Starting phenix.real_space_refine on Sun Aug 24 17:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q84_18246/08_2025/8q84_18246.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q84_18246/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q84_18246/08_2025/8q84_18246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q84_18246/08_2025/8q84_18246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q84_18246/08_2025/8q84_18246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q84_18246/08_2025/8q84_18246.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'GLU:plan': 39, 'TRP:plan': 1, 'ASN:plan1': 20, 'HIS:plan': 6, 'ARG:plan': 13, 'PHE:plan': 6, 'ASP:plan': 15, 'TYR:plan': 3} 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: {'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 17, 'GLN:plan1': 16, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5, 'HIS:plan': 1} 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, 'GLU:plan': 39, 'TRP:plan': 1, 'ASN:plan1': 20, 'HIS:plan': 6, 'ARG:plan': 13, 'PHE:plan': 6, 'ASP:plan': 15, 'TYR:plan': 3} 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: {'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 17, 'GLN:plan1': 16, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5, 'HIS:plan': 1} 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: 5.32, per 1000 atoms: 0.24 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: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.61 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: 4.57 Time building geometry restraints manager: 2.99 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: 4.170 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.640 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- 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 : 12.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.51 (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 ARG 0.017 0.001 ARG O 176 TYR 0.045 0.002 TYR Z 16 PHE 0.022 0.002 PHE M 60 TRP 0.016 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00342 (21992) covalent geometry : angle 0.73983 (29877) hydrogen bonds : bond 0.08914 ( 2257) hydrogen bonds : angle 4.69122 ( 6720) *********************** 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 : 0.933 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: U 66 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8769 (mmmm) REVERT: V 136 ARG cc_start: 0.9135 (tmm-80) cc_final: 0.8744 (tmm-80) 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: 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: 0.8295 (t80) REVERT: b 8 GLU cc_start: 0.7480 (tp30) cc_final: 0.7155 (tp30) outliers start: 11 outliers final: 6 residues processed: 380 average time/residue: 0.1591 time to fit residues: 93.7652 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 : 1.005 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN W 72 GLN Y 19 ASN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 GLN c 6 GLN c 36 GLN c 44 GLN d 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.145467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.098976 restraints weight = 77851.784| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.59 r_work: 0.3433 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21992 Z= 0.161 Angle : 0.615 11.209 29877 Z= 0.324 Chirality : 0.038 0.244 3629 Planarity : 0.004 0.071 3977 Dihedral : 4.326 44.741 3251 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.06 % Favored : 97.87 % Rotamer: Outliers : 3.42 % Allowed : 18.41 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.15), residues: 3057 helix: 3.06 (0.10), residues: 2533 sheet: -0.24 (0.89), residues: 32 loop : -0.30 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 24 TYR 0.040 0.002 TYR Z 16 PHE 0.033 0.002 PHE a 246 TRP 0.009 0.001 TRP P 59 HIS 0.007 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00342 (21992) covalent geometry : angle 0.61525 (29877) hydrogen bonds : bond 0.04523 ( 2257) hydrogen bonds : angle 3.99531 ( 6720) *********************** 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: 65 poor density : 352 time to evaluate : 0.931 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: I 69 GLU cc_start: 0.8770 (mp0) cc_final: 0.8537 (mp0) REVERT: J 72 ASP cc_start: 0.9207 (m-30) cc_final: 0.8917 (m-30) REVERT: K 77 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8550 (t0) REVERT: K 85 ASP cc_start: 0.8816 (t0) cc_final: 0.8587 (t0) REVERT: N 32 GLU cc_start: 0.9201 (tp30) cc_final: 0.8972 (tp30) REVERT: N 35 TYR cc_start: 0.6994 (m-80) cc_final: 0.6780 (m-80) REVERT: N 83 LYS cc_start: 0.9385 (tppp) cc_final: 0.9084 (tppp) REVERT: N 87 GLU cc_start: 0.8526 (pp20) cc_final: 0.8283 (pp20) REVERT: O 232 GLN cc_start: 0.9305 (pp30) cc_final: 0.8842 (pp30) REVERT: P 65 GLN cc_start: 0.8513 (tt0) cc_final: 0.7830 (tp-100) REVERT: Q 33 MET cc_start: 0.8995 (tmm) cc_final: 0.8752 (tmm) REVERT: U 61 GLN cc_start: 0.9303 (mt0) cc_final: 0.9031 (mm110) REVERT: U 66 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9017 (mmmm) REVERT: U 123 ASP cc_start: 0.8994 (t0) cc_final: 0.8677 (t0) REVERT: X 58 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8549 (tm-30) REVERT: Z 11 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8535 (pp20) REVERT: Z 35 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: a 168 PHE cc_start: 0.9199 (m-80) cc_final: 0.8541 (m-80) REVERT: a 179 TYR cc_start: 0.8386 (t80) cc_final: 0.8183 (t80) REVERT: a 188 MET cc_start: 0.4741 (ppp) cc_final: 0.4483 (ppp) REVERT: a 201 PHE cc_start: 0.8604 (t80) cc_final: 0.8361 (t80) REVERT: b 1 MET cc_start: 0.6975 (tmm) cc_final: 0.5797 (ppp) REVERT: d 85 GLN cc_start: 0.9697 (pp30) cc_final: 0.9363 (pp30) REVERT: d 98 ASN cc_start: 0.7909 (m110) cc_final: 0.6770 (t0) outliers start: 65 outliers final: 31 residues processed: 396 average time/residue: 0.1549 time to fit residues: 95.7387 Evaluate side-chains 336 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 303 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 40.0000 chunk 80 optimal weight: 50.0000 chunk 120 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 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** V 134 ASN W 72 GLN a 57 HIS a 195 GLN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN c 44 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.144527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.144513 restraints weight = 64855.577| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 0.02 r_work: 0.4231 rms_B_bonded: 0.22 restraints_weight: 0.5000 r_work: 0.4050 rms_B_bonded: 0.45 restraints_weight: 0.2500 r_work: 0.3948 rms_B_bonded: 0.82 restraints_weight: 0.1250 r_work: 0.3767 rms_B_bonded: 2.42 restraints_weight: 0.0625 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21992 Z= 0.207 Angle : 0.625 9.659 29877 Z= 0.329 Chirality : 0.039 0.372 3629 Planarity : 0.004 0.058 3977 Dihedral : 4.109 44.933 3243 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.19 % Favored : 97.74 % Rotamer: Outliers : 3.95 % Allowed : 19.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.82 (0.15), residues: 3057 helix: 3.03 (0.10), residues: 2563 sheet: -0.37 (1.07), residues: 22 loop : -0.45 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 24 TYR 0.022 0.002 TYR a 85 PHE 0.035 0.002 PHE O 168 TRP 0.009 0.001 TRP P 59 HIS 0.009 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00455 (21992) covalent geometry : angle 0.62486 (29877) hydrogen bonds : bond 0.04511 ( 2257) hydrogen bonds : angle 3.93217 ( 6720) *********************** 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 410 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 335 time to evaluate : 0.917 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: J 72 ASP cc_start: 0.8916 (m-30) cc_final: 0.8676 (m-30) REVERT: K 20 LYS cc_start: 0.8320 (mttm) cc_final: 0.8063 (mmtm) REVERT: K 85 ASP cc_start: 0.8342 (t0) cc_final: 0.7966 (t0) REVERT: N 24 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8718 (pttm) REVERT: N 32 GLU cc_start: 0.8878 (tp30) cc_final: 0.8118 (tp30) REVERT: N 83 LYS cc_start: 0.9428 (tppp) cc_final: 0.9164 (tppp) REVERT: P 8 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7511 (tm-30) REVERT: R 1 MET cc_start: 0.7087 (mmm) cc_final: 0.6812 (mmm) REVERT: U 66 LYS cc_start: 0.9279 (mmtt) cc_final: 0.8920 (mmmm) REVERT: U 123 ASP cc_start: 0.8563 (t0) cc_final: 0.8280 (t0) REVERT: X 58 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8135 (tm-30) REVERT: Z 22 ASP cc_start: 0.7865 (p0) cc_final: 0.7656 (p0) REVERT: a 168 PHE cc_start: 0.8626 (m-80) cc_final: 0.8223 (m-80) REVERT: a 179 TYR cc_start: 0.8358 (t80) cc_final: 0.7994 (t80) REVERT: a 188 MET cc_start: 0.5212 (ppp) cc_final: 0.4989 (ppp) REVERT: a 201 PHE cc_start: 0.8463 (t80) cc_final: 0.8045 (t80) REVERT: b 1 MET cc_start: 0.5534 (tmm) cc_final: 0.5130 (tmm) REVERT: b 8 GLU cc_start: 0.7531 (tp30) cc_final: 0.7069 (tp30) REVERT: b 58 GLU cc_start: 0.8436 (tp30) cc_final: 0.8074 (tm-30) REVERT: d 98 ASN cc_start: 0.7174 (m110) cc_final: 0.6158 (t0) REVERT: d 108 MET cc_start: 0.2016 (tmm) cc_final: 0.1174 (pmm) outliers start: 75 outliers final: 48 residues processed: 386 average time/residue: 0.1493 time to fit residues: 90.9478 Evaluate side-chains 342 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 100 SER 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 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 13 LEU 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 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 V residue 99 VAL Chi-restraints excluded: chain V residue 124 MET Chi-restraints excluded: chain V residue 144 THR 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 69 LEU Chi-restraints excluded: chain X residue 77 SER 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 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 160 THR Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 243 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 19 optimal weight: 30.0000 chunk 29 optimal weight: 40.0000 chunk 172 optimal weight: 0.0670 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 50.0000 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 overall best weight: 0.8922 ------------------------------------------------------------------------------- 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 34 ASN 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 U 147 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** a 173 GLN a 236 ASN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.140963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.091297 restraints weight = 70140.574| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.49 r_work: 0.3424 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1748 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= 0.144 Angle : 0.587 9.548 29877 Z= 0.308 Chirality : 0.037 0.268 3629 Planarity : 0.004 0.059 3977 Dihedral : 4.042 45.311 3243 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 3.79 % Allowed : 20.67 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.92 (0.15), residues: 3057 helix: 3.11 (0.10), residues: 2552 sheet: -0.34 (0.88), residues: 32 loop : -0.40 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 78 TYR 0.023 0.002 TYR Z 16 PHE 0.022 0.002 PHE O 168 TRP 0.009 0.001 TRP P 59 HIS 0.008 0.001 HIS a 57 Details of bonding type rmsd covalent geometry : bond 0.00301 (21992) covalent geometry : angle 0.58662 (29877) hydrogen bonds : bond 0.04331 ( 2257) hydrogen bonds : angle 3.80730 ( 6720) *********************** 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 416 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 344 time to evaluate : 1.261 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: 0.8682 (OUTLIER) cc_final: 0.8372 (pp) REVERT: I 69 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8816 (mp0) REVERT: J 72 ASP cc_start: 0.9157 (m-30) cc_final: 0.8893 (m-30) REVERT: K 20 LYS cc_start: 0.8412 (mttm) cc_final: 0.8113 (mmtm) REVERT: K 85 ASP cc_start: 0.8769 (t0) cc_final: 0.8316 (t0) REVERT: N 24 LYS cc_start: 0.9295 (mtmm) cc_final: 0.8898 (pttm) REVERT: N 83 LYS cc_start: 0.9411 (tppp) cc_final: 0.9061 (tppt) REVERT: O 205 PHE cc_start: 0.7720 (m-80) cc_final: 0.7206 (t80) REVERT: P 8 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7799 (tm-30) REVERT: Q 33 MET cc_start: 0.8967 (tmm) cc_final: 0.8538 (tmm) REVERT: R 1 MET cc_start: 0.7529 (mmm) cc_final: 0.7304 (mmm) REVERT: U 66 LYS cc_start: 0.9403 (mmtt) cc_final: 0.9061 (mmmm) REVERT: U 123 ASP cc_start: 0.9068 (t0) cc_final: 0.8785 (t0) REVERT: V 98 GLU cc_start: 0.9053 (tp30) cc_final: 0.8801 (tp30) REVERT: X 58 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8512 (tm-30) REVERT: X 60 GLN cc_start: 0.8863 (tp40) cc_final: 0.8388 (pm20) REVERT: X 74 GLU cc_start: 0.7951 (mp0) cc_final: 0.7675 (mp0) REVERT: Y 6 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8135 (mm-30) REVERT: Z 35 TYR cc_start: 0.8423 (t80) cc_final: 0.7791 (t80) REVERT: a 168 PHE cc_start: 0.9068 (m-80) cc_final: 0.8557 (m-80) REVERT: a 179 TYR cc_start: 0.8444 (t80) cc_final: 0.8054 (t80) REVERT: a 188 MET cc_start: 0.4808 (ppp) cc_final: 0.4538 (ppp) REVERT: a 201 PHE cc_start: 0.8774 (t80) cc_final: 0.8267 (t80) REVERT: b 1 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.5778 (tmm) REVERT: b 8 GLU cc_start: 0.7807 (tp30) cc_final: 0.7249 (tp30) REVERT: b 58 GLU cc_start: 0.8838 (tp30) cc_final: 0.8435 (tm-30) REVERT: d 81 MET cc_start: 0.3265 (mmt) cc_final: 0.2859 (tpt) REVERT: d 85 GLN cc_start: 0.9715 (pp30) cc_final: 0.9418 (pp30) REVERT: d 98 ASN cc_start: 0.7696 (m110) cc_final: 0.6678 (t0) REVERT: d 108 MET cc_start: 0.2788 (tmm) cc_final: 0.1814 (pmm) outliers start: 72 outliers final: 44 residues processed: 394 average time/residue: 0.1551 time to fit residues: 95.4596 Evaluate side-chains 353 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 M residue 8 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 33 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 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 VAL 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 164 LEU 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 33 LEU 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 214 MET 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 57 ARG 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 76 optimal weight: 40.0000 chunk 133 optimal weight: 0.0770 chunk 87 optimal weight: 50.0000 chunk 140 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 209 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 29 GLN O 36 GLN Q 2 ASN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 ASN R 93 GLN U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 45 ASN W 72 GLN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.142758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.096866 restraints weight = 70836.336| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 4.28 r_work: 0.3370 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21992 Z= 0.167 Angle : 0.594 12.839 29877 Z= 0.316 Chirality : 0.037 0.244 3629 Planarity : 0.004 0.056 3977 Dihedral : 4.009 45.844 3243 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 3.79 % Allowed : 21.04 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.96 (0.15), residues: 3057 helix: 3.13 (0.10), residues: 2562 sheet: -0.27 (0.89), residues: 32 loop : -0.37 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 78 TYR 0.038 0.002 TYR a 230 PHE 0.021 0.002 PHE M 60 TRP 0.008 0.001 TRP P 59 HIS 0.008 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00360 (21992) covalent geometry : angle 0.59421 (29877) hydrogen bonds : bond 0.04325 ( 2257) hydrogen bonds : angle 3.77201 ( 6720) *********************** 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 415 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 343 time to evaluate : 0.945 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 63 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8267 (pp) REVERT: I 69 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8858 (mp0) REVERT: J 72 ASP cc_start: 0.9160 (m-30) cc_final: 0.8914 (m-30) REVERT: K 20 LYS cc_start: 0.8516 (mttm) cc_final: 0.8270 (mttp) REVERT: K 85 ASP cc_start: 0.8852 (t0) cc_final: 0.8375 (t0) REVERT: N 32 GLU cc_start: 0.9283 (tp30) cc_final: 0.8980 (tp30) REVERT: N 35 TYR cc_start: 0.7572 (m-80) cc_final: 0.7321 (t80) REVERT: N 83 LYS cc_start: 0.9446 (tppp) cc_final: 0.9119 (ttmm) REVERT: O 57 HIS cc_start: 0.8404 (p-80) cc_final: 0.8188 (p-80) REVERT: O 175 GLN cc_start: 0.8986 (mm110) cc_final: 0.8770 (mm110) REVERT: O 205 PHE cc_start: 0.7697 (m-80) cc_final: 0.7443 (m-80) REVERT: O 230 TYR cc_start: 0.9042 (t80) cc_final: 0.8792 (t80) REVERT: O 232 GLN cc_start: 0.9340 (pp30) cc_final: 0.9057 (pp30) REVERT: O 237 TYR cc_start: 0.7797 (t80) cc_final: 0.7510 (t80) REVERT: O 261 MET cc_start: 0.2550 (ptt) cc_final: 0.2048 (ppp) REVERT: P 8 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7779 (tm-30) REVERT: Q 33 MET cc_start: 0.9119 (tmm) cc_final: 0.8660 (tmm) REVERT: U 66 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9078 (mmmm) REVERT: U 123 ASP cc_start: 0.9191 (t0) cc_final: 0.8958 (t0) REVERT: V 148 ASP cc_start: 0.7923 (t0) cc_final: 0.7426 (p0) REVERT: W 124 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.8002 (ptm) REVERT: X 58 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8426 (tm-30) REVERT: Y 6 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8308 (mm-30) REVERT: Z 19 LEU cc_start: 0.9484 (tt) cc_final: 0.9249 (mm) REVERT: Z 35 TYR cc_start: 0.8591 (t80) cc_final: 0.7901 (t80) REVERT: Z 58 ARG cc_start: 0.5944 (mmt180) cc_final: 0.5540 (mtt180) REVERT: a 19 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8786 (mmm) REVERT: a 168 PHE cc_start: 0.9143 (m-80) cc_final: 0.8540 (m-80) REVERT: a 179 TYR cc_start: 0.8444 (t80) cc_final: 0.7965 (t80) REVERT: a 188 MET cc_start: 0.4804 (ppp) cc_final: 0.4525 (ppp) REVERT: b 1 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5746 (tmm) REVERT: b 8 GLU cc_start: 0.7944 (tp30) cc_final: 0.7352 (tp30) REVERT: d 20 LYS cc_start: 0.9302 (tppt) cc_final: 0.8886 (tppt) REVERT: d 81 MET cc_start: 0.3180 (OUTLIER) cc_final: 0.2816 (tpt) REVERT: d 85 GLN cc_start: 0.9706 (pp30) cc_final: 0.9403 (pp30) REVERT: d 98 ASN cc_start: 0.7752 (m110) cc_final: 0.6744 (t0) REVERT: e 16 GLU cc_start: 0.8611 (pm20) cc_final: 0.8407 (pm20) outliers start: 72 outliers final: 46 residues processed: 398 average time/residue: 0.1510 time to fit residues: 94.4141 Evaluate side-chains 360 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 309 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 M residue 8 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 15 LYS 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 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 246 PHE Chi-restraints excluded: chain Q residue 27 THR 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 164 LEU 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 Y residue 65 THR Chi-restraints excluded: chain Z residue 33 LEU 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 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 2 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 92 optimal weight: 10.0000 chunk 190 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 138 optimal weight: 0.8980 chunk 113 optimal weight: 0.0010 chunk 135 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 44 optimal weight: 50.0000 chunk 288 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.099500 restraints weight = 75514.339| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.39 r_work: 0.3464 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21992 Z= 0.136 Angle : 0.600 11.746 29877 Z= 0.315 Chirality : 0.037 0.243 3629 Planarity : 0.003 0.054 3977 Dihedral : 3.995 46.078 3243 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.81 % Rotamer: Outliers : 3.05 % Allowed : 22.78 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.06 (0.15), residues: 3057 helix: 3.21 (0.10), residues: 2552 sheet: -0.18 (0.91), residues: 32 loop : -0.38 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 78 TYR 0.024 0.001 TYR Z 16 PHE 0.026 0.002 PHE a 201 TRP 0.017 0.001 TRP a 221 HIS 0.007 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00281 (21992) covalent geometry : angle 0.60045 (29877) hydrogen bonds : bond 0.04206 ( 2257) hydrogen bonds : angle 3.68925 ( 6720) *********************** 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 402 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 344 time to evaluate : 0.938 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: I 112 VAL cc_start: 0.9075 (t) cc_final: 0.8806 (p) REVERT: J 72 ASP cc_start: 0.9107 (m-30) cc_final: 0.8842 (m-30) REVERT: K 12 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7911 (mtm-85) REVERT: K 20 LYS cc_start: 0.8370 (mttm) cc_final: 0.8051 (mttm) REVERT: K 85 ASP cc_start: 0.8770 (t0) cc_final: 0.8294 (t0) REVERT: N 35 TYR cc_start: 0.7426 (m-80) cc_final: 0.7203 (t80) REVERT: O 205 PHE cc_start: 0.7723 (m-80) cc_final: 0.7276 (m-80) REVERT: O 230 TYR cc_start: 0.8960 (t80) cc_final: 0.8730 (t80) REVERT: O 237 TYR cc_start: 0.7670 (t80) cc_final: 0.7470 (t80) REVERT: O 261 MET cc_start: 0.2295 (ptt) cc_final: 0.1887 (ppp) REVERT: R 20 LYS cc_start: 0.9257 (mmmt) cc_final: 0.9024 (tptp) REVERT: R 85 GLN cc_start: 0.9802 (tp-100) cc_final: 0.9511 (tm-30) REVERT: U 66 LYS cc_start: 0.9417 (mmtt) cc_final: 0.9155 (mmmm) REVERT: U 123 ASP cc_start: 0.9034 (t0) cc_final: 0.8802 (t0) REVERT: V 148 ASP cc_start: 0.7728 (t0) cc_final: 0.7222 (p0) REVERT: W 126 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7239 (tmm-80) REVERT: X 58 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8527 (tm-30) REVERT: X 60 GLN cc_start: 0.8819 (tp40) cc_final: 0.8416 (pm20) REVERT: X 74 GLU cc_start: 0.7876 (mp0) cc_final: 0.7582 (mp0) REVERT: Y 6 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8236 (mm-30) REVERT: Z 29 THR cc_start: 0.8522 (m) cc_final: 0.8302 (m) REVERT: Z 35 TYR cc_start: 0.8443 (t80) cc_final: 0.7753 (t80) REVERT: Z 58 ARG cc_start: 0.5846 (mmt180) cc_final: 0.5500 (mtt180) REVERT: a 19 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8773 (mmm) REVERT: a 168 PHE cc_start: 0.9050 (m-80) cc_final: 0.8561 (m-80) REVERT: a 188 MET cc_start: 0.4781 (ppp) cc_final: 0.4467 (ppp) REVERT: b 1 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5447 (tmm) REVERT: b 8 GLU cc_start: 0.7768 (tp30) cc_final: 0.7170 (tp30) REVERT: c 24 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8355 (tm-30) REVERT: c 33 MET cc_start: 0.9354 (ttt) cc_final: 0.9063 (ttt) REVERT: d 20 LYS cc_start: 0.9235 (tppt) cc_final: 0.8822 (tppt) REVERT: d 48 ARG cc_start: 0.9175 (tpt170) cc_final: 0.8953 (ttm-80) REVERT: d 75 ASP cc_start: 0.9053 (p0) cc_final: 0.8760 (p0) REVERT: d 81 MET cc_start: 0.3105 (OUTLIER) cc_final: 0.2637 (tpt) REVERT: d 85 GLN cc_start: 0.9714 (pp30) cc_final: 0.9422 (pp30) REVERT: d 98 ASN cc_start: 0.7679 (m110) cc_final: 0.6730 (t0) REVERT: d 108 MET cc_start: 0.2356 (ppp) cc_final: 0.1316 (pmm) REVERT: e 16 GLU cc_start: 0.8416 (pm20) cc_final: 0.8215 (pm20) outliers start: 58 outliers final: 40 residues processed: 386 average time/residue: 0.1540 time to fit residues: 92.7971 Evaluate side-chains 356 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 GLU 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 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 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR 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 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 65 THR Chi-restraints excluded: chain Z residue 33 LEU 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 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 203 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 71 optimal weight: 40.0000 chunk 17 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 201 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 2 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 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 a 57 HIS ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.140071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.092876 restraints weight = 69328.385| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.36 r_work: 0.3349 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21992 Z= 0.195 Angle : 0.650 12.739 29877 Z= 0.340 Chirality : 0.038 0.243 3629 Planarity : 0.004 0.053 3977 Dihedral : 3.992 46.252 3243 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 3.95 % Allowed : 22.67 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.01 (0.15), residues: 3057 helix: 3.15 (0.10), residues: 2567 sheet: -0.20 (0.91), residues: 32 loop : -0.35 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 78 TYR 0.040 0.002 TYR Z 16 PHE 0.022 0.002 PHE M 60 TRP 0.013 0.001 TRP a 221 HIS 0.011 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00430 (21992) covalent geometry : angle 0.64995 (29877) hydrogen bonds : bond 0.04287 ( 2257) hydrogen bonds : angle 3.76670 ( 6720) *********************** 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 401 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 326 time to evaluate : 0.935 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: 0.9231 (mt-10) cc_final: 0.8850 (mp0) REVERT: J 72 ASP cc_start: 0.9170 (m-30) cc_final: 0.8915 (m-30) REVERT: J 77 MET cc_start: 0.9102 (ppp) cc_final: 0.8719 (ppp) REVERT: K 20 LYS cc_start: 0.8646 (mttm) cc_final: 0.8283 (mttm) REVERT: K 85 ASP cc_start: 0.9017 (t0) cc_final: 0.8563 (t0) REVERT: N 35 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7185 (t80) REVERT: O 237 TYR cc_start: 0.7709 (t80) cc_final: 0.7453 (t80) REVERT: O 261 MET cc_start: 0.2746 (ptt) cc_final: 0.2512 (ppp) REVERT: Q 33 MET cc_start: 0.9033 (tmm) cc_final: 0.8664 (tmm) REVERT: R 1 MET cc_start: 0.7247 (mmt) cc_final: 0.6810 (mmm) REVERT: U 66 LYS cc_start: 0.9430 (mmtt) cc_final: 0.9159 (mmmm) REVERT: U 123 ASP cc_start: 0.9214 (t0) cc_final: 0.9005 (t0) REVERT: V 148 ASP cc_start: 0.7774 (t0) cc_final: 0.7238 (p0) REVERT: W 75 GLU cc_start: 0.8745 (tp30) cc_final: 0.8503 (tp30) REVERT: W 126 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7593 (tmm-80) REVERT: X 58 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8410 (tm-30) REVERT: Z 29 THR cc_start: 0.8532 (m) cc_final: 0.8311 (m) REVERT: Z 35 TYR cc_start: 0.8670 (t80) cc_final: 0.7885 (t80) REVERT: Z 83 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9025 (ptpp) REVERT: a 19 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8797 (mmm) REVERT: a 168 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: a 188 MET cc_start: 0.4855 (ppp) cc_final: 0.4487 (ppp) REVERT: b 1 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5573 (tmm) REVERT: b 8 GLU cc_start: 0.7976 (tp30) cc_final: 0.7498 (tp30) REVERT: c 24 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8464 (tm-30) REVERT: c 33 MET cc_start: 0.9401 (ttt) cc_final: 0.9186 (ttt) REVERT: d 20 LYS cc_start: 0.9271 (tppt) cc_final: 0.8855 (tppt) REVERT: d 81 MET cc_start: 0.3466 (mmt) cc_final: 0.3037 (tpt) REVERT: d 85 GLN cc_start: 0.9725 (pp30) cc_final: 0.9431 (pp30) REVERT: d 98 ASN cc_start: 0.7565 (m110) cc_final: 0.6510 (t0) REVERT: d 108 MET cc_start: 0.2585 (ppp) cc_final: 0.1608 (pmm) outliers start: 75 outliers final: 56 residues processed: 381 average time/residue: 0.1519 time to fit residues: 91.1218 Evaluate side-chains 362 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 SER 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 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 15 LYS 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 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 Q residue 27 THR Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 164 LEU 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 65 THR Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 33 LEU 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 Z residue 85 GLU 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 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 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 169 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 119 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 50.0000 chunk 241 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN V 127 GLN d 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.142975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.096125 restraints weight = 69540.641| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.16 r_work: 0.3414 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2546 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= 0.136 Angle : 0.639 11.367 29877 Z= 0.333 Chirality : 0.037 0.245 3629 Planarity : 0.004 0.051 3977 Dihedral : 3.974 46.276 3243 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 3.16 % Allowed : 24.20 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.12 (0.15), residues: 3057 helix: 3.23 (0.09), residues: 2560 sheet: -0.09 (0.92), residues: 32 loop : -0.32 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 78 TYR 0.045 0.001 TYR Z 16 PHE 0.023 0.002 PHE M 60 TRP 0.015 0.001 TRP a 221 HIS 0.024 0.001 HIS a 57 Details of bonding type rmsd covalent geometry : bond 0.00279 (21992) covalent geometry : angle 0.63905 (29877) hydrogen bonds : bond 0.04170 ( 2257) hydrogen bonds : angle 3.66346 ( 6720) *********************** 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 401 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 341 time to evaluate : 0.928 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: I 69 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8865 (mp0) REVERT: I 112 VAL cc_start: 0.9094 (t) cc_final: 0.8835 (p) REVERT: J 72 ASP cc_start: 0.9242 (m-30) cc_final: 0.9010 (m-30) REVERT: J 77 MET cc_start: 0.9082 (ppp) cc_final: 0.8795 (ppp) REVERT: K 12 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7839 (mpp80) REVERT: K 20 LYS cc_start: 0.8532 (mttm) cc_final: 0.8189 (mttm) REVERT: K 85 ASP cc_start: 0.9045 (t0) cc_final: 0.8570 (t0) REVERT: M 16 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8804 (tt) REVERT: N 35 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.7363 (t80) REVERT: O 205 PHE cc_start: 0.7523 (m-80) cc_final: 0.7141 (t80) REVERT: O 230 TYR cc_start: 0.8892 (t80) cc_final: 0.8593 (t80) REVERT: O 237 TYR cc_start: 0.7783 (t80) cc_final: 0.7494 (t80) REVERT: O 261 MET cc_start: 0.2622 (ptt) cc_final: 0.2377 (ppp) REVERT: Q 11 GLN cc_start: 0.8591 (pp30) cc_final: 0.7899 (pp30) REVERT: R 1 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6716 (mmm) REVERT: R 20 LYS cc_start: 0.9276 (mmmt) cc_final: 0.9074 (tptp) REVERT: U 66 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9169 (mmmm) REVERT: U 69 GLU cc_start: 0.9289 (pt0) cc_final: 0.9059 (pt0) REVERT: U 78 ASP cc_start: 0.9199 (t0) cc_final: 0.8991 (t70) REVERT: U 93 ASP cc_start: 0.8731 (t0) cc_final: 0.8373 (t0) REVERT: V 148 ASP cc_start: 0.7761 (t0) cc_final: 0.7206 (p0) REVERT: W 41 GLU cc_start: 0.8908 (tp30) cc_final: 0.8649 (tp30) REVERT: W 126 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7223 (tmm-80) REVERT: X 60 GLN cc_start: 0.8928 (tp40) cc_final: 0.8473 (pm20) REVERT: Y 40 ARG cc_start: 0.8995 (mmm-85) cc_final: 0.8620 (ttp80) REVERT: Z 29 THR cc_start: 0.8463 (m) cc_final: 0.8262 (m) REVERT: Z 35 TYR cc_start: 0.8661 (t80) cc_final: 0.7838 (t80) REVERT: Z 58 ARG cc_start: 0.5846 (mmt180) cc_final: 0.5434 (mtt180) REVERT: a 19 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8431 (mmm) REVERT: a 168 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: a 179 TYR cc_start: 0.8493 (t80) cc_final: 0.8067 (t80) REVERT: a 188 MET cc_start: 0.4967 (ppp) cc_final: 0.4612 (ppp) REVERT: b 1 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5310 (tmm) REVERT: b 8 GLU cc_start: 0.7941 (tp30) cc_final: 0.7311 (tp30) REVERT: c 24 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8495 (tm-30) REVERT: d 20 LYS cc_start: 0.9301 (tppt) cc_final: 0.8965 (tppt) REVERT: d 81 MET cc_start: 0.3287 (mmt) cc_final: 0.2939 (tpt) REVERT: d 85 GLN cc_start: 0.9736 (pp30) cc_final: 0.9435 (pp30) REVERT: d 98 ASN cc_start: 0.7541 (m-40) cc_final: 0.6636 (t0) REVERT: d 108 MET cc_start: 0.2831 (ppp) cc_final: 0.1793 (pmm) outliers start: 60 outliers final: 43 residues processed: 380 average time/residue: 0.1560 time to fit residues: 91.8516 Evaluate side-chains 376 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 326 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain K residue 3 SER 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 M residue 16 ILE Chi-restraints excluded: chain N residue 15 LYS 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 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain P residue 8 GLU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 109 SER 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 W residue 126 ARG Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU 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 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 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 62 optimal weight: 20.0000 chunk 186 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 chunk 55 optimal weight: 30.0000 chunk 198 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 75 optimal weight: 10.0000 chunk 238 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 61 ASN O 36 GLN Q 2 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.137355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.086763 restraints weight = 66524.415| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.41 r_work: 0.3277 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21992 Z= 0.291 Angle : 0.746 11.749 29877 Z= 0.393 Chirality : 0.042 0.268 3629 Planarity : 0.004 0.054 3977 Dihedral : 4.113 46.643 3243 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 3.73 % Allowed : 24.25 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.78 (0.15), residues: 3057 helix: 2.96 (0.10), residues: 2591 sheet: -0.24 (0.92), residues: 32 loop : -0.40 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 78 TYR 0.036 0.002 TYR Z 16 PHE 0.021 0.002 PHE O 226 TRP 0.036 0.002 TRP a 221 HIS 0.013 0.002 HIS N 38 Details of bonding type rmsd covalent geometry : bond 0.00643 (21992) covalent geometry : angle 0.74626 (29877) hydrogen bonds : bond 0.04562 ( 2257) hydrogen bonds : angle 3.91787 ( 6720) *********************** 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 395 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 0.928 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: I 69 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8827 (mp0) REVERT: J 72 ASP cc_start: 0.9102 (m-30) cc_final: 0.8834 (m-30) REVERT: K 20 LYS cc_start: 0.8756 (mttm) cc_final: 0.8547 (mmtp) REVERT: K 85 ASP cc_start: 0.9018 (t0) cc_final: 0.8561 (t0) REVERT: K 129 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9252 (p) REVERT: N 32 GLU cc_start: 0.9210 (tp30) cc_final: 0.8818 (tp30) REVERT: N 35 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.7305 (t80) REVERT: O 175 GLN cc_start: 0.9034 (mm110) cc_final: 0.8759 (mm110) REVERT: O 230 TYR cc_start: 0.8967 (t80) cc_final: 0.8650 (t80) REVERT: O 261 MET cc_start: 0.2841 (ptt) cc_final: 0.2446 (ppp) REVERT: R 1 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6909 (mmm) REVERT: U 69 GLU cc_start: 0.9320 (pt0) cc_final: 0.9119 (pt0) REVERT: V 148 ASP cc_start: 0.7773 (t0) cc_final: 0.7226 (p0) REVERT: W 126 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7672 (tmm-80) REVERT: Z 29 THR cc_start: 0.8491 (m) cc_final: 0.8274 (m) REVERT: Z 35 TYR cc_start: 0.8821 (t80) cc_final: 0.8025 (t80) REVERT: a 19 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8850 (mmm) REVERT: a 168 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: a 188 MET cc_start: 0.5084 (ppp) cc_final: 0.4662 (ppp) REVERT: b 1 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5426 (tmm) REVERT: b 8 GLU cc_start: 0.8090 (tp30) cc_final: 0.7649 (tp30) REVERT: b 58 GLU cc_start: 0.8806 (tp30) cc_final: 0.8320 (tm-30) REVERT: c 24 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8337 (tm-30) REVERT: d 20 LYS cc_start: 0.9251 (tppt) cc_final: 0.8976 (tppt) REVERT: d 59 LYS cc_start: 0.8692 (pttm) cc_final: 0.8457 (pttm) REVERT: d 81 MET cc_start: 0.3430 (mmt) cc_final: 0.3015 (tpt) REVERT: d 85 GLN cc_start: 0.9787 (pp30) cc_final: 0.9516 (pp30) REVERT: d 98 ASN cc_start: 0.7707 (m-40) cc_final: 0.6828 (t0) REVERT: d 108 MET cc_start: 0.3168 (ppp) cc_final: 0.2178 (pmm) outliers start: 71 outliers final: 49 residues processed: 376 average time/residue: 0.1552 time to fit residues: 91.0989 Evaluate side-chains 353 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 99 VAL Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 3 SER 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 129 VAL 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 15 LYS 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 235 HIS Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 1 MET 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 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 33 LEU 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 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 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 50.0000 chunk 226 optimal weight: 0.9980 chunk 24 optimal weight: 50.0000 chunk 168 optimal weight: 0.0040 chunk 100 optimal weight: 30.0000 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 250 optimal weight: 0.3980 chunk 290 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN O 36 GLN Q 2 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.145546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.098416 restraints weight = 75043.460| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.36 r_work: 0.3440 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2893 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= 0.146 Angle : 0.706 13.405 29877 Z= 0.367 Chirality : 0.039 0.247 3629 Planarity : 0.004 0.054 3977 Dihedral : 4.076 46.787 3243 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.93 % Favored : 98.00 % Rotamer: Outliers : 2.63 % Allowed : 25.88 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.00 (0.15), residues: 3057 helix: 3.15 (0.10), residues: 2566 sheet: 0.01 (0.93), residues: 32 loop : -0.38 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG d 86 TYR 0.029 0.001 TYR Z 16 PHE 0.039 0.002 PHE a 201 TRP 0.029 0.002 TRP a 221 HIS 0.008 0.001 HIS a 31 Details of bonding type rmsd covalent geometry : bond 0.00308 (21992) covalent geometry : angle 0.70626 (29877) hydrogen bonds : bond 0.04261 ( 2257) hydrogen bonds : angle 3.70976 ( 6720) ********************** 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 377 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 327 time to evaluate : 0.950 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: I 69 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8852 (mp0) REVERT: I 112 VAL cc_start: 0.9078 (t) cc_final: 0.8812 (p) REVERT: J 72 ASP cc_start: 0.9109 (m-30) cc_final: 0.8839 (m-30) REVERT: J 77 MET cc_start: 0.9039 (ppp) cc_final: 0.8760 (ppp) REVERT: K 20 LYS cc_start: 0.8515 (mttm) cc_final: 0.8277 (mttp) REVERT: K 85 ASP cc_start: 0.8926 (t0) cc_final: 0.8452 (t0) REVERT: O 175 GLN cc_start: 0.8959 (mm110) cc_final: 0.8661 (mm110) REVERT: O 205 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6873 (t80) REVERT: O 230 TYR cc_start: 0.8883 (t80) cc_final: 0.8442 (t80) REVERT: O 261 MET cc_start: 0.2125 (ptt) cc_final: 0.1892 (ppp) REVERT: R 1 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6445 (mmm) REVERT: U 69 GLU cc_start: 0.9312 (pt0) cc_final: 0.9042 (pt0) REVERT: U 78 ASP cc_start: 0.8944 (t0) cc_final: 0.8742 (t70) REVERT: W 126 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7303 (tmm-80) REVERT: X 60 GLN cc_start: 0.8836 (tp40) cc_final: 0.8423 (pm20) REVERT: X 74 GLU cc_start: 0.7866 (mp0) cc_final: 0.7598 (mp0) REVERT: Z 2 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7882 (tm-30) REVERT: Z 35 TYR cc_start: 0.8493 (t80) cc_final: 0.7860 (t80) REVERT: Z 58 ARG cc_start: 0.5651 (mmt180) cc_final: 0.5345 (mmt180) REVERT: a 19 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8404 (mmm) REVERT: a 168 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: a 179 TYR cc_start: 0.8772 (t80) cc_final: 0.8498 (t80) REVERT: a 188 MET cc_start: 0.4984 (ppp) cc_final: 0.4572 (ppp) REVERT: b 1 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5621 (tmm) REVERT: c 24 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8379 (tm-30) REVERT: d 20 LYS cc_start: 0.9261 (tppt) cc_final: 0.9041 (tppt) REVERT: d 81 MET cc_start: 0.3294 (mmt) cc_final: 0.2812 (tpt) REVERT: d 85 GLN cc_start: 0.9766 (pp30) cc_final: 0.9487 (pp30) REVERT: d 98 ASN cc_start: 0.7459 (m-40) cc_final: 0.6622 (t0) REVERT: d 108 MET cc_start: 0.2951 (ppp) cc_final: 0.1836 (pmm) outliers start: 50 outliers final: 36 residues processed: 363 average time/residue: 0.1566 time to fit residues: 88.4392 Evaluate side-chains 343 residues out of total 2924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 3 SER 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 M residue 44 LEU Chi-restraints excluded: chain N residue 15 LYS 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 205 PHE 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 Q residue 27 THR Chi-restraints excluded: chain R residue 1 MET 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 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 69 LEU Chi-restraints excluded: chain Y residue 69 LYS 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 66 VAL Chi-restraints excluded: chain a residue 168 PHE 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 d residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 87 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 chunk 284 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 268 optimal weight: 0.1980 chunk 41 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 102 optimal weight: 30.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** N 34 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN X 46 ASN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.145130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.098778 restraints weight = 75556.368| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.40 r_work: 0.3443 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21992 Z= 0.157 Angle : 0.712 13.323 29877 Z= 0.373 Chirality : 0.040 0.448 3629 Planarity : 0.004 0.083 3977 Dihedral : 4.065 46.575 3243 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.94 % Rotamer: Outliers : 2.89 % Allowed : 25.72 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.04 (0.15), residues: 3057 helix: 3.15 (0.10), residues: 2573 sheet: 0.10 (0.93), residues: 32 loop : -0.27 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG V 167 TYR 0.026 0.002 TYR Z 16 PHE 0.049 0.002 PHE a 201 TRP 0.027 0.001 TRP a 221 HIS 0.008 0.001 HIS N 38 Details of bonding type rmsd covalent geometry : bond 0.00342 (21992) covalent geometry : angle 0.71235 (29877) hydrogen bonds : bond 0.04218 ( 2257) hydrogen bonds : angle 3.70975 ( 6720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12327.00 seconds wall clock time: 210 minutes 11.94 seconds (12611.94 seconds total)