Starting phenix.real_space_refine on Sun Aug 24 21:48:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl0_41358/08_2025/8tl0_41358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl0_41358/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tl0_41358/08_2025/8tl0_41358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl0_41358/08_2025/8tl0_41358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tl0_41358/08_2025/8tl0_41358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl0_41358/08_2025/8tl0_41358.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 129 5.16 5 C 14421 2.51 5 N 4281 2.21 5 O 4274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23119 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 28, 'TRANS': 449} Chain breaks: 3 Chain: "B" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3700 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 27, 'TRANS': 449} Chain breaks: 3 Chain: "C" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3678 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 26, 'TRANS': 446} Chain breaks: 3 Chain: "D" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3708 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 27, 'TRANS': 450} Chain breaks: 3 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "I" Number of atoms: 3711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3711 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 450} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "K" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2084 Classifications: {'peptide': 267} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 250} Chain breaks: 1 Chain: "L" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2089 Classifications: {'peptide': 268} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "N" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.22 Number of scatterers: 23119 At special positions: 0 Unit cell: (108.1, 121.26, 157.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 P 14 15.00 O 4274 8.00 N 4281 7.00 C 14421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5418 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 27 sheets defined 40.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 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: 3.66 Time building geometry restraints manager: 2.21 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: 8.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.790 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.15), residues: 2878 helix: 0.35 (0.16), residues: 928 sheet: -0.58 (0.20), residues: 690 loop : -1.81 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 243 TYR 0.034 0.002 TYR D 446 PHE 0.016 0.002 PHE D 453 TRP 0.019 0.001 TRP D 282 HIS 0.013 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00714 (23700) covalent geometry : angle 0.83630 (32291) hydrogen bonds : bond 0.17791 ( 947) hydrogen bonds : angle 6.88922 ( 2775) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.770 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: 0.1559 time to fit residues: 48.4633 Evaluate side-chains 163 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN K 247 ASN L 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.089328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065567 restraints weight = 55143.561| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.69 r_work: 0.2850 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23700 Z= 0.168 Angle : 0.576 7.084 32291 Z= 0.301 Chirality : 0.043 0.159 3537 Planarity : 0.005 0.059 4208 Dihedral : 5.653 42.510 3474 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.60 % Allowed : 5.85 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.16), residues: 2878 helix: 1.34 (0.17), residues: 954 sheet: -0.49 (0.19), residues: 703 loop : -1.63 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 199 TYR 0.026 0.001 TYR L 114 PHE 0.013 0.001 PHE B 453 TRP 0.010 0.001 TRP B 283 HIS 0.004 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00381 (23700) covalent geometry : angle 0.57614 (32291) hydrogen bonds : bond 0.04428 ( 947) hydrogen bonds : angle 4.97767 ( 2775) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 328 GLU cc_start: 0.8712 (mp0) cc_final: 0.8438 (mp0) REVERT: B 35 ILE cc_start: 0.9129 (mm) cc_final: 0.8924 (mt) REVERT: B 203 ASP cc_start: 0.7800 (t0) cc_final: 0.7510 (t0) REVERT: B 357 ASP cc_start: 0.9051 (m-30) cc_final: 0.8584 (m-30) REVERT: C 176 MET cc_start: 0.9031 (mtp) cc_final: 0.8808 (mtp) REVERT: C 219 ASP cc_start: 0.8936 (p0) cc_final: 0.8571 (p0) REVERT: D 143 ARG cc_start: 0.8106 (tmm-80) cc_final: 0.7657 (ptm-80) REVERT: I 173 GLU cc_start: 0.8710 (tt0) cc_final: 0.8379 (tp30) REVERT: I 176 MET cc_start: 0.8676 (mmt) cc_final: 0.8155 (mmt) REVERT: I 381 VAL cc_start: 0.9025 (t) cc_final: 0.8774 (p) REVERT: K 38 CYS cc_start: 0.8853 (m) cc_final: 0.8557 (m) REVERT: K 87 ASP cc_start: 0.8760 (t70) cc_final: 0.8484 (t0) REVERT: K 142 GLN cc_start: 0.6345 (pm20) cc_final: 0.5854 (pm20) REVERT: K 251 ARG cc_start: 0.6865 (tpm170) cc_final: 0.6363 (tpp-160) REVERT: L 176 MET cc_start: 0.8362 (mtp) cc_final: 0.8117 (mtp) REVERT: L 220 THR cc_start: 0.8815 (p) cc_final: 0.8583 (p) REVERT: L 223 MET cc_start: 0.8034 (ttm) cc_final: 0.7782 (ttm) outliers start: 14 outliers final: 10 residues processed: 189 average time/residue: 0.1591 time to fit residues: 46.6508 Evaluate side-chains 173 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain L residue 56 ASN Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 166 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 259 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 HIS ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 425 HIS ** K 22 GLN ** 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 = 0.3476 r_free = 0.3476 target = 0.089667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.065852 restraints weight = 55228.904| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.71 r_work: 0.2853 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23700 Z= 0.145 Angle : 0.520 6.907 32291 Z= 0.269 Chirality : 0.041 0.145 3537 Planarity : 0.004 0.062 4208 Dihedral : 5.309 41.983 3474 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.03 % Allowed : 7.52 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.16), residues: 2878 helix: 1.85 (0.17), residues: 951 sheet: -0.49 (0.19), residues: 706 loop : -1.45 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 342 TYR 0.019 0.001 TYR I 446 PHE 0.013 0.001 PHE K 98 TRP 0.010 0.001 TRP D 283 HIS 0.005 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00332 (23700) covalent geometry : angle 0.52032 (32291) hydrogen bonds : bond 0.03722 ( 947) hydrogen bonds : angle 4.53721 ( 2775) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: B 357 ASP cc_start: 0.9042 (m-30) cc_final: 0.8581 (m-30) REVERT: C 176 MET cc_start: 0.9073 (mtp) cc_final: 0.8850 (mtp) REVERT: C 219 ASP cc_start: 0.8936 (p0) cc_final: 0.8590 (p0) REVERT: I 169 GLU cc_start: 0.8531 (mp0) cc_final: 0.8310 (pm20) REVERT: I 176 MET cc_start: 0.8691 (mmt) cc_final: 0.8238 (mmt) REVERT: I 381 VAL cc_start: 0.9102 (t) cc_final: 0.8833 (p) REVERT: K 38 CYS cc_start: 0.8838 (m) cc_final: 0.8553 (m) REVERT: K 87 ASP cc_start: 0.8745 (t70) cc_final: 0.8469 (t0) REVERT: K 142 GLN cc_start: 0.6390 (pm20) cc_final: 0.5912 (pm20) REVERT: K 176 MET cc_start: 0.6628 (mtp) cc_final: 0.6074 (mtp) REVERT: K 240 ASN cc_start: 0.7392 (m110) cc_final: 0.7147 (m110) REVERT: K 251 ARG cc_start: 0.6955 (tpm170) cc_final: 0.6447 (tpp-160) REVERT: K 282 TRP cc_start: 0.6928 (m-10) cc_final: 0.6700 (m-10) REVERT: L 176 MET cc_start: 0.8454 (mtp) cc_final: 0.7359 (mtp) REVERT: L 220 THR cc_start: 0.8807 (p) cc_final: 0.8556 (p) REVERT: L 223 MET cc_start: 0.8302 (ttm) cc_final: 0.8041 (ttp) outliers start: 24 outliers final: 17 residues processed: 182 average time/residue: 0.1911 time to fit residues: 53.1107 Evaluate side-chains 174 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 69 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 48 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 HIS C 375 HIS ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 425 HIS K 22 GLN K 247 ASN L 33 ASN L 56 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063525 restraints weight = 56106.757| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.67 r_work: 0.2800 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 23700 Z= 0.249 Angle : 0.580 6.846 32291 Z= 0.299 Chirality : 0.043 0.154 3537 Planarity : 0.004 0.061 4208 Dihedral : 5.320 44.101 3474 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.84 % Allowed : 8.93 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2878 helix: 2.16 (0.17), residues: 951 sheet: -0.53 (0.20), residues: 702 loop : -1.36 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 342 TYR 0.019 0.002 TYR I 446 PHE 0.020 0.001 PHE B 453 TRP 0.011 0.001 TRP A 180 HIS 0.006 0.001 HIS C 331 Details of bonding type rmsd covalent geometry : bond 0.00577 (23700) covalent geometry : angle 0.57966 (32291) hydrogen bonds : bond 0.04115 ( 947) hydrogen bonds : angle 4.51121 ( 2775) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8410 (t70) cc_final: 0.7498 (t0) REVERT: B 357 ASP cc_start: 0.9068 (m-30) cc_final: 0.8596 (m-30) REVERT: C 219 ASP cc_start: 0.8916 (p0) cc_final: 0.8645 (p0) REVERT: I 173 GLU cc_start: 0.8817 (tt0) cc_final: 0.8460 (tp30) REVERT: I 176 MET cc_start: 0.8686 (mmt) cc_final: 0.8322 (mmt) REVERT: I 381 VAL cc_start: 0.9110 (t) cc_final: 0.8837 (p) REVERT: K 38 CYS cc_start: 0.8815 (m) cc_final: 0.8495 (m) REVERT: K 87 ASP cc_start: 0.8758 (t70) cc_final: 0.8477 (t0) REVERT: K 142 GLN cc_start: 0.6596 (pm20) cc_final: 0.6129 (pm20) REVERT: K 176 MET cc_start: 0.6677 (mtp) cc_final: 0.6077 (mtp) REVERT: K 223 MET cc_start: 0.7848 (ttp) cc_final: 0.7520 (ttp) REVERT: K 251 ARG cc_start: 0.6948 (tpm170) cc_final: 0.6625 (tpp-160) REVERT: K 282 TRP cc_start: 0.7118 (m-10) cc_final: 0.6885 (m-10) REVERT: L 220 THR cc_start: 0.8821 (p) cc_final: 0.8572 (p) REVERT: L 223 MET cc_start: 0.8543 (ttp) cc_final: 0.8260 (ttp) outliers start: 43 outliers final: 31 residues processed: 183 average time/residue: 0.1853 time to fit residues: 52.5098 Evaluate side-chains 186 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 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 139 VAL 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 L residue 56 ASN Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 200 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** C 452 HIS I 33 ASN I 481 HIS 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 = 0.3453 r_free = 0.3453 target = 0.090000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066691 restraints weight = 55590.514| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.68 r_work: 0.2818 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23700 Z= 0.171 Angle : 0.524 7.370 32291 Z= 0.269 Chirality : 0.042 0.151 3537 Planarity : 0.004 0.060 4208 Dihedral : 5.182 44.110 3474 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.75 % Allowed : 10.17 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2878 helix: 2.27 (0.17), residues: 950 sheet: -0.53 (0.20), residues: 698 loop : -1.26 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 46 TYR 0.019 0.001 TYR L 101 PHE 0.014 0.001 PHE B 453 TRP 0.010 0.001 TRP C 283 HIS 0.004 0.001 HIS L 54 Details of bonding type rmsd covalent geometry : bond 0.00397 (23700) covalent geometry : angle 0.52446 (32291) hydrogen bonds : bond 0.03626 ( 947) hydrogen bonds : angle 4.35021 ( 2775) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 188 ASP cc_start: 0.8270 (t70) cc_final: 0.7272 (t0) REVERT: B 357 ASP cc_start: 0.9021 (m-30) cc_final: 0.8545 (m-30) REVERT: C 176 MET cc_start: 0.8996 (mtp) cc_final: 0.7749 (mtp) REVERT: C 219 ASP cc_start: 0.8884 (p0) cc_final: 0.8595 (p0) REVERT: I 169 GLU cc_start: 0.8501 (mp0) cc_final: 0.8201 (pt0) REVERT: I 173 GLU cc_start: 0.8717 (tt0) cc_final: 0.8397 (tp30) REVERT: I 176 MET cc_start: 0.8570 (mmt) cc_final: 0.8239 (mmt) REVERT: K 38 CYS cc_start: 0.8758 (m) cc_final: 0.8459 (m) REVERT: K 87 ASP cc_start: 0.8711 (t70) cc_final: 0.8435 (t0) REVERT: K 142 GLN cc_start: 0.6402 (pm20) cc_final: 0.5964 (pm20) REVERT: K 176 MET cc_start: 0.6522 (mtp) cc_final: 0.5865 (mtp) REVERT: K 223 MET cc_start: 0.7907 (ttp) cc_final: 0.7602 (ttp) REVERT: K 251 ARG cc_start: 0.6946 (tpm170) cc_final: 0.6595 (tpp-160) REVERT: K 282 TRP cc_start: 0.7034 (m-10) cc_final: 0.6825 (m-10) REVERT: L 220 THR cc_start: 0.8732 (p) cc_final: 0.8477 (p) REVERT: L 223 MET cc_start: 0.8508 (ttp) cc_final: 0.8198 (ttp) REVERT: L 227 GLU cc_start: 0.8361 (mp0) cc_final: 0.7932 (mp0) outliers start: 41 outliers final: 27 residues processed: 181 average time/residue: 0.1722 time to fit residues: 49.0829 Evaluate side-chains 180 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 336 LEU 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 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 241 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 114 optimal weight: 0.8980 chunk 215 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064904 restraints weight = 55563.578| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.68 r_work: 0.2833 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23700 Z= 0.160 Angle : 0.510 8.195 32291 Z= 0.262 Chirality : 0.041 0.153 3537 Planarity : 0.004 0.060 4208 Dihedral : 5.061 43.230 3474 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.71 % Allowed : 10.94 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.16), residues: 2878 helix: 2.40 (0.17), residues: 950 sheet: -0.48 (0.20), residues: 698 loop : -1.22 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 199 TYR 0.014 0.001 TYR I 446 PHE 0.015 0.001 PHE K 98 TRP 0.010 0.001 TRP C 283 HIS 0.005 0.001 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00372 (23700) covalent geometry : angle 0.51024 (32291) hydrogen bonds : bond 0.03447 ( 947) hydrogen bonds : angle 4.24946 ( 2775) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.828 Fit side-chains REVERT: A 188 ASP cc_start: 0.8263 (t70) cc_final: 0.7235 (t0) REVERT: B 357 ASP cc_start: 0.9030 (m-30) cc_final: 0.8555 (m-30) REVERT: C 176 MET cc_start: 0.9036 (mtp) cc_final: 0.7750 (mtp) REVERT: C 219 ASP cc_start: 0.8892 (p0) cc_final: 0.8580 (p0) REVERT: I 169 GLU cc_start: 0.8498 (mp0) cc_final: 0.8214 (pt0) REVERT: I 173 GLU cc_start: 0.8729 (tt0) cc_final: 0.8400 (tp30) REVERT: I 176 MET cc_start: 0.8611 (mmt) cc_final: 0.8283 (mmt) REVERT: I 340 ARG cc_start: 0.7681 (mpt180) cc_final: 0.7324 (ptp90) REVERT: I 346 GLU cc_start: 0.7760 (mp0) cc_final: 0.7537 (mp0) REVERT: K 38 CYS cc_start: 0.8791 (m) cc_final: 0.8498 (m) REVERT: K 87 ASP cc_start: 0.8704 (t70) cc_final: 0.8426 (t0) REVERT: K 142 GLN cc_start: 0.6521 (pm20) cc_final: 0.6027 (pm20) REVERT: K 223 MET cc_start: 0.7937 (ttp) cc_final: 0.7714 (ttp) REVERT: K 240 ASN cc_start: 0.7253 (m110) cc_final: 0.6947 (m110) REVERT: K 251 ARG cc_start: 0.6885 (tpm170) cc_final: 0.6497 (tpp-160) REVERT: L 220 THR cc_start: 0.8770 (p) cc_final: 0.8496 (p) REVERT: L 223 MET cc_start: 0.8550 (ttp) cc_final: 0.8253 (ttm) REVERT: L 227 GLU cc_start: 0.8347 (mp0) cc_final: 0.7946 (mp0) outliers start: 40 outliers final: 33 residues processed: 188 average time/residue: 0.1826 time to fit residues: 53.3846 Evaluate side-chains 186 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 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 338 GLU 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 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 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 224 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 221 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.065421 restraints weight = 55248.763| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.71 r_work: 0.2834 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1904 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= 0.144 Angle : 0.504 9.463 32291 Z= 0.256 Chirality : 0.041 0.150 3537 Planarity : 0.004 0.059 4208 Dihedral : 4.962 42.489 3474 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.58 % Allowed : 11.79 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.16), residues: 2878 helix: 2.48 (0.17), residues: 949 sheet: -0.43 (0.20), residues: 704 loop : -1.18 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 46 TYR 0.021 0.001 TYR K 114 PHE 0.015 0.001 PHE K 98 TRP 0.010 0.001 TRP D 283 HIS 0.003 0.001 HIS D 278 Details of bonding type rmsd covalent geometry : bond 0.00335 (23700) covalent geometry : angle 0.50357 (32291) hydrogen bonds : bond 0.03329 ( 947) hydrogen bonds : angle 4.16025 ( 2775) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.990 Fit side-chains REVERT: A 188 ASP cc_start: 0.8186 (t70) cc_final: 0.7185 (t0) REVERT: B 357 ASP cc_start: 0.9021 (m-30) cc_final: 0.8535 (m-30) REVERT: C 176 MET cc_start: 0.9035 (mtp) cc_final: 0.7767 (mtp) REVERT: C 219 ASP cc_start: 0.8890 (p0) cc_final: 0.8583 (p0) REVERT: I 169 GLU cc_start: 0.8467 (mp0) cc_final: 0.8164 (pt0) REVERT: I 173 GLU cc_start: 0.8716 (tt0) cc_final: 0.8380 (tp30) REVERT: I 176 MET cc_start: 0.8591 (mmt) cc_final: 0.8309 (mmt) REVERT: I 340 ARG cc_start: 0.7675 (mpt180) cc_final: 0.7433 (mtm-85) REVERT: I 346 GLU cc_start: 0.7707 (mp0) cc_final: 0.7444 (mp0) REVERT: K 38 CYS cc_start: 0.8795 (m) cc_final: 0.8509 (m) REVERT: K 87 ASP cc_start: 0.8693 (t70) cc_final: 0.8449 (t0) REVERT: K 176 MET cc_start: 0.6379 (mtp) cc_final: 0.5903 (mtp) REVERT: K 240 ASN cc_start: 0.7327 (m110) cc_final: 0.7021 (m110) REVERT: K 251 ARG cc_start: 0.6848 (tpm170) cc_final: 0.6453 (tpp-160) REVERT: L 176 MET cc_start: 0.8072 (mmm) cc_final: 0.7336 (mmm) REVERT: L 220 THR cc_start: 0.8724 (p) cc_final: 0.8450 (p) REVERT: L 223 MET cc_start: 0.8572 (ttp) cc_final: 0.8252 (ttp) REVERT: L 227 GLU cc_start: 0.8260 (mp0) cc_final: 0.7823 (mp0) outliers start: 37 outliers final: 35 residues processed: 183 average time/residue: 0.1818 time to fit residues: 51.5330 Evaluate side-chains 192 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 336 LEU 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 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 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 SER Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 184 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 0.0030 chunk 131 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.066469 restraints weight = 54831.440| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.66 r_work: 0.2865 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- 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 0.052 23700 Z= 0.109 Angle : 0.489 9.109 32291 Z= 0.249 Chirality : 0.041 0.178 3537 Planarity : 0.004 0.058 4208 Dihedral : 4.872 41.424 3474 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.32 % Allowed : 12.73 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 2878 helix: 2.52 (0.17), residues: 949 sheet: -0.38 (0.20), residues: 706 loop : -1.12 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 46 TYR 0.013 0.001 TYR L 114 PHE 0.016 0.001 PHE K 98 TRP 0.010 0.001 TRP D 283 HIS 0.003 0.001 HIS D 388 Details of bonding type rmsd covalent geometry : bond 0.00253 (23700) covalent geometry : angle 0.48884 (32291) hydrogen bonds : bond 0.03078 ( 947) hydrogen bonds : angle 4.06133 ( 2775) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.191 Fit side-chains REVERT: A 188 ASP cc_start: 0.8195 (t70) cc_final: 0.7215 (t0) REVERT: B 357 ASP cc_start: 0.9036 (m-30) cc_final: 0.8549 (m-30) REVERT: C 176 MET cc_start: 0.9111 (mtp) cc_final: 0.7855 (mtp) REVERT: C 219 ASP cc_start: 0.8893 (p0) cc_final: 0.8569 (p0) REVERT: I 169 GLU cc_start: 0.8542 (mp0) cc_final: 0.8244 (pt0) REVERT: I 173 GLU cc_start: 0.8739 (tt0) cc_final: 0.8393 (tp30) REVERT: I 346 GLU cc_start: 0.7828 (mp0) cc_final: 0.7553 (mp0) REVERT: K 27 LEU cc_start: 0.7755 (mt) cc_final: 0.7492 (mt) REVERT: K 38 CYS cc_start: 0.8892 (m) cc_final: 0.8602 (m) REVERT: K 87 ASP cc_start: 0.8711 (t70) cc_final: 0.8463 (t0) REVERT: K 142 GLN cc_start: 0.7569 (pm20) cc_final: 0.7263 (pm20) REVERT: K 176 MET cc_start: 0.6567 (mtp) cc_final: 0.6022 (mtp) REVERT: K 240 ASN cc_start: 0.7300 (m110) cc_final: 0.6940 (m110) REVERT: K 243 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6564 (ptt-90) REVERT: K 251 ARG cc_start: 0.6891 (tpm170) cc_final: 0.6478 (tpp-160) REVERT: L 176 MET cc_start: 0.8162 (mmm) cc_final: 0.7415 (mmm) REVERT: L 220 THR cc_start: 0.8844 (p) cc_final: 0.8585 (p) REVERT: L 223 MET cc_start: 0.8621 (ttp) cc_final: 0.8324 (ttp) REVERT: L 227 GLU cc_start: 0.8265 (mp0) cc_final: 0.7880 (mp0) outliers start: 31 outliers final: 26 residues processed: 188 average time/residue: 0.1753 time to fit residues: 51.8272 Evaluate side-chains 185 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 407 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 243 ARG Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 282 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 56 ASN L 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.065978 restraints weight = 55128.037| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.72 r_work: 0.2848 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2075 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= 0.143 Angle : 0.507 8.484 32291 Z= 0.256 Chirality : 0.041 0.173 3537 Planarity : 0.004 0.059 4208 Dihedral : 4.847 41.286 3474 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.58 % Allowed : 12.82 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.16), residues: 2878 helix: 2.54 (0.17), residues: 949 sheet: -0.37 (0.20), residues: 709 loop : -1.08 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 46 TYR 0.023 0.001 TYR K 114 PHE 0.016 0.001 PHE K 98 TRP 0.010 0.001 TRP K 77 HIS 0.003 0.001 HIS D 278 Details of bonding type rmsd covalent geometry : bond 0.00334 (23700) covalent geometry : angle 0.50694 (32291) hydrogen bonds : bond 0.03241 ( 947) hydrogen bonds : angle 4.09586 ( 2775) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.930 Fit side-chains REVERT: A 188 ASP cc_start: 0.8187 (t70) cc_final: 0.7195 (t0) REVERT: B 357 ASP cc_start: 0.9015 (m-30) cc_final: 0.8534 (m-30) REVERT: C 176 MET cc_start: 0.9061 (mtp) cc_final: 0.7808 (mtp) REVERT: C 219 ASP cc_start: 0.8898 (p0) cc_final: 0.8536 (p0) REVERT: I 173 GLU cc_start: 0.8733 (tt0) cc_final: 0.8377 (tp30) REVERT: I 346 GLU cc_start: 0.7760 (mp0) cc_final: 0.7483 (mp0) REVERT: K 27 LEU cc_start: 0.7723 (mt) cc_final: 0.7470 (mt) REVERT: K 38 CYS cc_start: 0.8822 (m) cc_final: 0.8538 (m) REVERT: K 87 ASP cc_start: 0.8685 (t70) cc_final: 0.8446 (t0) REVERT: K 142 GLN cc_start: 0.7612 (pm20) cc_final: 0.7259 (pm20) REVERT: K 176 MET cc_start: 0.6405 (mtp) cc_final: 0.5868 (mtp) REVERT: K 240 ASN cc_start: 0.7329 (m110) cc_final: 0.6997 (m110) REVERT: K 243 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6541 (ptt-90) REVERT: K 251 ARG cc_start: 0.6859 (tpm170) cc_final: 0.6453 (tpp-160) REVERT: L 173 GLU cc_start: 0.7941 (tp30) cc_final: 0.7683 (tp30) REVERT: L 176 MET cc_start: 0.8061 (mmm) cc_final: 0.7317 (mmm) REVERT: L 220 THR cc_start: 0.8772 (p) cc_final: 0.8517 (p) REVERT: L 223 MET cc_start: 0.8565 (ttp) cc_final: 0.8267 (ttp) REVERT: L 227 GLU cc_start: 0.8198 (mp0) cc_final: 0.7779 (mp0) outliers start: 37 outliers final: 31 residues processed: 186 average time/residue: 0.1761 time to fit residues: 51.6532 Evaluate side-chains 189 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 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 402 MET Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 243 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 264 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 56 ASN L 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.069088 restraints weight = 54813.634| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.53 r_work: 0.2864 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23700 Z= 0.132 Angle : 0.507 8.393 32291 Z= 0.255 Chirality : 0.041 0.170 3537 Planarity : 0.004 0.058 4208 Dihedral : 4.831 41.167 3474 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.50 % Allowed : 12.64 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2878 helix: 2.56 (0.17), residues: 949 sheet: -0.36 (0.20), residues: 709 loop : -1.08 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 46 TYR 0.016 0.001 TYR L 114 PHE 0.017 0.001 PHE K 258 TRP 0.013 0.001 TRP K 77 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00309 (23700) covalent geometry : angle 0.50741 (32291) hydrogen bonds : bond 0.03173 ( 947) hydrogen bonds : angle 4.06427 ( 2775) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5756 Ramachandran restraints generated. 2878 Oldfield, 0 Emsley, 2878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.951 Fit side-chains REVERT: A 188 ASP cc_start: 0.8176 (t70) cc_final: 0.7197 (t0) REVERT: B 357 ASP cc_start: 0.9014 (m-30) cc_final: 0.8532 (m-30) REVERT: C 176 MET cc_start: 0.9066 (mtp) cc_final: 0.7776 (mtp) REVERT: C 219 ASP cc_start: 0.8890 (p0) cc_final: 0.8527 (p0) REVERT: I 169 GLU cc_start: 0.8460 (mp0) cc_final: 0.8162 (pt0) REVERT: I 173 GLU cc_start: 0.8729 (tt0) cc_final: 0.8370 (tp30) REVERT: I 346 GLU cc_start: 0.7798 (mp0) cc_final: 0.7505 (mp0) REVERT: K 27 LEU cc_start: 0.7776 (mt) cc_final: 0.7524 (mt) REVERT: K 38 CYS cc_start: 0.8851 (m) cc_final: 0.8551 (m) REVERT: K 87 ASP cc_start: 0.8720 (t70) cc_final: 0.8469 (t0) REVERT: K 142 GLN cc_start: 0.7670 (pm20) cc_final: 0.7304 (pm20) REVERT: K 176 MET cc_start: 0.6519 (mtp) cc_final: 0.5984 (mtp) REVERT: K 240 ASN cc_start: 0.7338 (m110) cc_final: 0.6964 (m110) REVERT: K 243 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6578 (ptt-90) REVERT: K 251 ARG cc_start: 0.6925 (tpm170) cc_final: 0.6510 (tpp-160) REVERT: L 173 GLU cc_start: 0.7949 (tp30) cc_final: 0.7676 (tp30) REVERT: L 176 MET cc_start: 0.8106 (mmm) cc_final: 0.7356 (mmm) REVERT: L 220 THR cc_start: 0.8792 (p) cc_final: 0.8534 (p) REVERT: L 223 MET cc_start: 0.8599 (ttp) cc_final: 0.8298 (ttp) REVERT: L 227 GLU cc_start: 0.8202 (mp0) cc_final: 0.7789 (mp0) outliers start: 35 outliers final: 32 residues processed: 183 average time/residue: 0.1767 time to fit residues: 50.7135 Evaluate side-chains 190 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain 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 402 MET Chi-restraints excluded: chain I residue 461 LEU Chi-restraints excluded: chain I residue 506 VAL Chi-restraints excluded: chain K residue 122 GLN Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 209 SER Chi-restraints excluded: chain K residue 243 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 10 optimal weight: 0.8980 chunk 211 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 197 optimal weight: 0.5980 chunk 233 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 265 optimal weight: 0.8980 chunk 207 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 56 ASN L 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.092338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070131 restraints weight = 54420.709| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.53 r_work: 0.2880 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2206 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= 0.104 Angle : 0.495 8.855 32291 Z= 0.248 Chirality : 0.041 0.164 3537 Planarity : 0.004 0.058 4208 Dihedral : 4.764 40.402 3474 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.45 % Allowed : 12.77 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.16), residues: 2878 helix: 2.54 (0.17), residues: 950 sheet: -0.32 (0.20), residues: 706 loop : -1.08 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 46 TYR 0.024 0.001 TYR K 114 PHE 0.017 0.001 PHE K 98 TRP 0.013 0.001 TRP K 77 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00241 (23700) covalent geometry : angle 0.49479 (32291) hydrogen bonds : bond 0.02976 ( 947) hydrogen bonds : angle 3.99583 ( 2775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.74 seconds wall clock time: 95 minutes 17.71 seconds (5717.71 seconds total)