Starting phenix.real_space_refine on Fri Jun 20 01:47:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl0_41358/06_2025/8tl0_41358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl0_41358/06_2025/8tl0_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_41358/06_2025/8tl0_41358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl0_41358/06_2025/8tl0_41358.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl0_41358/06_2025/8tl0_41358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl0_41358/06_2025/8tl0_41358.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.93, per 1000 atoms: 0.69 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: 5.77 Conformation dependent library (CDL) restraints added in 2.8 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: 3.24 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: 8.46 Time building geometry restraints manager: 6.82 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: 31526 2.36 - 4.72: 655 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: 2563 0.048 - 0.096: 716 0.096 - 0.144: 234 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: 8.410 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: 0.900 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 53.920 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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= 0.314 Angle : 0.836 11.806 32291 Z= 0.473 Chirality : 0.049 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.001 TRP D 282 HIS 0.013 0.001 HIS L 54 PHE 0.016 0.002 PHE D 453 TYR 0.034 0.002 TYR D 446 ARG 0.020 0.001 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.17791 ( 947) hydrogen bonds : angle 6.88922 ( 2775) covalent geometry : bond 0.00714 (23700) covalent geometry : angle 0.83630 (32291) *********************** 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 : 2.690 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: 0.4158 time to fit residues: 131.4972 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 : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 260 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS C 56 ASN C 452 HIS D 56 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 247 ASN L 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066896 restraints weight = 54715.313| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.74 r_work: 0.2870 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23700 Z= 0.127 Angle : 0.556 7.002 32291 Z= 0.288 Chirality : 0.042 0.158 3537 Planarity : 0.004 0.056 4208 Dihedral : 5.578 42.040 3474 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.51 % Allowed : 5.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2878 helix: 1.33 (0.17), residues: 947 sheet: -0.49 (0.19), residues: 708 loop : -1.61 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.005 0.001 HIS L 54 PHE 0.013 0.001 PHE K 98 TYR 0.026 0.001 TYR L 114 ARG 0.007 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 947) hydrogen bonds : angle 4.88731 ( 2775) covalent geometry : bond 0.00282 (23700) covalent geometry : angle 0.55583 (32291) *********************** 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 202 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8705 (mp0) cc_final: 0.8395 (mp0) REVERT: B 35 ILE cc_start: 0.9097 (mm) cc_final: 0.8884 (mt) REVERT: B 357 ASP cc_start: 0.9027 (m-30) cc_final: 0.8576 (m-30) REVERT: C 176 MET cc_start: 0.9002 (mtp) cc_final: 0.8733 (mtp) REVERT: C 219 ASP cc_start: 0.8929 (p0) cc_final: 0.8541 (p0) REVERT: I 173 GLU cc_start: 0.8689 (tt0) cc_final: 0.8355 (tp30) REVERT: I 176 MET cc_start: 0.8635 (mmt) cc_final: 0.8109 (mmt) REVERT: I 381 VAL cc_start: 0.9004 (t) cc_final: 0.8754 (p) REVERT: K 38 CYS cc_start: 0.8834 (m) cc_final: 0.8581 (m) REVERT: K 87 ASP cc_start: 0.8733 (t70) cc_final: 0.8468 (t0) REVERT: K 142 GLN cc_start: 0.6200 (pm20) cc_final: 0.5744 (pm20) REVERT: K 182 SER cc_start: 0.6552 (t) cc_final: 0.5719 (m) REVERT: K 251 ARG cc_start: 0.6827 (tpm170) cc_final: 0.6341 (tpp-160) REVERT: L 176 MET cc_start: 0.8307 (mtp) cc_final: 0.8055 (mtp) REVERT: L 220 THR cc_start: 0.8762 (p) cc_final: 0.8523 (p) REVERT: L 223 MET cc_start: 0.7937 (ttm) cc_final: 0.7690 (ttm) outliers start: 12 outliers final: 8 residues processed: 197 average time/residue: 0.3914 time to fit residues: 118.3250 Evaluate side-chains 170 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 2.740 ------------------------------------------------------------------------------- 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 341 LYS Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain L residue 56 ASN 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 122 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 279 optimal weight: 0.0570 chunk 176 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 254 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 425 HIS ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3459 r_free = 0.3459 target = 0.088771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065077 restraints weight = 54915.243| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.67 r_work: 0.2837 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23700 Z= 0.193 Angle : 0.544 6.553 32291 Z= 0.281 Chirality : 0.042 0.147 3537 Planarity : 0.004 0.065 4208 Dihedral : 5.331 42.086 3474 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.28 % Allowed : 7.35 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2878 helix: 1.87 (0.17), residues: 952 sheet: -0.51 (0.19), residues: 701 loop : -1.42 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 283 HIS 0.005 0.001 HIS L 54 PHE 0.015 0.001 PHE B 453 TYR 0.020 0.001 TYR I 446 ARG 0.007 0.000 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 947) hydrogen bonds : angle 4.57636 ( 2775) covalent geometry : bond 0.00447 (23700) covalent geometry : angle 0.54446 (32291) *********************** 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 193 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 2.488 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8301 (t70) cc_final: 0.7360 (t0) REVERT: B 357 ASP cc_start: 0.9050 (m-30) cc_final: 0.8594 (m-30) REVERT: C 176 MET cc_start: 0.9055 (mtp) cc_final: 0.8832 (mtp) REVERT: C 219 ASP cc_start: 0.8946 (p0) cc_final: 0.8607 (p0) REVERT: I 169 GLU cc_start: 0.8507 (mp0) cc_final: 0.8281 (pm20) REVERT: I 173 GLU cc_start: 0.8760 (tt0) cc_final: 0.8422 (tp30) REVERT: I 176 MET cc_start: 0.8663 (mmt) cc_final: 0.8213 (mmt) REVERT: I 381 VAL cc_start: 0.9059 (t) cc_final: 0.8796 (p) REVERT: K 38 CYS cc_start: 0.8845 (m) cc_final: 0.8566 (m) REVERT: K 87 ASP cc_start: 0.8756 (t70) cc_final: 0.8488 (t0) REVERT: K 142 GLN cc_start: 0.6411 (pm20) cc_final: 0.5925 (pm20) REVERT: K 176 MET cc_start: 0.6603 (mtp) cc_final: 0.6050 (mtp) REVERT: K 240 ASN cc_start: 0.7409 (m110) cc_final: 0.7159 (m110) REVERT: K 251 ARG cc_start: 0.6976 (tpm170) cc_final: 0.6466 (tpp-160) REVERT: K 282 TRP cc_start: 0.6958 (m-10) cc_final: 0.6726 (m-10) REVERT: L 176 MET cc_start: 0.8422 (mtp) cc_final: 0.7348 (mtp) REVERT: L 220 THR cc_start: 0.8774 (p) cc_final: 0.8526 (p) REVERT: L 223 MET cc_start: 0.8320 (ttm) cc_final: 0.8054 (ttp) outliers start: 30 outliers final: 22 residues processed: 176 average time/residue: 0.3655 time to fit residues: 101.1295 Evaluate side-chains 177 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 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 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 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 223 MET 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 260 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 198 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS I 33 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 ASN L 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066915 restraints weight = 55190.239| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.69 r_work: 0.2876 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23700 Z= 0.113 Angle : 0.491 7.171 32291 Z= 0.252 Chirality : 0.041 0.149 3537 Planarity : 0.004 0.056 4208 Dihedral : 5.099 41.725 3474 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.11 % Allowed : 8.76 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2878 helix: 2.11 (0.17), residues: 953 sheet: -0.49 (0.20), residues: 698 loop : -1.28 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 283 HIS 0.003 0.001 HIS I 375 PHE 0.013 0.001 PHE K 98 TYR 0.015 0.001 TYR I 446 ARG 0.005 0.000 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 947) hydrogen bonds : angle 4.26685 ( 2775) covalent geometry : bond 0.00258 (23700) covalent geometry : angle 0.49079 (32291) *********************** 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 206 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 2.533 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8208 (t70) cc_final: 0.7233 (t0) REVERT: B 46 ARG cc_start: 0.8295 (mmm160) cc_final: 0.8062 (mmm160) REVERT: B 357 ASP cc_start: 0.9020 (m-30) cc_final: 0.8554 (m-30) REVERT: C 176 MET cc_start: 0.9059 (mtp) cc_final: 0.8810 (mtp) REVERT: C 219 ASP cc_start: 0.8913 (p0) cc_final: 0.8568 (p0) REVERT: I 169 GLU cc_start: 0.8516 (mp0) cc_final: 0.8246 (pt0) REVERT: I 173 GLU cc_start: 0.8728 (tt0) cc_final: 0.8380 (tp30) REVERT: I 176 MET cc_start: 0.8661 (mmt) cc_final: 0.8292 (mmt) REVERT: I 381 VAL cc_start: 0.9133 (t) cc_final: 0.8856 (p) REVERT: K 38 CYS cc_start: 0.8827 (m) cc_final: 0.8566 (m) REVERT: K 87 ASP cc_start: 0.8732 (t70) cc_final: 0.8460 (t0) REVERT: K 142 GLN cc_start: 0.6347 (pm20) cc_final: 0.5900 (pm20) REVERT: K 240 ASN cc_start: 0.7292 (m110) cc_final: 0.7016 (m110) REVERT: K 251 ARG cc_start: 0.6971 (tpm170) cc_final: 0.6652 (tpp-160) REVERT: L 176 MET cc_start: 0.8430 (mtp) cc_final: 0.8148 (mtp) REVERT: L 220 THR cc_start: 0.8759 (p) cc_final: 0.8494 (p) REVERT: L 223 MET cc_start: 0.8485 (ttp) cc_final: 0.8189 (ttp) REVERT: L 227 GLU cc_start: 0.8437 (mp0) cc_final: 0.8012 (mp0) outliers start: 26 outliers final: 18 residues processed: 197 average time/residue: 0.3930 time to fit residues: 120.4145 Evaluate side-chains 183 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 407 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 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 I residue 461 LEU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 154 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN C 184 GLN C 375 HIS ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 22 GLN L 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063994 restraints weight = 55800.779| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.68 r_work: 0.2810 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 23700 Z= 0.244 Angle : 0.561 6.517 32291 Z= 0.288 Chirality : 0.043 0.151 3537 Planarity : 0.004 0.063 4208 Dihedral : 5.130 43.013 3474 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.96 % Allowed : 9.65 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2878 helix: 2.32 (0.17), residues: 952 sheet: -0.48 (0.19), residues: 702 loop : -1.24 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 180 HIS 0.006 0.001 HIS L 54 PHE 0.018 0.001 PHE B 453 TYR 0.020 0.001 TYR L 101 ARG 0.006 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 947) hydrogen bonds : angle 4.36791 ( 2775) covalent geometry : bond 0.00568 (23700) covalent geometry : angle 0.56058 (32291) *********************** 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 205 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8372 (t70) cc_final: 0.7389 (t0) REVERT: B 357 ASP cc_start: 0.9061 (m-30) cc_final: 0.8595 (m-30) REVERT: C 219 ASP cc_start: 0.8919 (p0) cc_final: 0.8611 (p0) REVERT: I 173 GLU cc_start: 0.8772 (tt0) cc_final: 0.8436 (tp30) REVERT: I 176 MET cc_start: 0.8689 (mmt) cc_final: 0.8359 (mmt) REVERT: I 346 GLU cc_start: 0.7863 (mp0) cc_final: 0.7596 (mp0) REVERT: I 381 VAL cc_start: 0.9139 (t) cc_final: 0.8843 (p) REVERT: K 38 CYS cc_start: 0.8838 (m) cc_final: 0.8539 (m) REVERT: K 87 ASP cc_start: 0.8754 (t70) cc_final: 0.8474 (t0) REVERT: K 142 GLN cc_start: 0.6608 (pm20) cc_final: 0.6110 (pm20) REVERT: K 176 MET cc_start: 0.6476 (mtp) cc_final: 0.6009 (mtp) REVERT: K 251 ARG cc_start: 0.6964 (tpm170) cc_final: 0.6616 (tpp-160) REVERT: L 176 MET cc_start: 0.8498 (mtp) cc_final: 0.7409 (mtp) REVERT: L 220 THR cc_start: 0.8796 (p) cc_final: 0.8507 (p) REVERT: L 223 MET cc_start: 0.8575 (ttp) cc_final: 0.8261 (ttm) REVERT: L 227 GLU cc_start: 0.8462 (mp0) cc_final: 0.8047 (mp0) outliers start: 46 outliers final: 31 residues processed: 183 average time/residue: 0.3676 time to fit residues: 105.1164 Evaluate side-chains 182 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 2.714 ------------------------------------------------------------------------------- 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 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 245 ILE Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain I residue 33 ASN 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 K residue 223 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 88 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 425 HIS I 481 HIS K 22 GLN L 33 ASN L 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.089377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.065847 restraints weight = 54804.894| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.70 r_work: 0.2846 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23700 Z= 0.130 Angle : 0.499 7.421 32291 Z= 0.256 Chirality : 0.041 0.154 3537 Planarity : 0.004 0.059 4208 Dihedral : 5.010 42.791 3474 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.50 % Allowed : 10.89 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2878 helix: 2.39 (0.17), residues: 950 sheet: -0.39 (0.20), residues: 701 loop : -1.18 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 283 HIS 0.003 0.001 HIS D 278 PHE 0.015 0.001 PHE K 98 TYR 0.013 0.001 TYR K 114 ARG 0.013 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 947) hydrogen bonds : angle 4.19422 ( 2775) covalent geometry : bond 0.00301 (23700) covalent geometry : angle 0.49911 (32291) *********************** 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 196 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 3.022 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8217 (t70) cc_final: 0.7169 (t0) REVERT: B 357 ASP cc_start: 0.9032 (m-30) cc_final: 0.8567 (m-30) REVERT: C 176 MET cc_start: 0.9062 (mtp) cc_final: 0.7821 (mtp) REVERT: C 219 ASP cc_start: 0.8907 (p0) cc_final: 0.8600 (p0) REVERT: I 169 GLU cc_start: 0.8502 (mp0) cc_final: 0.8240 (pt0) REVERT: I 173 GLU cc_start: 0.8733 (tt0) cc_final: 0.8390 (tp30) REVERT: I 176 MET cc_start: 0.8626 (mmt) cc_final: 0.8293 (mmt) REVERT: I 346 GLU cc_start: 0.7824 (mp0) cc_final: 0.7526 (mp0) REVERT: I 381 VAL cc_start: 0.9071 (t) cc_final: 0.8772 (p) REVERT: K 27 LEU cc_start: 0.7768 (mt) cc_final: 0.7462 (mt) REVERT: K 38 CYS cc_start: 0.8818 (m) cc_final: 0.8520 (m) REVERT: K 87 ASP cc_start: 0.8712 (t70) cc_final: 0.8436 (t0) REVERT: K 142 GLN cc_start: 0.6502 (pm20) cc_final: 0.6027 (pm20) REVERT: K 176 MET cc_start: 0.6348 (mtp) cc_final: 0.5944 (mtp) REVERT: K 240 ASN cc_start: 0.7273 (m110) cc_final: 0.6932 (m110) REVERT: K 251 ARG cc_start: 0.6858 (tpm170) cc_final: 0.6482 (tpp-160) REVERT: L 176 MET cc_start: 0.8400 (mtp) cc_final: 0.7303 (mtp) REVERT: L 220 THR cc_start: 0.8753 (p) cc_final: 0.8472 (p) REVERT: L 223 MET cc_start: 0.8565 (ttp) cc_final: 0.8129 (ttp) REVERT: L 227 GLU cc_start: 0.8386 (mp0) cc_final: 0.7983 (mp0) outliers start: 35 outliers final: 28 residues processed: 180 average time/residue: 0.4125 time to fit residues: 116.7212 Evaluate side-chains 182 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 2.454 ------------------------------------------------------------------------------- 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 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 336 LEU Chi-restraints excluded: chain C residue 341 LYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 193 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 248 optimal weight: 0.0040 chunk 202 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 182 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067359 restraints weight = 55033.106| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.68 r_work: 0.2883 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23700 Z= 0.099 Angle : 0.474 8.129 32291 Z= 0.242 Chirality : 0.040 0.152 3537 Planarity : 0.004 0.059 4208 Dihedral : 4.826 40.793 3474 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.37 % Allowed : 11.36 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2878 helix: 2.49 (0.17), residues: 951 sheet: -0.28 (0.20), residues: 702 loop : -1.13 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 283 HIS 0.006 0.001 HIS L 54 PHE 0.016 0.001 PHE K 98 TYR 0.013 0.001 TYR I 446 ARG 0.010 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 947) hydrogen bonds : angle 4.03752 ( 2775) covalent geometry : bond 0.00228 (23700) covalent geometry : angle 0.47420 (32291) *********************** 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 205 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 2.561 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8157 (t70) cc_final: 0.7152 (t0) REVERT: B 357 ASP cc_start: 0.9022 (m-30) cc_final: 0.8571 (m-30) REVERT: C 176 MET cc_start: 0.9110 (mtp) cc_final: 0.7865 (mtp) REVERT: C 219 ASP cc_start: 0.8900 (p0) cc_final: 0.8552 (p0) REVERT: I 169 GLU cc_start: 0.8513 (mp0) cc_final: 0.8257 (pt0) REVERT: I 173 GLU cc_start: 0.8744 (tt0) cc_final: 0.8390 (tp30) REVERT: I 176 MET cc_start: 0.8674 (mmt) cc_final: 0.8300 (mmt) REVERT: I 346 GLU cc_start: 0.7843 (mp0) cc_final: 0.7536 (mp0) REVERT: K 27 LEU cc_start: 0.7707 (mt) cc_final: 0.7461 (mt) REVERT: K 38 CYS cc_start: 0.8877 (m) cc_final: 0.8590 (m) REVERT: K 87 ASP cc_start: 0.8708 (t70) cc_final: 0.8465 (t0) REVERT: K 142 GLN cc_start: 0.6640 (pm20) cc_final: 0.6139 (pm20) REVERT: K 176 MET cc_start: 0.6356 (mtp) cc_final: 0.5897 (mtp) REVERT: K 240 ASN cc_start: 0.7269 (m110) cc_final: 0.6942 (m110) REVERT: K 251 ARG cc_start: 0.6916 (tpm170) cc_final: 0.6554 (tpp-160) REVERT: L 176 MET cc_start: 0.8455 (mtp) cc_final: 0.7163 (mtp) REVERT: L 220 THR cc_start: 0.8835 (p) cc_final: 0.8565 (p) REVERT: L 223 MET cc_start: 0.8599 (ttp) cc_final: 0.8317 (ttp) REVERT: L 227 GLU cc_start: 0.8295 (mp0) cc_final: 0.7944 (mp0) outliers start: 32 outliers final: 26 residues processed: 191 average time/residue: 0.3954 time to fit residues: 118.8803 Evaluate side-chains 187 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 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 128 VAL Chi-restraints excluded: chain I residue 461 LEU 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 223 MET Chi-restraints excluded: chain L residue 127 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 261 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN L 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.088051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064682 restraints weight = 55679.131| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.64 r_work: 0.2823 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 23700 Z= 0.233 Angle : 0.553 9.085 32291 Z= 0.281 Chirality : 0.042 0.148 3537 Planarity : 0.004 0.061 4208 Dihedral : 4.907 42.470 3474 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.71 % Allowed : 11.70 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2878 helix: 2.58 (0.17), residues: 950 sheet: -0.40 (0.20), residues: 703 loop : -1.09 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 77 HIS 0.006 0.001 HIS C 331 PHE 0.017 0.001 PHE B 453 TYR 0.022 0.001 TYR K 114 ARG 0.011 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 947) hydrogen bonds : angle 4.21724 ( 2775) covalent geometry : bond 0.00545 (23700) covalent geometry : angle 0.55301 (32291) *********************** 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 200 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 3.252 Fit side-chains revert: symmetry clash REVERT: B 357 ASP cc_start: 0.9053 (m-30) cc_final: 0.8561 (m-30) REVERT: C 176 MET cc_start: 0.9145 (mtp) cc_final: 0.7981 (mtp) REVERT: C 219 ASP cc_start: 0.8930 (p0) cc_final: 0.8612 (p0) REVERT: I 173 GLU cc_start: 0.8768 (tt0) cc_final: 0.8415 (tp30) REVERT: I 176 MET cc_start: 0.8633 (mmt) cc_final: 0.8355 (mmt) REVERT: I 340 ARG cc_start: 0.7691 (mpt180) cc_final: 0.7463 (mtm-85) REVERT: I 346 GLU cc_start: 0.7892 (mp0) cc_final: 0.7572 (mp0) REVERT: K 38 CYS cc_start: 0.8878 (m) cc_final: 0.8577 (m) REVERT: K 87 ASP cc_start: 0.8740 (t70) cc_final: 0.8459 (t0) REVERT: K 176 MET cc_start: 0.6454 (mtp) cc_final: 0.5954 (mtp) REVERT: K 240 ASN cc_start: 0.7309 (m110) cc_final: 0.6824 (m110) REVERT: K 251 ARG cc_start: 0.6949 (tpm170) cc_final: 0.6427 (tpp-160) REVERT: L 176 MET cc_start: 0.8460 (mtp) cc_final: 0.7267 (mtp) REVERT: L 220 THR cc_start: 0.8823 (p) cc_final: 0.8534 (p) REVERT: L 223 MET cc_start: 0.8630 (ttp) cc_final: 0.8258 (ttp) REVERT: L 227 GLU cc_start: 0.8362 (mp0) cc_final: 0.7903 (mp0) outliers start: 40 outliers final: 33 residues processed: 182 average time/residue: 0.4014 time to fit residues: 116.0236 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 : 2.866 ------------------------------------------------------------------------------- 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 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 56 ASN 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 245 ILE 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 K residue 69 SER 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 223 MET Chi-restraints excluded: chain L residue 127 THR 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 231 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 98 optimal weight: 0.0870 chunk 221 optimal weight: 0.4980 chunk 225 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 285 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066099 restraints weight = 54952.824| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.65 r_work: 0.2859 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23700 Z= 0.129 Angle : 0.508 9.581 32291 Z= 0.257 Chirality : 0.041 0.154 3537 Planarity : 0.004 0.059 4208 Dihedral : 4.863 42.300 3474 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.37 % Allowed : 12.17 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2878 helix: 2.56 (0.17), residues: 949 sheet: -0.35 (0.20), residues: 705 loop : -1.09 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 77 HIS 0.003 0.001 HIS D 388 PHE 0.022 0.001 PHE K 258 TYR 0.018 0.001 TYR K 114 ARG 0.012 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 947) hydrogen bonds : angle 4.11930 ( 2775) covalent geometry : bond 0.00301 (23700) covalent geometry : angle 0.50768 (32291) *********************** 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: 32 poor density : 165 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 357 ASP cc_start: 0.9032 (m-30) cc_final: 0.8551 (m-30) REVERT: C 176 MET cc_start: 0.9117 (mtp) cc_final: 0.7902 (mtp) REVERT: C 219 ASP cc_start: 0.8908 (p0) cc_final: 0.8583 (p0) REVERT: I 169 GLU cc_start: 0.8465 (mp0) cc_final: 0.8188 (pt0) REVERT: I 173 GLU cc_start: 0.8740 (tt0) cc_final: 0.8383 (tp30) REVERT: I 176 MET cc_start: 0.8631 (mmt) cc_final: 0.8342 (mmt) REVERT: I 346 GLU cc_start: 0.7825 (mp0) cc_final: 0.7512 (mp0) REVERT: K 27 LEU cc_start: 0.7850 (mt) cc_final: 0.7597 (mt) REVERT: K 38 CYS cc_start: 0.8855 (m) cc_final: 0.8567 (m) REVERT: K 87 ASP cc_start: 0.8706 (t70) cc_final: 0.8461 (t0) REVERT: K 142 GLN cc_start: 0.7322 (pm20) cc_final: 0.7036 (pm20) REVERT: K 176 MET cc_start: 0.6422 (mtp) cc_final: 0.5915 (mtp) REVERT: K 251 ARG cc_start: 0.6929 (tpm170) cc_final: 0.6410 (tpp-160) REVERT: L 176 MET cc_start: 0.8392 (mtp) cc_final: 0.7187 (mtp) REVERT: L 220 THR cc_start: 0.8792 (p) cc_final: 0.8505 (p) REVERT: L 223 MET cc_start: 0.8626 (ttp) cc_final: 0.8316 (ttp) REVERT: L 227 GLU cc_start: 0.8294 (mp0) cc_final: 0.7853 (mp0) outliers start: 32 outliers final: 28 residues processed: 183 average time/residue: 0.3631 time to fit residues: 106.1343 Evaluate side-chains 189 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 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 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 D residue 407 LEU 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 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 223 MET Chi-restraints excluded: chain L residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 258 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 191 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.066808 restraints weight = 55094.991| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.64 r_work: 0.2874 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23700 Z= 0.117 Angle : 0.497 9.711 32291 Z= 0.250 Chirality : 0.041 0.147 3537 Planarity : 0.004 0.057 4208 Dihedral : 4.764 40.744 3474 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.41 % Allowed : 12.39 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2878 helix: 2.62 (0.17), residues: 950 sheet: -0.30 (0.20), residues: 708 loop : -1.08 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 77 HIS 0.004 0.001 HIS B 463 PHE 0.018 0.001 PHE K 98 TYR 0.014 0.001 TYR K 114 ARG 0.013 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 947) hydrogen bonds : angle 4.02865 ( 2775) covalent geometry : bond 0.00273 (23700) covalent geometry : angle 0.49703 (32291) ********************** 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 204 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 357 ASP cc_start: 0.9020 (m-30) cc_final: 0.8533 (m-30) REVERT: C 176 MET cc_start: 0.9150 (mtp) cc_final: 0.7944 (mtp) REVERT: C 219 ASP cc_start: 0.8897 (p0) cc_final: 0.8538 (p0) REVERT: D 169 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: I 169 GLU cc_start: 0.8499 (mp0) cc_final: 0.8207 (pt0) REVERT: I 173 GLU cc_start: 0.8749 (tt0) cc_final: 0.8381 (tp30) REVERT: I 176 MET cc_start: 0.8615 (mmt) cc_final: 0.8321 (mmt) REVERT: I 346 GLU cc_start: 0.7850 (mp0) cc_final: 0.7525 (mp0) REVERT: K 27 LEU cc_start: 0.7781 (mt) cc_final: 0.7547 (mt) REVERT: K 38 CYS cc_start: 0.8924 (m) cc_final: 0.8666 (m) REVERT: K 87 ASP cc_start: 0.8729 (t70) cc_final: 0.8476 (t0) REVERT: K 142 GLN cc_start: 0.7414 (pm20) cc_final: 0.6994 (pm20) REVERT: K 176 MET cc_start: 0.6400 (mtp) cc_final: 0.5874 (mtp) REVERT: K 251 ARG cc_start: 0.6949 (tpm170) cc_final: 0.6422 (tpp-160) REVERT: L 173 GLU cc_start: 0.7955 (tp30) cc_final: 0.7723 (tp30) REVERT: L 176 MET cc_start: 0.8414 (mtp) cc_final: 0.7245 (mtp) REVERT: L 220 THR cc_start: 0.8886 (p) cc_final: 0.8629 (p) REVERT: L 223 MET cc_start: 0.8648 (ttp) cc_final: 0.8345 (ttp) REVERT: L 227 GLU cc_start: 0.8255 (mp0) cc_final: 0.7837 (mp0) outliers start: 33 outliers final: 28 residues processed: 190 average time/residue: 0.4094 time to fit residues: 124.8218 Evaluate side-chains 188 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 2.376 ------------------------------------------------------------------------------- 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 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 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 169 GLU 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 D residue 407 LEU 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 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 223 MET Chi-restraints excluded: chain L residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 181 optimal weight: 0.0050 chunk 89 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.066661 restraints weight = 55249.013| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.66 r_work: 0.2873 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2192 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= 0.133 Angle : 0.505 9.556 32291 Z= 0.254 Chirality : 0.041 0.147 3537 Planarity : 0.004 0.057 4208 Dihedral : 4.738 40.710 3474 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.28 % Allowed : 12.47 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.16), residues: 2878 helix: 2.60 (0.17), residues: 950 sheet: -0.30 (0.20), residues: 709 loop : -1.07 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 77 HIS 0.004 0.001 HIS B 463 PHE 0.017 0.001 PHE K 98 TYR 0.014 0.001 TYR L 114 ARG 0.012 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 947) hydrogen bonds : angle 4.02743 ( 2775) covalent geometry : bond 0.00312 (23700) covalent geometry : angle 0.50458 (32291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11848.96 seconds wall clock time: 207 minutes 50.03 seconds (12470.03 seconds total)