Starting phenix.real_space_refine on Wed May 21 15:47:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q84_18246/05_2025/8q84_18246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q84_18246/05_2025/8q84_18246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q84_18246/05_2025/8q84_18246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q84_18246/05_2025/8q84_18246.map" model { file = "/net/cci-nas-00/data/ceres_data/8q84_18246/05_2025/8q84_18246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q84_18246/05_2025/8q84_18246.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 13453 2.51 5 N 3918 2.21 5 O 4351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21802 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1463 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 2, 'TRANS': 291} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 966 Unresolved non-hydrogen angles: 1196 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 20, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 490 Chain: "B" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1180 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'PTRANS': 1, 'TRANS': 235} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 785 Unresolved non-hydrogen angles: 987 Unresolved non-hydrogen dihedrals: 617 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 17, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 398 Chain: "F" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1463 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 2, 'TRANS': 291} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 966 Unresolved non-hydrogen angles: 1196 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 20, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 490 Chain: "G" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1175 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 1, 'TRANS': 234} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 983 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 17, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 398 Chain: "I" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "K" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 485 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "O" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1929 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "P" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 527 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Q" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "V" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "W" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "X" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 535 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "Z" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "a" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1925 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Chain: "b" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "c" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "d" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "e" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 14.99, per 1000 atoms: 0.69 Number of scatterers: 21802 At special positions: 0 Unit cell: (296.8, 157.94, 263.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 4351 8.00 N 3918 7.00 C 13453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.91 Conformation dependent library (CDL) restraints added in 3.2 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 8 sheets defined 86.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 372 through 393 removed outlier: 4.420A pdb=" N GLY A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.757A pdb=" N ASN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 479 removed outlier: 3.794A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.619A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.846A pdb=" N LEU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 663 Processing helix chain 'B' and resid 212 through 244 removed outlier: 3.543A pdb=" N GLU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 244 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 252 through 307 removed outlier: 3.708A pdb=" N SER B 256 " --> pdb=" O MET B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 337 Processing helix chain 'B' and resid 339 through 386 Processing helix chain 'B' and resid 386 through 401 Processing helix chain 'B' and resid 405 through 446 removed outlier: 3.547A pdb=" N ASN B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 393 removed outlier: 4.527A pdb=" N GLY F 376 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.841A pdb=" N ASN F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 479 removed outlier: 3.874A pdb=" N GLN F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU F 479 " --> pdb=" O SER F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 489 removed outlier: 3.776A pdb=" N LEU F 488 " --> pdb=" O ASN F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'F' and resid 506 through 511 removed outlier: 3.743A pdb=" N LEU F 510 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 663 Processing helix chain 'G' and resid 213 through 244 removed outlier: 4.057A pdb=" N LEU G 237 " --> pdb=" O GLN G 233 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER G 239 " --> pdb=" O VAL G 235 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU G 244 " --> pdb=" O ASN G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 248 Processing helix chain 'G' and resid 252 through 307 removed outlier: 3.735A pdb=" N SER G 256 " --> pdb=" O MET G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 337 Processing helix chain 'G' and resid 339 through 386 Processing helix chain 'G' and resid 386 through 401 Processing helix chain 'G' and resid 405 through 446 removed outlier: 3.559A pdb=" N ASN G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET G 446 " --> pdb=" O TYR G 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 110 Proline residue: I 65 - end of helix Processing helix chain 'I' and resid 120 through 151 Processing helix chain 'J' and resid 61 through 126 removed outlier: 4.433A pdb=" N LEU J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Proline residue: J 90 - end of helix removed outlier: 3.655A pdb=" N ASP J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 143 removed outlier: 3.817A pdb=" N LEU J 130 " --> pdb=" O ASP J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 176 Processing helix chain 'K' and resid 3 through 54 Processing helix chain 'K' and resid 54 through 67 removed outlier: 3.800A pdb=" N SER K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 3.545A pdb=" N GLN K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR K 73 " --> pdb=" O GLY K 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 68 through 73' Processing helix chain 'K' and resid 74 through 79 removed outlier: 3.602A pdb=" N TYR K 78 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU K 79 " --> pdb=" O GLY K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'L' and resid 16 through 57 Processing helix chain 'L' and resid 58 through 67 removed outlier: 3.958A pdb=" N VAL L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 65 removed outlier: 3.695A pdb=" N GLN M 7 " --> pdb=" O ASN M 3 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASN M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 65 " --> pdb=" O ASN M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 35 Processing helix chain 'N' and resid 53 through 65 removed outlier: 3.827A pdb=" N ASP N 59 " --> pdb=" O GLN N 55 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS N 63 " --> pdb=" O ASP N 59 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY N 65 " --> pdb=" O GLU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 94 removed outlier: 3.753A pdb=" N LYS N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 94 " --> pdb=" O GLY N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 Processing helix chain 'O' and resid 28 through 38 removed outlier: 3.568A pdb=" N ASN O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 51 removed outlier: 3.811A pdb=" N ARG O 45 " --> pdb=" O LYS O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 63 Processing helix chain 'O' and resid 81 through 99 Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.521A pdb=" N TYR O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS O 118 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU O 121 " --> pdb=" O ASN O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 168 Processing helix chain 'O' and resid 171 through 184 Processing helix chain 'O' and resid 206 through 221 Processing helix chain 'O' and resid 223 through 265 removed outlier: 3.647A pdb=" N LEU O 253 " --> pdb=" O LYS O 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 57 removed outlier: 3.698A pdb=" N GLU P 11 " --> pdb=" O GLU P 7 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE P 40 " --> pdb=" O THR P 36 " (cutoff:3.500A) Proline residue: P 41 - end of helix Processing helix chain 'P' and resid 57 through 69 removed outlier: 4.271A pdb=" N THR P 67 " --> pdb=" O MET P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 40 removed outlier: 3.591A pdb=" N HIS Q 14 " --> pdb=" O ASN Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 63 Processing helix chain 'R' and resid 2 through 40 Proline residue: R 32 - end of helix removed outlier: 4.112A pdb=" N MET R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 65 Processing helix chain 'R' and resid 65 through 108 Processing helix chain 'U' and resid 58 through 111 Proline residue: U 65 - end of helix removed outlier: 3.556A pdb=" N CYS U 111 " --> pdb=" O SER U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 151 Processing helix chain 'V' and resid 61 through 126 removed outlier: 4.450A pdb=" N LEU V 89 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Proline residue: V 90 - end of helix removed outlier: 3.809A pdb=" N ASP V 126 " --> pdb=" O LYS V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 143 Processing helix chain 'V' and resid 146 through 150 Processing helix chain 'V' and resid 151 through 176 Processing helix chain 'W' and resid 3 through 67 removed outlier: 4.562A pdb=" N ASN W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP W 56 " --> pdb=" O LEU W 52 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP W 57 " --> pdb=" O MET W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 73 Processing helix chain 'W' and resid 75 through 79 removed outlier: 3.812A pdb=" N GLU W 79 " --> pdb=" O GLY W 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 84 Processing helix chain 'X' and resid 14 through 57 Processing helix chain 'X' and resid 58 through 67 removed outlier: 4.080A pdb=" N VAL X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 80 Processing helix chain 'Y' and resid 4 through 42 removed outlier: 4.041A pdb=" N VAL Y 8 " --> pdb=" O PRO Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 65 Processing helix chain 'Z' and resid 6 through 35 Processing helix chain 'Z' and resid 53 through 65 removed outlier: 3.922A pdb=" N ASP Z 59 " --> pdb=" O GLN Z 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS Z 63 " --> pdb=" O ASP Z 59 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY Z 65 " --> pdb=" O GLU Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 94 removed outlier: 3.827A pdb=" N LYS Z 72 " --> pdb=" O GLY Z 68 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 22 Processing helix chain 'a' and resid 29 through 37 Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'a' and resid 56 through 63 Processing helix chain 'a' and resid 81 through 99 Processing helix chain 'a' and resid 111 through 125 removed outlier: 4.221A pdb=" N LYS a 118 " --> pdb=" O VAL a 114 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU a 121 " --> pdb=" O ASN a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 168 Processing helix chain 'a' and resid 171 through 183 Processing helix chain 'a' and resid 206 through 221 Processing helix chain 'a' and resid 223 through 265 removed outlier: 4.272A pdb=" N SER a 242 " --> pdb=" O GLU a 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 38 Processing helix chain 'b' and resid 38 through 57 Processing helix chain 'b' and resid 57 through 69 Processing helix chain 'c' and resid 2 through 39 Processing helix chain 'c' and resid 44 through 63 Processing helix chain 'd' and resid 2 through 40 Proline residue: d 32 - end of helix removed outlier: 3.741A pdb=" N THR d 39 " --> pdb=" O ASN d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 65 Processing helix chain 'd' and resid 65 through 108 Processing sheet with id=AA1, first strand: chain 'I' and resid 112 through 114 Processing sheet with id=AA2, first strand: chain 'O' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'O' and resid 64 through 67 Processing sheet with id=AA4, first strand: chain 'O' and resid 185 through 189 Processing sheet with id=AA5, first strand: chain 'U' and resid 112 through 113 Processing sheet with id=AA6, first strand: chain 'a' and resid 52 through 54 removed outlier: 3.660A pdb=" N ILE W 127 " --> pdb=" O ARG d 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'a' and resid 185 through 189 2257 hydrogen bonds defined for protein. 6720 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: 7.21 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5190 1.33 - 1.45: 3923 1.45 - 1.58: 12737 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 21992 Sorted by residual: bond pdb=" N LYS N 72 " pdb=" CA LYS N 72 " ideal model delta sigma weight residual 1.459 1.405 0.054 1.17e-02 7.31e+03 2.13e+01 bond pdb=" C LEU N 71 " pdb=" N LYS N 72 " ideal model delta sigma weight residual 1.334 1.298 0.036 1.23e-02 6.61e+03 8.47e+00 bond pdb=" CA LYS N 72 " pdb=" CB LYS N 72 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.57e-02 4.06e+03 7.95e+00 bond pdb=" C LYS N 72 " pdb=" O LYS N 72 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.15e-02 7.56e+03 4.89e+00 bond pdb=" CA LYS N 72 " pdb=" C LYS N 72 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.24e-02 6.50e+03 2.98e+00 ... (remaining 21987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 29429 2.60 - 5.20: 383 5.20 - 7.79: 43 7.79 - 10.39: 18 10.39 - 12.99: 4 Bond angle restraints: 29877 Sorted by residual: angle pdb=" CA MET I 143 " pdb=" CB MET I 143 " pdb=" CG MET I 143 " ideal model delta sigma weight residual 114.10 123.86 -9.76 2.00e+00 2.50e-01 2.38e+01 angle pdb=" CA MET U 143 " pdb=" CB MET U 143 " pdb=" CG MET U 143 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CA ARG d 57 " pdb=" CB ARG d 57 " pdb=" CG ARG d 57 " ideal model delta sigma weight residual 114.10 122.47 -8.37 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA TYR Z 16 " pdb=" CB TYR Z 16 " pdb=" CG TYR Z 16 " ideal model delta sigma weight residual 113.90 121.42 -7.52 1.80e+00 3.09e-01 1.75e+01 angle pdb=" CA GLN d 85 " pdb=" CB GLN d 85 " pdb=" CG GLN d 85 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 ... (remaining 29872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 12030 17.22 - 34.43: 1131 34.43 - 51.65: 316 51.65 - 68.86: 57 68.86 - 86.08: 27 Dihedral angle restraints: 13561 sinusoidal: 4396 harmonic: 9165 Sorted by residual: dihedral pdb=" CA ILE Z 53 " pdb=" C ILE Z 53 " pdb=" N LEU Z 54 " pdb=" CA LEU Z 54 " ideal model delta harmonic sigma weight residual -180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LEU I 63 " pdb=" C LEU I 63 " pdb=" N LEU I 64 " pdb=" CA LEU I 64 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP O 119 " pdb=" CB ASP O 119 " pdb=" CG ASP O 119 " pdb=" OD1 ASP O 119 " ideal model delta sinusoidal sigma weight residual -30.00 -89.96 59.96 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 13558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3265 0.066 - 0.132: 337 0.132 - 0.197: 22 0.197 - 0.263: 3 0.263 - 0.329: 2 Chirality restraints: 3629 Sorted by residual: chirality pdb=" CG LEU R 97 " pdb=" CB LEU R 97 " pdb=" CD1 LEU R 97 " pdb=" CD2 LEU R 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL O 251 " pdb=" CA VAL O 251 " pdb=" CG1 VAL O 251 " pdb=" CG2 VAL O 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU Z 78 " pdb=" CB LEU Z 78 " pdb=" CD1 LEU Z 78 " pdb=" CD2 LEU Z 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3626 not shown) Planarity restraints: 3977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 64 " 0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO I 65 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO I 65 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 65 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP U 120 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C ASP U 120 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP U 120 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE U 121 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 58 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C GLU X 58 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU X 58 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE X 59 " -0.016 2.00e-02 2.50e+03 ... (remaining 3974 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 267 2.62 - 3.19: 21632 3.19 - 3.76: 38930 3.76 - 4.33: 44268 4.33 - 4.90: 72870 Nonbonded interactions: 177967 Sorted by model distance: nonbonded pdb=" O ILE O 247 " pdb=" OH TYR R 95 " model vdw 2.054 3.040 nonbonded pdb=" OG SER W 3 " pdb=" OD1 ASP W 5 " model vdw 2.125 3.040 nonbonded pdb=" OE1 GLU a 182 " pdb=" ND2 ASN a 183 " model vdw 2.143 3.120 nonbonded pdb=" NZ LYS V 79 " pdb=" OD2 ASP Z 22 " model vdw 2.182 3.120 nonbonded pdb=" OE2 GLU U 96 " pdb=" N ILE a 29 " model vdw 2.185 3.120 ... (remaining 177962 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' selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 212 through 447) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = (chain 'X' and resid 15 through 75) } ncs_group { reference = chain 'M' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = (chain 'Z' and resid 3 through 94) } ncs_group { reference = (chain 'O' and resid 3 through 265) selection = chain 'a' } ncs_group { reference = chain 'P' selection = (chain 'b' and resid 5 through 69) } ncs_group { reference = chain 'Q' selection = chain 'c' } ncs_group { reference = chain 'R' selection = chain 'd' } 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: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.220 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21992 Z= 0.171 Angle : 0.740 12.988 29877 Z= 0.400 Chirality : 0.040 0.329 3629 Planarity : 0.004 0.085 3977 Dihedral : 15.742 86.080 7539 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 0.58 % Allowed : 22.99 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.15), residues: 3057 helix: 2.80 (0.10), residues: 2543 sheet: 0.06 (0.97), residues: 32 loop : -0.32 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.045 0.002 TYR Z 16 ARG 0.017 0.001 ARG O 176 Details of bonding type rmsd hydrogen bonds : bond 0.08914 ( 2257) hydrogen bonds : angle 4.69122 ( 6720) covalent geometry : bond 0.00342 (21992) covalent geometry : angle 0.73983 (29877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 377 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 GLN cc_start: 0.8449 (tt0) cc_final: 0.7800 (tp40) REVERT: Q 6 GLN cc_start: 0.9398 (mt0) cc_final: 0.9067 (mm-40) REVERT: U 66 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8769 (mmmm) REVERT: W 41 GLU cc_start: 0.8434 (tp30) cc_final: 0.8067 (tp30) REVERT: W 47 ASP cc_start: 0.8972 (t0) cc_final: 0.8651 (p0) REVERT: Z 11 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8235 (tm-30) REVERT: a 168 PHE cc_start: 0.8271 (m-80) cc_final: 0.7960 (m-80) REVERT: a 201 PHE cc_start: 0.8544 (t80) cc_final: 0.8290 (t80) outliers start: 11 outliers final: 6 residues processed: 380 average time/residue: 0.3278 time to fit residues: 192.1333 Evaluate side-chains 318 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 312 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain V residue 144 THR Chi-restraints excluded: chain W residue 72 GLN Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain d residue 98 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 77 optimal weight: 50.0000 chunk 153 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 142 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN V 134 ASN W 72 GLN Y 19 ASN b 22 GLN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 44 GLN d 105 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.099298 restraints weight = 77613.763| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.53 r_work: 0.3452 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21992 Z= 0.156 Angle : 0.612 11.066 29877 Z= 0.321 Chirality : 0.038 0.242 3629 Planarity : 0.004 0.071 3977 Dihedral : 4.316 44.722 3251 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.81 % Rotamer: Outliers : 3.58 % Allowed : 18.36 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.15), residues: 3057 helix: 3.08 (0.10), residues: 2533 sheet: -0.23 (0.89), residues: 32 loop : -0.30 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.006 0.001 HIS a 31 PHE 0.034 0.002 PHE a 246 TYR 0.040 0.002 TYR Z 16 ARG 0.007 0.001 ARG X 24 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 2257) hydrogen bonds : angle 3.99155 ( 6720) covalent geometry : bond 0.00330 (21992) covalent geometry : angle 0.61209 (29877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 349 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 69 GLU cc_start: 0.8767 (mp0) cc_final: 0.8540 (mp0) REVERT: J 72 ASP cc_start: 0.9282 (m-30) cc_final: 0.8986 (m-30) REVERT: K 77 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8633 (t0) REVERT: K 85 ASP cc_start: 0.8754 (t0) cc_final: 0.8526 (t0) REVERT: N 32 GLU cc_start: 0.9256 (tp30) cc_final: 0.9013 (tp30) REVERT: N 35 TYR cc_start: 0.6983 (m-80) cc_final: 0.6752 (m-80) REVERT: P 65 GLN cc_start: 0.8519 (tt0) cc_final: 0.7815 (tp-100) REVERT: Q 33 MET cc_start: 0.8968 (tmm) cc_final: 0.8726 (tmm) REVERT: U 61 GLN cc_start: 0.9320 (mt0) cc_final: 0.9048 (mm110) REVERT: U 66 LYS cc_start: 0.9418 (mmtt) cc_final: 0.9068 (mmmm) REVERT: U 123 ASP cc_start: 0.9043 (t0) cc_final: 0.8726 (t0) REVERT: V 140 GLU cc_start: 0.7797 (mp0) cc_final: 0.7041 (pm20) REVERT: X 58 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8545 (tm-30) REVERT: Z 29 THR cc_start: 0.8681 (m) cc_final: 0.8477 (m) REVERT: Z 35 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8205 (m-80) REVERT: a 168 PHE cc_start: 0.9092 (m-80) cc_final: 0.8506 (m-80) REVERT: a 179 TYR cc_start: 0.8426 (t80) cc_final: 0.8214 (t80) REVERT: a 188 MET cc_start: 0.4737 (ppp) cc_final: 0.4494 (ppp) REVERT: a 201 PHE cc_start: 0.8626 (t80) cc_final: 0.8369 (t80) REVERT: b 1 MET cc_start: 0.6740 (tmm) cc_final: 0.5694 (ppp) REVERT: d 85 GLN cc_start: 0.9721 (pp30) cc_final: 0.9422 (pp30) REVERT: d 98 ASN cc_start: 0.7645 (m110) cc_final: 0.6477 (t0) outliers start: 68 outliers final: 31 residues processed: 397 average time/residue: 0.3163 time to fit residues: 196.1553 Evaluate side-chains 338 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 83 PHE Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain V residue 124 MET Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 77 SER Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain b residue 2 ASP Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 187 optimal weight: 0.9980 chunk 5 optimal weight: 40.0000 chunk 222 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 266 optimal weight: 0.9990 chunk 242 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 22 optimal weight: 50.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 GLN K 31 GLN L 29 GLN M 61 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN a 57 HIS a 173 GLN a 195 GLN c 6 GLN c 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.146121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.099817 restraints weight = 75910.060| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.42 r_work: 0.3468 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21992 Z= 0.147 Angle : 0.595 11.354 29877 Z= 0.310 Chirality : 0.038 0.372 3629 Planarity : 0.004 0.059 3977 Dihedral : 4.051 44.643 3243 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 2.89 % Allowed : 19.83 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.15), residues: 3057 helix: 3.12 (0.10), residues: 2550 sheet: -0.34 (1.06), residues: 22 loop : -0.37 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 59 HIS 0.007 0.001 HIS a 31 PHE 0.019 0.002 PHE M 60 TYR 0.023 0.001 TYR Z 16 ARG 0.007 0.001 ARG X 24 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 2257) hydrogen bonds : angle 3.83090 ( 6720) covalent geometry : bond 0.00309 (21992) covalent geometry : angle 0.59459 (29877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 72 ASP cc_start: 0.9190 (m-30) cc_final: 0.8944 (m-30) REVERT: K 12 ARG cc_start: 0.8345 (mpp80) cc_final: 0.8106 (mtt90) REVERT: K 20 LYS cc_start: 0.8224 (mttm) cc_final: 0.7857 (mmtp) REVERT: K 85 ASP cc_start: 0.8747 (t0) cc_final: 0.8376 (t0) REVERT: N 28 GLU cc_start: 0.9346 (tp30) cc_final: 0.9140 (tp30) REVERT: N 32 GLU cc_start: 0.9202 (tp30) cc_final: 0.8474 (tp30) REVERT: N 59 ASP cc_start: 0.8552 (t0) cc_final: 0.8351 (t0) REVERT: N 83 LYS cc_start: 0.9384 (tppp) cc_final: 0.9145 (tppp) REVERT: N 87 GLU cc_start: 0.8455 (pp20) cc_final: 0.8238 (pp20) REVERT: P 65 GLN cc_start: 0.8561 (tt0) cc_final: 0.7881 (tp-100) REVERT: Q 6 GLN cc_start: 0.9329 (mt0) cc_final: 0.9062 (mm-40) REVERT: Q 33 MET cc_start: 0.9030 (tmm) cc_final: 0.8669 (tmm) REVERT: R 1 MET cc_start: 0.6768 (mmt) cc_final: 0.6525 (mmt) REVERT: R 81 MET cc_start: 0.7313 (mmp) cc_final: 0.6967 (mmm) REVERT: U 61 GLN cc_start: 0.9302 (mt0) cc_final: 0.9007 (mm110) REVERT: U 66 LYS cc_start: 0.9442 (mmtt) cc_final: 0.9055 (mmmm) REVERT: U 123 ASP cc_start: 0.9031 (t0) cc_final: 0.8744 (t0) REVERT: U 135 GLU cc_start: 0.9397 (mm-30) cc_final: 0.8705 (pp20) REVERT: V 148 ASP cc_start: 0.7883 (t0) cc_final: 0.7445 (p0) REVERT: W 79 GLU cc_start: 0.7895 (mp0) cc_final: 0.7579 (pm20) REVERT: X 58 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8554 (tm-30) REVERT: X 60 GLN cc_start: 0.8879 (tp40) cc_final: 0.8403 (pm20) REVERT: Z 19 LEU cc_start: 0.9449 (tt) cc_final: 0.9223 (mm) REVERT: Z 22 ASP cc_start: 0.7889 (p0) cc_final: 0.7679 (p0) REVERT: Z 29 THR cc_start: 0.8723 (m) cc_final: 0.8502 (m) REVERT: Z 35 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8353 (t80) REVERT: a 168 PHE cc_start: 0.9010 (m-80) cc_final: 0.8518 (m-80) REVERT: a 179 TYR cc_start: 0.8365 (t80) cc_final: 0.8003 (t80) REVERT: a 188 MET cc_start: 0.4992 (ppp) cc_final: 0.4776 (ppp) REVERT: a 201 PHE cc_start: 0.8748 (t80) cc_final: 0.8260 (t80) REVERT: b 1 MET cc_start: 0.6489 (tmm) cc_final: 0.6038 (tmm) REVERT: d 98 ASN cc_start: 0.7627 (m110) cc_final: 0.6574 (t0) REVERT: d 108 MET cc_start: 0.2591 (tmm) cc_final: 0.1581 (pmm) outliers start: 55 outliers final: 35 residues processed: 391 average time/residue: 0.3193 time to fit residues: 197.0768 Evaluate side-chains 344 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain b residue 2 ASP Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 122 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 218 optimal weight: 0.6980 chunk 204 optimal weight: 0.6980 chunk 265 optimal weight: 6.9990 chunk 72 optimal weight: 50.0000 chunk 111 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 40.0000 chunk 49 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 31 GLN L 29 GLN N 41 GLN Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN W 45 ASN a 57 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.146269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.100078 restraints weight = 76806.893| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.42 r_work: 0.3478 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21992 Z= 0.139 Angle : 0.575 9.615 29877 Z= 0.303 Chirality : 0.037 0.263 3629 Planarity : 0.004 0.053 3977 Dihedral : 3.969 44.897 3243 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Rotamer: Outliers : 3.95 % Allowed : 20.04 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.15), residues: 3057 helix: 3.20 (0.10), residues: 2549 sheet: -0.25 (0.86), residues: 32 loop : -0.36 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 59 HIS 0.008 0.001 HIS a 57 PHE 0.026 0.002 PHE O 168 TYR 0.026 0.002 TYR Z 16 ARG 0.009 0.001 ARG R 78 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 2257) hydrogen bonds : angle 3.74558 ( 6720) covalent geometry : bond 0.00288 (21992) covalent geometry : angle 0.57511 (29877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 346 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8268 (pp) REVERT: I 69 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8772 (mp0) REVERT: J 72 ASP cc_start: 0.9209 (m-30) cc_final: 0.8941 (m-30) REVERT: K 20 LYS cc_start: 0.8313 (mttm) cc_final: 0.7921 (mmtm) REVERT: K 85 ASP cc_start: 0.8762 (t0) cc_final: 0.8329 (t0) REVERT: N 24 LYS cc_start: 0.9249 (mtmm) cc_final: 0.8959 (pttm) REVERT: N 59 ASP cc_start: 0.8647 (t0) cc_final: 0.8384 (t0) REVERT: N 83 LYS cc_start: 0.9419 (tppp) cc_final: 0.9163 (tppp) REVERT: O 205 PHE cc_start: 0.7729 (m-80) cc_final: 0.7281 (t80) REVERT: O 232 GLN cc_start: 0.9393 (pp30) cc_final: 0.8946 (pp30) REVERT: U 61 GLN cc_start: 0.9290 (mt0) cc_final: 0.8993 (mm110) REVERT: U 66 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9041 (mmmm) REVERT: U 123 ASP cc_start: 0.9041 (t0) cc_final: 0.8778 (t0) REVERT: V 148 ASP cc_start: 0.7802 (t0) cc_final: 0.7311 (p0) REVERT: X 58 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8412 (tm-30) REVERT: X 74 GLU cc_start: 0.7899 (mp0) cc_final: 0.7663 (mp0) REVERT: Y 6 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8092 (mm-30) REVERT: Z 29 THR cc_start: 0.8690 (m) cc_final: 0.8401 (m) REVERT: Z 35 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8270 (t80) REVERT: a 168 PHE cc_start: 0.8990 (m-80) cc_final: 0.8489 (m-80) REVERT: a 179 TYR cc_start: 0.8435 (t80) cc_final: 0.8002 (t80) REVERT: a 188 MET cc_start: 0.4932 (ppp) cc_final: 0.4660 (ppp) REVERT: a 201 PHE cc_start: 0.8745 (t80) cc_final: 0.8244 (t80) REVERT: b 1 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5466 (tmm) REVERT: d 50 VAL cc_start: 0.8482 (t) cc_final: 0.7990 (m) REVERT: d 85 GLN cc_start: 0.9699 (pp30) cc_final: 0.9384 (pp30) REVERT: d 98 ASN cc_start: 0.7671 (m110) cc_final: 0.6666 (t0) REVERT: d 108 MET cc_start: 0.2686 (tmm) cc_final: 0.1694 (pmm) REVERT: e 16 GLU cc_start: 0.8435 (pm20) cc_final: 0.8163 (pm20) REVERT: e 17 TYR cc_start: 0.8576 (t80) cc_final: 0.8374 (t80) outliers start: 75 outliers final: 40 residues processed: 397 average time/residue: 0.3188 time to fit residues: 197.9904 Evaluate side-chains 362 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 129 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 286 optimal weight: 1.9990 chunk 3 optimal weight: 50.0000 chunk 282 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 ASN a 57 HIS c 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.143194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.096706 restraints weight = 70158.086| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.60 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21992 Z= 0.162 Angle : 0.599 13.220 29877 Z= 0.315 Chirality : 0.037 0.243 3629 Planarity : 0.004 0.053 3977 Dihedral : 3.946 45.246 3243 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 3.89 % Allowed : 20.67 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.15), residues: 3057 helix: 3.20 (0.10), residues: 2556 sheet: -0.23 (0.89), residues: 32 loop : -0.36 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.013 0.001 HIS a 57 PHE 0.020 0.002 PHE M 60 TYR 0.026 0.002 TYR Z 16 ARG 0.007 0.001 ARG R 78 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 2257) hydrogen bonds : angle 3.72461 ( 6720) covalent geometry : bond 0.00348 (21992) covalent geometry : angle 0.59917 (29877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 348 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8206 (pp) REVERT: J 72 ASP cc_start: 0.9115 (m-30) cc_final: 0.8830 (m-30) REVERT: K 8 ILE cc_start: 0.7899 (mm) cc_final: 0.7584 (mm) REVERT: K 12 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7995 (mpp80) REVERT: K 20 LYS cc_start: 0.8487 (mttm) cc_final: 0.8102 (mmtp) REVERT: K 85 ASP cc_start: 0.8733 (t0) cc_final: 0.8259 (t0) REVERT: N 13 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8653 (mm) REVERT: N 17 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8850 (mppt) REVERT: N 24 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8716 (pttm) REVERT: N 32 GLU cc_start: 0.8897 (tp30) cc_final: 0.8584 (tp30) REVERT: N 59 ASP cc_start: 0.8494 (t0) cc_final: 0.8180 (t0) REVERT: N 83 LYS cc_start: 0.9375 (tppp) cc_final: 0.9005 (tppt) REVERT: O 175 GLN cc_start: 0.8955 (mm110) cc_final: 0.8690 (mm110) REVERT: P 38 ASP cc_start: 0.7911 (m-30) cc_final: 0.7703 (m-30) REVERT: Q 33 MET cc_start: 0.8968 (tmm) cc_final: 0.8512 (tmm) REVERT: U 66 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9039 (mmmm) REVERT: U 93 ASP cc_start: 0.8236 (t0) cc_final: 0.7273 (t0) REVERT: U 123 ASP cc_start: 0.8831 (t0) cc_final: 0.8597 (t0) REVERT: V 148 ASP cc_start: 0.8121 (t0) cc_final: 0.7534 (p0) REVERT: W 40 LYS cc_start: 0.8848 (tppt) cc_final: 0.8633 (tptp) REVERT: X 58 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8367 (tm-30) REVERT: X 60 GLN cc_start: 0.8765 (tp40) cc_final: 0.8358 (pm20) REVERT: Y 6 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8016 (mm-30) REVERT: Z 29 THR cc_start: 0.8393 (m) cc_final: 0.8150 (m) REVERT: Z 35 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8227 (t80) REVERT: a 19 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8701 (mmm) REVERT: a 168 PHE cc_start: 0.8980 (m-80) cc_final: 0.8478 (m-80) REVERT: a 188 MET cc_start: 0.4658 (ppp) cc_final: 0.4400 (ppp) REVERT: b 1 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5780 (tmm) REVERT: b 58 GLU cc_start: 0.8176 (tp30) cc_final: 0.7799 (tm-30) REVERT: d 81 MET cc_start: 0.2936 (OUTLIER) cc_final: 0.2485 (tpt) REVERT: d 85 GLN cc_start: 0.9714 (pp30) cc_final: 0.9428 (pp30) REVERT: d 98 ASN cc_start: 0.7444 (m110) cc_final: 0.6486 (t0) outliers start: 74 outliers final: 45 residues processed: 397 average time/residue: 0.3172 time to fit residues: 194.4093 Evaluate side-chains 373 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 124 MET Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 200 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 261 optimal weight: 0.8980 chunk 133 optimal weight: 0.0980 chunk 183 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 36 GLN Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.143602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.096555 restraints weight = 70994.276| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.49 r_work: 0.3359 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21992 Z= 0.152 Angle : 0.603 10.461 29877 Z= 0.317 Chirality : 0.037 0.242 3629 Planarity : 0.004 0.053 3977 Dihedral : 3.947 45.418 3243 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 3.73 % Allowed : 21.62 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.15), residues: 3057 helix: 3.24 (0.09), residues: 2554 sheet: -0.17 (0.89), residues: 32 loop : -0.32 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.009 0.001 HIS a 57 PHE 0.026 0.002 PHE a 201 TYR 0.025 0.001 TYR Z 16 ARG 0.010 0.001 ARG R 78 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 2257) hydrogen bonds : angle 3.70053 ( 6720) covalent geometry : bond 0.00323 (21992) covalent geometry : angle 0.60279 (29877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 346 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8253 (pp) REVERT: I 69 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8798 (mp0) REVERT: I 112 VAL cc_start: 0.9097 (t) cc_final: 0.8823 (p) REVERT: J 72 ASP cc_start: 0.9241 (m-30) cc_final: 0.8978 (m-30) REVERT: K 16 GLN cc_start: 0.8463 (pp30) cc_final: 0.8198 (pp30) REVERT: K 20 LYS cc_start: 0.8468 (mttm) cc_final: 0.8050 (mmtm) REVERT: K 85 ASP cc_start: 0.8879 (t0) cc_final: 0.8413 (t0) REVERT: N 32 GLU cc_start: 0.9316 (tp30) cc_final: 0.9023 (tp30) REVERT: N 35 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7665 (t80) REVERT: N 83 LYS cc_start: 0.9436 (tppp) cc_final: 0.8932 (tppt) REVERT: O 205 PHE cc_start: 0.7848 (m-80) cc_final: 0.7401 (t80) REVERT: O 230 TYR cc_start: 0.8883 (t80) cc_final: 0.8628 (t80) REVERT: P 38 ASP cc_start: 0.8372 (m-30) cc_final: 0.8170 (m-30) REVERT: Q 6 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8842 (mp10) REVERT: Q 33 MET cc_start: 0.9024 (tmm) cc_final: 0.8602 (tmm) REVERT: U 66 LYS cc_start: 0.9454 (mmtt) cc_final: 0.9142 (mmmm) REVERT: U 123 ASP cc_start: 0.9173 (t0) cc_final: 0.8939 (t0) REVERT: V 98 GLU cc_start: 0.9139 (tp30) cc_final: 0.8861 (tp30) REVERT: V 148 ASP cc_start: 0.7959 (t0) cc_final: 0.7391 (p0) REVERT: W 126 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7209 (tmm-80) REVERT: X 58 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8576 (tm-30) REVERT: X 60 GLN cc_start: 0.8915 (tp40) cc_final: 0.8442 (pm20) REVERT: X 74 GLU cc_start: 0.7887 (mp0) cc_final: 0.7597 (mp0) REVERT: Y 6 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8246 (mm-30) REVERT: Y 40 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8626 (ttp80) REVERT: Z 29 THR cc_start: 0.8554 (m) cc_final: 0.8303 (m) REVERT: Z 35 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8311 (t80) REVERT: Z 83 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9004 (pttm) REVERT: a 19 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8787 (mmm) REVERT: a 168 PHE cc_start: 0.9177 (m-80) cc_final: 0.8612 (m-80) REVERT: a 188 MET cc_start: 0.4777 (ppp) cc_final: 0.4463 (ppp) REVERT: b 1 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5647 (tmm) REVERT: b 8 GLU cc_start: 0.7846 (tp30) cc_final: 0.7426 (tp30) REVERT: b 58 GLU cc_start: 0.8854 (tp30) cc_final: 0.8418 (tm-30) REVERT: c 33 MET cc_start: 0.9373 (ttt) cc_final: 0.9116 (ttt) REVERT: d 20 LYS cc_start: 0.9305 (tppt) cc_final: 0.8889 (tppt) REVERT: d 81 MET cc_start: 0.3233 (OUTLIER) cc_final: 0.2744 (tpt) REVERT: d 85 GLN cc_start: 0.9744 (pp30) cc_final: 0.9482 (pp30) REVERT: d 98 ASN cc_start: 0.7757 (m110) cc_final: 0.6810 (t0) REVERT: d 108 MET cc_start: 0.2610 (ppp) cc_final: 0.1665 (pmm) outliers start: 71 outliers final: 50 residues processed: 394 average time/residue: 0.3149 time to fit residues: 192.9788 Evaluate side-chains 374 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain Q residue 6 GLN Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 235 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 79 optimal weight: 50.0000 chunk 176 optimal weight: 0.8980 chunk 74 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 4 optimal weight: 0.1980 chunk 89 optimal weight: 30.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 34 ASN O 36 GLN Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 132 ASN d 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.142618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.096172 restraints weight = 70303.973| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.31 r_work: 0.3381 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21992 Z= 0.169 Angle : 0.622 10.170 29877 Z= 0.328 Chirality : 0.038 0.241 3629 Planarity : 0.003 0.051 3977 Dihedral : 3.954 45.623 3243 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % Rotamer: Outliers : 3.79 % Allowed : 22.99 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.15), residues: 3057 helix: 3.22 (0.09), residues: 2566 sheet: -0.07 (0.89), residues: 32 loop : -0.35 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 59 HIS 0.008 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.022 0.002 TYR Z 16 ARG 0.006 0.001 ARG R 78 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 2257) hydrogen bonds : angle 3.70224 ( 6720) covalent geometry : bond 0.00368 (21992) covalent geometry : angle 0.62201 (29877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 333 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8218 (pp) REVERT: I 69 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8802 (mp0) REVERT: I 112 VAL cc_start: 0.9116 (t) cc_final: 0.8865 (p) REVERT: J 72 ASP cc_start: 0.9278 (m-30) cc_final: 0.9014 (m-30) REVERT: J 77 MET cc_start: 0.9118 (ppp) cc_final: 0.8796 (ppp) REVERT: K 20 LYS cc_start: 0.8524 (mttm) cc_final: 0.8277 (mttp) REVERT: K 85 ASP cc_start: 0.8934 (t0) cc_final: 0.8473 (t0) REVERT: N 32 GLU cc_start: 0.9326 (tp30) cc_final: 0.8960 (tp30) REVERT: N 35 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7593 (t80) REVERT: O 205 PHE cc_start: 0.7714 (m-80) cc_final: 0.7118 (t80) REVERT: O 230 TYR cc_start: 0.8853 (t80) cc_final: 0.8548 (t80) REVERT: O 261 MET cc_start: 0.1840 (OUTLIER) cc_final: 0.1578 (ppp) REVERT: P 38 ASP cc_start: 0.8461 (m-30) cc_final: 0.8227 (m-30) REVERT: U 66 LYS cc_start: 0.9408 (mmtt) cc_final: 0.9116 (mmmm) REVERT: W 126 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7362 (tmm-80) REVERT: X 58 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8390 (tm-30) REVERT: X 60 GLN cc_start: 0.8931 (tp40) cc_final: 0.8658 (tp40) REVERT: Y 6 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8332 (mm-30) REVERT: Z 29 THR cc_start: 0.8515 (m) cc_final: 0.8261 (m) REVERT: Z 35 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8302 (t80) REVERT: Z 83 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8972 (pttm) REVERT: a 17 ASP cc_start: 0.9500 (t0) cc_final: 0.9285 (m-30) REVERT: a 19 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8841 (mmm) REVERT: a 168 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: a 188 MET cc_start: 0.4820 (ppp) cc_final: 0.4493 (ppp) REVERT: b 1 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5729 (tmm) REVERT: b 8 GLU cc_start: 0.7970 (tp30) cc_final: 0.7464 (tp30) REVERT: b 58 GLU cc_start: 0.8846 (tp30) cc_final: 0.8425 (tm-30) REVERT: c 33 MET cc_start: 0.9406 (ttt) cc_final: 0.9183 (ttt) REVERT: d 20 LYS cc_start: 0.9285 (tppt) cc_final: 0.8858 (tppt) REVERT: d 81 MET cc_start: 0.3017 (OUTLIER) cc_final: 0.2565 (tpt) REVERT: d 85 GLN cc_start: 0.9744 (pp30) cc_final: 0.9451 (pp30) REVERT: d 98 ASN cc_start: 0.7499 (m-40) cc_final: 0.6560 (t0) REVERT: d 108 MET cc_start: 0.2702 (ppp) cc_final: 0.1583 (pmm) outliers start: 72 outliers final: 51 residues processed: 380 average time/residue: 0.3253 time to fit residues: 192.3812 Evaluate side-chains 370 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 309 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 286 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 294 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 72 optimal weight: 50.0000 chunk 281 optimal weight: 0.6980 chunk 0 optimal weight: 70.0000 chunk 51 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 55 optimal weight: 40.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.141794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.094790 restraints weight = 70103.568| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 4.20 r_work: 0.3353 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21992 Z= 0.200 Angle : 0.658 11.282 29877 Z= 0.346 Chirality : 0.039 0.245 3629 Planarity : 0.004 0.052 3977 Dihedral : 3.998 45.990 3243 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.81 % Rotamer: Outliers : 4.05 % Allowed : 23.20 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.15), residues: 3057 helix: 3.18 (0.09), residues: 2569 sheet: -0.13 (0.91), residues: 32 loop : -0.34 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 221 HIS 0.008 0.001 HIS a 31 PHE 0.040 0.002 PHE a 201 TYR 0.020 0.002 TYR a 237 ARG 0.008 0.001 ARG R 78 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 2257) hydrogen bonds : angle 3.73666 ( 6720) covalent geometry : bond 0.00439 (21992) covalent geometry : angle 0.65804 (29877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 327 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8149 (pp) REVERT: I 69 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8828 (mp0) REVERT: I 120 ASP cc_start: 0.8843 (p0) cc_final: 0.8569 (p0) REVERT: I 123 ASP cc_start: 0.8834 (t0) cc_final: 0.8542 (t0) REVERT: J 72 ASP cc_start: 0.9237 (m-30) cc_final: 0.8971 (m-30) REVERT: K 20 LYS cc_start: 0.8665 (mttm) cc_final: 0.8364 (mttp) REVERT: K 85 ASP cc_start: 0.9008 (t0) cc_final: 0.8532 (t0) REVERT: M 16 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8911 (tt) REVERT: N 32 GLU cc_start: 0.9334 (tp30) cc_final: 0.8928 (tp30) REVERT: N 35 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7606 (t80) REVERT: N 59 ASP cc_start: 0.8880 (t0) cc_final: 0.8566 (t0) REVERT: O 230 TYR cc_start: 0.8896 (t80) cc_final: 0.8585 (t80) REVERT: O 261 MET cc_start: 0.1776 (OUTLIER) cc_final: 0.1492 (ppp) REVERT: P 38 ASP cc_start: 0.8560 (m-30) cc_final: 0.8267 (m-30) REVERT: Q 11 GLN cc_start: 0.8657 (pp30) cc_final: 0.8089 (pp30) REVERT: R 1 MET cc_start: 0.7251 (mmt) cc_final: 0.6841 (mmt) REVERT: U 66 LYS cc_start: 0.9420 (mmtt) cc_final: 0.9179 (mmmt) REVERT: V 148 ASP cc_start: 0.7642 (t0) cc_final: 0.7120 (p0) REVERT: W 126 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7423 (tmm-80) REVERT: X 58 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8359 (tm-30) REVERT: Z 29 THR cc_start: 0.8466 (m) cc_final: 0.8170 (m) REVERT: Z 35 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8253 (t80) REVERT: Z 83 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9035 (pttm) REVERT: a 19 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8504 (mmm) REVERT: a 168 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: a 188 MET cc_start: 0.5062 (ppp) cc_final: 0.4712 (ppp) REVERT: b 1 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5514 (tmm) REVERT: b 8 GLU cc_start: 0.8105 (tp30) cc_final: 0.7575 (tp30) REVERT: c 24 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8524 (tm-30) REVERT: d 20 LYS cc_start: 0.9289 (tppt) cc_final: 0.8956 (tppt) REVERT: d 81 MET cc_start: 0.3173 (OUTLIER) cc_final: 0.2783 (tpt) REVERT: d 85 GLN cc_start: 0.9762 (pp30) cc_final: 0.9471 (pp30) REVERT: d 98 ASN cc_start: 0.7683 (m-40) cc_final: 0.6760 (t0) REVERT: d 108 MET cc_start: 0.2970 (ppp) cc_final: 0.1887 (pmm) outliers start: 77 outliers final: 53 residues processed: 380 average time/residue: 0.3284 time to fit residues: 194.1666 Evaluate side-chains 366 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 45 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 124 MET Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 216 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 100 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 40.0000 chunk 213 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 127 GLN a 56 ASN a 57 HIS c 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.142731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.096077 restraints weight = 69845.187| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 4.29 r_work: 0.3370 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21992 Z= 0.150 Angle : 0.667 12.431 29877 Z= 0.350 Chirality : 0.038 0.280 3629 Planarity : 0.004 0.095 3977 Dihedral : 4.010 45.980 3243 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.09 % Favored : 97.84 % Rotamer: Outliers : 3.31 % Allowed : 24.72 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.15), residues: 3057 helix: 3.22 (0.10), residues: 2573 sheet: -0.08 (0.90), residues: 32 loop : -0.26 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP a 221 HIS 0.007 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.022 0.001 TYR Z 16 ARG 0.014 0.001 ARG d 86 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 2257) hydrogen bonds : angle 3.67533 ( 6720) covalent geometry : bond 0.00323 (21992) covalent geometry : angle 0.66676 (29877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 337 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8099 (pp) REVERT: I 69 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8850 (mp0) REVERT: I 112 VAL cc_start: 0.9083 (t) cc_final: 0.8822 (p) REVERT: I 120 ASP cc_start: 0.8806 (p0) cc_final: 0.8531 (p0) REVERT: I 123 ASP cc_start: 0.8807 (t0) cc_final: 0.8501 (t0) REVERT: J 72 ASP cc_start: 0.9247 (m-30) cc_final: 0.8982 (m-30) REVERT: J 77 MET cc_start: 0.9095 (ppp) cc_final: 0.8807 (ppp) REVERT: K 20 LYS cc_start: 0.8578 (mttm) cc_final: 0.8212 (mttm) REVERT: K 85 ASP cc_start: 0.9011 (t0) cc_final: 0.8527 (t0) REVERT: L 74 GLU cc_start: 0.8526 (mp0) cc_final: 0.8192 (mp0) REVERT: M 16 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8855 (tt) REVERT: N 32 GLU cc_start: 0.9294 (tp30) cc_final: 0.8875 (tp30) REVERT: N 35 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7577 (t80) REVERT: O 205 PHE cc_start: 0.7524 (m-80) cc_final: 0.7305 (t80) REVERT: O 230 TYR cc_start: 0.8855 (t80) cc_final: 0.8524 (t80) REVERT: O 261 MET cc_start: 0.1691 (OUTLIER) cc_final: 0.1399 (ppp) REVERT: P 38 ASP cc_start: 0.8462 (m-30) cc_final: 0.8181 (m-30) REVERT: Q 11 GLN cc_start: 0.8574 (pp30) cc_final: 0.7955 (pp30) REVERT: R 1 MET cc_start: 0.7014 (mmt) cc_final: 0.6609 (mmt) REVERT: U 61 GLN cc_start: 0.9295 (mt0) cc_final: 0.8985 (mm110) REVERT: U 66 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9196 (mmmt) REVERT: U 78 ASP cc_start: 0.9166 (t0) cc_final: 0.8962 (t70) REVERT: V 148 ASP cc_start: 0.7557 (t0) cc_final: 0.7080 (p0) REVERT: X 58 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8509 (tm-30) REVERT: X 60 GLN cc_start: 0.8862 (tp40) cc_final: 0.8482 (pm20) REVERT: Y 40 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8610 (ttp80) REVERT: Z 29 THR cc_start: 0.8380 (m) cc_final: 0.8158 (m) REVERT: Z 35 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8233 (t80) REVERT: Z 83 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9103 (ptpp) REVERT: a 19 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8521 (mmm) REVERT: a 168 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8449 (m-80) REVERT: a 188 MET cc_start: 0.4988 (ppp) cc_final: 0.4630 (ppp) REVERT: b 1 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5716 (tmm) REVERT: b 8 GLU cc_start: 0.8107 (tp30) cc_final: 0.7570 (tp30) REVERT: c 24 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8493 (tm-30) REVERT: d 20 LYS cc_start: 0.9305 (tppt) cc_final: 0.9021 (tppt) REVERT: d 81 MET cc_start: 0.3039 (OUTLIER) cc_final: 0.2644 (tpt) REVERT: d 85 GLN cc_start: 0.9776 (pp30) cc_final: 0.9489 (pp30) REVERT: d 98 ASN cc_start: 0.7596 (m-40) cc_final: 0.6714 (t0) REVERT: d 108 MET cc_start: 0.2938 (ppp) cc_final: 0.1803 (pmm) outliers start: 63 outliers final: 47 residues processed: 380 average time/residue: 0.3188 time to fit residues: 189.7712 Evaluate side-chains 370 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 35 TYR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 8 GLU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 153 HIS Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 23 LEU Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 53 optimal weight: 50.0000 chunk 173 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 21 optimal weight: 50.0000 chunk 56 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 60 GLN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.144683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.097457 restraints weight = 74903.682| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.37 r_work: 0.3409 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21992 Z= 0.181 Angle : 0.696 12.583 29877 Z= 0.364 Chirality : 0.039 0.247 3629 Planarity : 0.004 0.052 3977 Dihedral : 4.006 45.937 3243 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 3.16 % Allowed : 25.14 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.15), residues: 3057 helix: 3.18 (0.10), residues: 2573 sheet: -0.05 (0.90), residues: 32 loop : -0.30 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 221 HIS 0.008 0.001 HIS a 31 PHE 0.021 0.002 PHE M 60 TYR 0.046 0.002 TYR Z 16 ARG 0.010 0.001 ARG K 12 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 2257) hydrogen bonds : angle 3.72080 ( 6720) covalent geometry : bond 0.00398 (21992) covalent geometry : angle 0.69618 (29877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 60 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8160 (pp30) REVERT: I 63 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8069 (pp) REVERT: I 69 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8867 (mp0) REVERT: I 112 VAL cc_start: 0.9106 (t) cc_final: 0.8854 (p) REVERT: I 120 ASP cc_start: 0.8691 (p0) cc_final: 0.8437 (p0) REVERT: I 123 ASP cc_start: 0.8748 (t0) cc_final: 0.8450 (t0) REVERT: J 72 ASP cc_start: 0.9146 (m-30) cc_final: 0.8865 (m-30) REVERT: J 77 MET cc_start: 0.9123 (ppp) cc_final: 0.8718 (ppp) REVERT: K 20 LYS cc_start: 0.8585 (mttm) cc_final: 0.8218 (mttm) REVERT: K 85 ASP cc_start: 0.8951 (t0) cc_final: 0.8473 (t0) REVERT: L 74 GLU cc_start: 0.8446 (mp0) cc_final: 0.8190 (mp0) REVERT: M 16 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8883 (tt) REVERT: N 32 GLU cc_start: 0.9226 (tp30) cc_final: 0.8811 (tp30) REVERT: N 59 ASP cc_start: 0.8739 (t0) cc_final: 0.8451 (t0) REVERT: O 205 PHE cc_start: 0.7588 (m-80) cc_final: 0.7320 (t80) REVERT: O 230 TYR cc_start: 0.8906 (t80) cc_final: 0.8560 (t80) REVERT: O 261 MET cc_start: 0.0960 (OUTLIER) cc_final: 0.0684 (ppp) REVERT: P 38 ASP cc_start: 0.8426 (m-30) cc_final: 0.8162 (m-30) REVERT: R 1 MET cc_start: 0.7116 (mmt) cc_final: 0.6714 (mmt) REVERT: U 66 LYS cc_start: 0.9437 (mmtt) cc_final: 0.9234 (mmmt) REVERT: U 69 GLU cc_start: 0.9332 (pt0) cc_final: 0.9088 (pt0) REVERT: V 140 GLU cc_start: 0.7506 (mp0) cc_final: 0.6859 (pm20) REVERT: V 148 ASP cc_start: 0.7603 (t0) cc_final: 0.7136 (p0) REVERT: W 41 GLU cc_start: 0.8816 (tp30) cc_final: 0.8547 (tp30) REVERT: X 58 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8470 (tm-30) REVERT: X 60 GLN cc_start: 0.8827 (tp40) cc_final: 0.8432 (pm20) REVERT: Z 2 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7844 (tm-30) REVERT: Z 29 THR cc_start: 0.8389 (m) cc_final: 0.8157 (m) REVERT: Z 35 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.8064 (t80) REVERT: Z 83 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8998 (pttm) REVERT: a 168 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: a 179 TYR cc_start: 0.8566 (t80) cc_final: 0.8114 (t80) REVERT: a 188 MET cc_start: 0.5036 (ppp) cc_final: 0.4643 (ppp) REVERT: b 1 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5597 (tmm) REVERT: b 8 GLU cc_start: 0.8086 (tp30) cc_final: 0.7597 (tp30) REVERT: c 24 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8395 (tm-30) REVERT: d 20 LYS cc_start: 0.9228 (tppt) cc_final: 0.8943 (tppt) REVERT: d 81 MET cc_start: 0.3145 (OUTLIER) cc_final: 0.2749 (tpt) REVERT: d 85 GLN cc_start: 0.9765 (pp30) cc_final: 0.9473 (pp30) REVERT: d 98 ASN cc_start: 0.7448 (m-40) cc_final: 0.6608 (t0) REVERT: d 108 MET cc_start: 0.2872 (ppp) cc_final: 0.1710 (pmm) outliers start: 60 outliers final: 47 residues processed: 359 average time/residue: 0.3016 time to fit residues: 169.7874 Evaluate side-chains 362 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 235 HIS Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 153 HIS Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 53 ILE Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 64 GLU Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 298 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 288 optimal weight: 2.9990 chunk 86 optimal weight: 40.0000 chunk 241 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 195 optimal weight: 0.2980 chunk 276 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.145956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.098875 restraints weight = 75336.806| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.40 r_work: 0.3439 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21992 Z= 0.146 Angle : 0.689 13.156 29877 Z= 0.359 Chirality : 0.039 0.244 3629 Planarity : 0.004 0.051 3977 Dihedral : 3.992 45.777 3243 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.06 % Favored : 97.87 % Rotamer: Outliers : 3.05 % Allowed : 25.51 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.15), residues: 3057 helix: 3.24 (0.10), residues: 2564 sheet: -0.02 (0.89), residues: 32 loop : -0.24 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 221 HIS 0.007 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.032 0.002 TYR Z 16 ARG 0.014 0.001 ARG V 167 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 2257) hydrogen bonds : angle 3.65486 ( 6720) covalent geometry : bond 0.00311 (21992) covalent geometry : angle 0.68935 (29877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20346.79 seconds wall clock time: 351 minutes 18.78 seconds (21078.78 seconds total)