Starting phenix.real_space_refine on Thu May 15 14:26:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itp_60874/05_2025/9itp_60874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itp_60874/05_2025/9itp_60874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itp_60874/05_2025/9itp_60874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itp_60874/05_2025/9itp_60874.map" model { file = "/net/cci-nas-00/data/ceres_data/9itp_60874/05_2025/9itp_60874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itp_60874/05_2025/9itp_60874.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 36 5.16 5 C 8709 2.51 5 N 2293 2.21 5 O 2383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13421 Number of models: 1 Model: "" Number of chains: 16 Chain: "Y" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1223 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "V" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1205 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "X" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1112 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "U" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1089 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 151} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "I" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "N" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "P" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Z" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2028 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 14, 'TRANS': 245} Chain breaks: 1 Chain: "T" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1630 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 74 Time building chain proxies: 9.24, per 1000 atoms: 0.69 Number of scatterers: 13421 At special positions: 0 Unit cell: (119.97, 127.41, 226.92, 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 36 16.00 O 2383 8.00 N 2293 7.00 C 8709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS Z 135 " - pdb=" SG CYS Z 173 " distance=2.98 Simple disulfide: pdb=" SG CYS T 135 " - pdb=" SG CYS T 173 " distance=2.30 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: 3.37 Conformation dependent library (CDL) restraints added in 1.9 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3306 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'Y' and resid 8 through 27 removed outlier: 3.784A pdb=" N ILE Y 12 " --> pdb=" O PRO Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 147 removed outlier: 3.589A pdb=" N VAL Y 33 " --> pdb=" O LEU Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 150 through 160 removed outlier: 4.194A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU Y 160 " --> pdb=" O SER Y 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 29 Processing helix chain 'V' and resid 29 through 120 removed outlier: 3.820A pdb=" N MET V 34 " --> pdb=" O TYR V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 132 removed outlier: 3.893A pdb=" N VAL V 132 " --> pdb=" O ILE V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 151 through 156 removed outlier: 4.185A pdb=" N SER V 156 " --> pdb=" O LEU V 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 41 removed outlier: 4.418A pdb=" N ARG X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Proline residue: X 32 - end of helix Processing helix chain 'X' and resid 42 through 94 removed outlier: 3.698A pdb=" N GLU X 46 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA X 61 " --> pdb=" O GLN X 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 95 through 122 removed outlier: 3.589A pdb=" N ARG X 100 " --> pdb=" O ALA X 96 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG X 104 " --> pdb=" O ARG X 100 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU X 107 " --> pdb=" O GLU X 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG X 119 " --> pdb=" O GLN X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 130 removed outlier: 3.583A pdb=" N ASP X 130 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 139 removed outlier: 3.721A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.954A pdb=" N ALA U 51 " --> pdb=" O SER U 47 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG U 63 " --> pdb=" O ALA U 59 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG U 110 " --> pdb=" O LYS U 106 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 146 removed outlier: 3.739A pdb=" N GLN U 145 " --> pdb=" O GLY U 141 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA U 146 " --> pdb=" O ALA U 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 141 through 146' Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.539A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 72 removed outlier: 4.444A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE H 55 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 17 removed outlier: 3.529A pdb=" N VAL I 13 " --> pdb=" O THR I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 38 removed outlier: 3.535A pdb=" N VAL I 22 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 72 removed outlier: 4.562A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 removed outlier: 4.192A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 71 removed outlier: 3.900A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE J 55 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU J 59 " --> pdb=" O PHE J 55 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 removed outlier: 3.885A pdb=" N VAL K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 38 Processing helix chain 'K' and resid 41 through 72 removed outlier: 4.183A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE K 66 " --> pdb=" O PHE K 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 18 through 38 removed outlier: 4.065A pdb=" N VAL L 22 " --> pdb=" O ILE L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 72 removed outlier: 4.082A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 17 removed outlier: 3.504A pdb=" N VAL M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 38 removed outlier: 3.521A pdb=" N VAL M 22 " --> pdb=" O ILE M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 71 removed outlier: 3.509A pdb=" N THR M 56 " --> pdb=" O GLY M 52 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 18 through 38 removed outlier: 5.198A pdb=" N ILE N 24 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 71 removed outlier: 4.300A pdb=" N TYR N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.715A pdb=" N VAL O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 42 through 72 removed outlier: 4.659A pdb=" N TYR O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.739A pdb=" N VAL P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL P 13 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 38 Processing helix chain 'P' and resid 41 through 71 removed outlier: 5.071A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA P 54 " --> pdb=" O PHE P 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.760A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 38 removed outlier: 4.094A pdb=" N VAL Q 22 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 72 removed outlier: 3.845A pdb=" N TYR Q 48 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 71 Processing helix chain 'Z' and resid 79 through 97 Processing helix chain 'Z' and resid 102 through 124 Proline residue: Z 108 - end of helix removed outlier: 3.611A pdb=" N THR Z 112 " --> pdb=" O PRO Z 108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE Z 119 " --> pdb=" O LEU Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 211 removed outlier: 3.625A pdb=" N PHE Z 195 " --> pdb=" O LEU Z 191 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Z 196 " --> pdb=" O ASN Z 192 " (cutoff:3.500A) Processing helix chain 'Z' and resid 227 through 267 removed outlier: 3.847A pdb=" N ILE Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 4.022A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.592A pdb=" N ALA Z 292 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.915A pdb=" N VAL T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 3.823A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.876A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.955A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 210 removed outlier: 3.605A pdb=" N ALA T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE T 197 " --> pdb=" O PHE T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 217 Processing helix chain 'T' and resid 228 through 268 removed outlier: 4.008A pdb=" N PHE T 236 " --> pdb=" O GLY T 232 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE T 237 " --> pdb=" O ILE T 233 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER T 238 " --> pdb=" O ILE T 234 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.679A pdb=" N GLY T 278 " --> pdb=" O LEU T 274 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE T 279 " --> pdb=" O PRO T 275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3588 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: 4.03 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4488 1.34 - 1.46: 2127 1.46 - 1.58: 6923 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 13606 Sorted by residual: bond pdb=" N ILE Z 39 " pdb=" CA ILE Z 39 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL Z 134 " pdb=" CA VAL Z 134 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.67e+00 bond pdb=" N ILE I 70 " pdb=" CA ILE I 70 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.66e+00 bond pdb=" N ILE J 70 " pdb=" CA ILE J 70 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.60e+00 bond pdb=" N ILE H 70 " pdb=" CA ILE H 70 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.44e+00 ... (remaining 13601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 17782 1.39 - 2.78: 554 2.78 - 4.17: 76 4.17 - 5.56: 27 5.56 - 6.95: 5 Bond angle restraints: 18444 Sorted by residual: angle pdb=" N THR T 172 " pdb=" CA THR T 172 " pdb=" C THR T 172 " ideal model delta sigma weight residual 112.38 105.71 6.67 1.22e+00 6.72e-01 2.99e+01 angle pdb=" N VAL N 22 " pdb=" CA VAL N 22 " pdb=" C VAL N 22 " ideal model delta sigma weight residual 112.96 108.02 4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" C ASP Z 41 " pdb=" CA ASP Z 41 " pdb=" CB ASP Z 41 " ideal model delta sigma weight residual 116.63 112.11 4.52 1.16e+00 7.43e-01 1.52e+01 angle pdb=" N PHE Z 40 " pdb=" CA PHE Z 40 " pdb=" C PHE Z 40 " ideal model delta sigma weight residual 113.50 108.94 4.56 1.23e+00 6.61e-01 1.37e+01 angle pdb=" N ILE O 70 " pdb=" CA ILE O 70 " pdb=" C ILE O 70 " ideal model delta sigma weight residual 110.72 107.04 3.68 1.01e+00 9.80e-01 1.33e+01 ... (remaining 18439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6924 17.90 - 35.80: 844 35.80 - 53.70: 225 53.70 - 71.60: 46 71.60 - 89.50: 23 Dihedral angle restraints: 8062 sinusoidal: 2925 harmonic: 5137 Sorted by residual: dihedral pdb=" CB CYS T 135 " pdb=" SG CYS T 135 " pdb=" SG CYS T 173 " pdb=" CB CYS T 173 " ideal model delta sinusoidal sigma weight residual 93.00 133.02 -40.02 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CB CYS Z 135 " pdb=" SG CYS Z 135 " pdb=" SG CYS Z 173 " pdb=" CB CYS Z 173 " ideal model delta sinusoidal sigma weight residual -86.00 -52.01 -33.99 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CA MET Z 264 " pdb=" C MET Z 264 " pdb=" N ALA Z 265 " pdb=" CA ALA Z 265 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 8059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1704 0.045 - 0.090: 424 0.090 - 0.135: 85 0.135 - 0.180: 16 0.180 - 0.225: 10 Chirality restraints: 2239 Sorted by residual: chirality pdb=" CA ILE L 70 " pdb=" N ILE L 70 " pdb=" C ILE L 70 " pdb=" CB ILE L 70 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE O 70 " pdb=" N ILE O 70 " pdb=" C ILE O 70 " pdb=" CB ILE O 70 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE M 70 " pdb=" N ILE M 70 " pdb=" C ILE M 70 " pdb=" CB ILE M 70 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2236 not shown) Planarity restraints: 2379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP T 171 " 0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C ASP T 171 " -0.068 2.00e-02 2.50e+03 pdb=" O ASP T 171 " 0.025 2.00e-02 2.50e+03 pdb=" N THR T 172 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY O 19 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO O 20 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO O 20 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 20 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 19 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO L 20 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO L 20 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 20 " -0.038 5.00e-02 4.00e+02 ... (remaining 2376 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3358 2.80 - 3.32: 14959 3.32 - 3.85: 23484 3.85 - 4.37: 25378 4.37 - 4.90: 42810 Nonbonded interactions: 109989 Sorted by model distance: nonbonded pdb=" O ASP V 130 " pdb=" OG1 THR V 133 " model vdw 2.270 3.040 nonbonded pdb=" O LEU X 134 " pdb=" OG SER X 137 " model vdw 2.274 3.040 nonbonded pdb=" OE2 GLU H 42 " pdb=" OH TYR Q 48 " model vdw 2.294 3.040 nonbonded pdb=" O GLU T 235 " pdb=" OG SER T 238 " model vdw 2.298 3.040 nonbonded pdb=" O GLU Y 143 " pdb=" N GLY Y 148 " model vdw 2.307 3.120 ... (remaining 109984 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 72) selection = chain 'Q' } ncs_group { reference = (chain 'T' and (resid 47 through 135 or resid 170 through 304)) selection = (chain 'Z' and ((resid 47 through 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 through 66 or (resid 67 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 120 or (resid 121 thro \ ugh 123 and (name N or name CA or name C or name O or name CB )) or resid 124 or \ (resid 125 through 127 and (name N or name CA or name C or name O or name CB )) \ or resid 128 or (resid 129 and (name N or name CA or name C or name O or name C \ B )) or resid 130 or (resid 131 through 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 or (resid 134 and (name N or name CA or name C \ or name O or name CB )) or resid 135 or resid 170 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 182 o \ r (resid 183 through 189 and (name N or name CA or name C or name O or name CB ) \ ) or resid 190 through 217 or (resid 218 through 225 and (name N or name CA or n \ ame C or name O or name CB )) or resid 226 or (resid 227 through 230 and (name N \ or name CA or name C or name O or name CB )) or resid 231 through 304)) } ncs_group { reference = (chain 'U' and (resid 8 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 139 or (resid 140 and (name N or na \ me CA or name C or name O or name CB )) or (resid 141 through 147 and (name N or \ name CA or name C or name O or name CB )) or resid 148 through 157)) selection = (chain 'V' and ((resid 8 through 45 and (name N or name CA or name C or name O o \ r name CB )) or resid 46 through 77 or (resid 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 157)) selection = (chain 'X' and ((resid 8 through 45 and (name N or name CA or name C or name O o \ r name CB )) or resid 46 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 141 through 147 and (name N or name CA or \ name C or name O or name CB )) or resid 148 through 157)) selection = (chain 'Y' and ((resid 8 through 45 and (name N or name CA or name C or name O o \ r name CB )) or resid 46 through 77 or (resid 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 139 or (resid 140 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 141 through 147 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 through 157)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.080 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.009 0.950 13608 Z= 0.487 Angle : 0.701 31.269 18448 Z= 0.414 Chirality : 0.043 0.225 2239 Planarity : 0.005 0.070 2379 Dihedral : 17.546 89.501 4750 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.63 % Allowed : 29.58 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1784 helix: 1.31 (0.14), residues: 1466 sheet: None (None), residues: 0 loop : -1.92 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 208 HIS 0.004 0.001 HIS Y 149 PHE 0.026 0.001 PHE Z 276 TYR 0.012 0.001 TYR Z 296 ARG 0.003 0.000 ARG V 40 Details of bonding type rmsd hydrogen bonds : bond 0.12909 ( 1200) hydrogen bonds : angle 5.55392 ( 3588) SS BOND : bond 0.69838 ( 2) SS BOND : angle 26.76995 ( 4) covalent geometry : bond 0.00418 (13606) covalent geometry : angle 0.57934 (18444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 499 time to evaluate : 1.598 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: Y 84 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8617 (tm-30) REVERT: Y 88 LYS cc_start: 0.9102 (pptt) cc_final: 0.8733 (pptt) REVERT: Y 90 GLN cc_start: 0.8364 (tp40) cc_final: 0.8158 (tp40) REVERT: Y 127 GLN cc_start: 0.9014 (tp40) cc_final: 0.8691 (tp-100) REVERT: Y 131 LEU cc_start: 0.9289 (tt) cc_final: 0.9086 (tt) REVERT: X 99 ARG cc_start: 0.8916 (mmp-170) cc_final: 0.8372 (mmp80) REVERT: X 126 SER cc_start: 0.8481 (p) cc_final: 0.8167 (p) REVERT: U 69 ILE cc_start: 0.9379 (mm) cc_final: 0.9109 (mm) REVERT: U 101 GLU cc_start: 0.9325 (tp30) cc_final: 0.8629 (tp30) REVERT: U 105 LEU cc_start: 0.9173 (mt) cc_final: 0.8583 (mt) REVERT: U 112 GLN cc_start: 0.8863 (mp10) cc_final: 0.8616 (mp10) REVERT: U 119 ARG cc_start: 0.9100 (mmm-85) cc_final: 0.8865 (ttp80) REVERT: U 120 MET cc_start: 0.8929 (mmt) cc_final: 0.8517 (mmt) REVERT: U 123 GLU cc_start: 0.8818 (pp20) cc_final: 0.8476 (pp20) REVERT: H 49 MET cc_start: 0.9234 (ttt) cc_final: 0.8773 (tmm) REVERT: I 4 LEU cc_start: 0.9417 (tp) cc_final: 0.9039 (tp) REVERT: I 6 LEU cc_start: 0.9074 (mt) cc_final: 0.8858 (mt) REVERT: I 15 LEU cc_start: 0.9080 (mt) cc_final: 0.8767 (tp) REVERT: I 56 THR cc_start: 0.9211 (p) cc_final: 0.8979 (p) REVERT: J 18 ILE cc_start: 0.9124 (mt) cc_final: 0.8648 (mt) REVERT: J 48 TYR cc_start: 0.8768 (m-80) cc_final: 0.8122 (m-80) REVERT: K 55 PHE cc_start: 0.8148 (m-80) cc_final: 0.7939 (m-10) REVERT: K 59 LEU cc_start: 0.9305 (mt) cc_final: 0.9071 (mp) REVERT: L 15 LEU cc_start: 0.9482 (mt) cc_final: 0.9149 (mp) REVERT: M 27 ILE cc_start: 0.9404 (mt) cc_final: 0.9173 (tt) REVERT: M 62 PHE cc_start: 0.9020 (m-10) cc_final: 0.8786 (m-10) REVERT: M 70 ILE cc_start: 0.8938 (mm) cc_final: 0.8591 (mm) REVERT: N 1 MET cc_start: 0.7923 (tpp) cc_final: 0.7063 (mmp) REVERT: N 7 VAL cc_start: 0.9599 (t) cc_final: 0.9349 (p) REVERT: O 20 PRO cc_start: 0.8965 (Cg_exo) cc_final: 0.8753 (Cg_endo) REVERT: O 48 TYR cc_start: 0.8656 (m-80) cc_final: 0.8124 (m-80) REVERT: Z 75 MET cc_start: 0.8766 (tpt) cc_final: 0.8514 (tpp) REVERT: Z 78 ARG cc_start: 0.4987 (tmt170) cc_final: 0.4288 (tpt90) REVERT: Z 80 LEU cc_start: 0.8343 (mm) cc_final: 0.8114 (tp) REVERT: Z 81 GLN cc_start: 0.7964 (tt0) cc_final: 0.7336 (tt0) REVERT: Z 85 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8116 (tt0) REVERT: Z 113 ILE cc_start: 0.9534 (mt) cc_final: 0.9289 (mt) REVERT: Z 115 LEU cc_start: 0.9148 (mt) cc_final: 0.8629 (mt) REVERT: Z 195 PHE cc_start: 0.8821 (m-80) cc_final: 0.8468 (m-80) REVERT: Z 280 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9134 (mm-30) REVERT: T 84 MET cc_start: 0.8996 (ttt) cc_final: 0.8683 (tmm) REVERT: T 115 LEU cc_start: 0.9184 (mt) cc_final: 0.8856 (pp) REVERT: T 170 HIS cc_start: 0.3723 (OUTLIER) cc_final: 0.3465 (m170) REVERT: T 203 VAL cc_start: 0.9332 (p) cc_final: 0.9044 (p) REVERT: T 206 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7859 (pp20) REVERT: T 249 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.8336 (ptp-170) outliers start: 8 outliers final: 2 residues processed: 506 average time/residue: 0.2241 time to fit residues: 168.3888 Evaluate side-chains 362 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 359 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 134 VAL Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain T residue 170 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 82 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 GLN ** V 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN X 112 GLN ** X 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN Z 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.084466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066332 restraints weight = 62836.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067994 restraints weight = 35398.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069102 restraints weight = 24314.855| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13608 Z= 0.154 Angle : 0.620 10.015 18448 Z= 0.324 Chirality : 0.043 0.323 2239 Planarity : 0.005 0.065 2379 Dihedral : 3.931 19.391 1936 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.51 % Allowed : 30.76 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1784 helix: 1.56 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -2.00 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 208 HIS 0.003 0.001 HIS Y 149 PHE 0.025 0.001 PHE J 62 TYR 0.017 0.002 TYR Z 92 ARG 0.004 0.000 ARG X 71 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 1200) hydrogen bonds : angle 3.97865 ( 3588) SS BOND : bond 0.00900 ( 2) SS BOND : angle 0.92424 ( 4) covalent geometry : bond 0.00335 (13606) covalent geometry : angle 0.61986 (18444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 385 time to evaluate : 1.635 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: Y 84 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8587 (tm-30) REVERT: Y 88 LYS cc_start: 0.9097 (pptt) cc_final: 0.8730 (pptt) REVERT: Y 90 GLN cc_start: 0.8364 (tp40) cc_final: 0.8162 (tp40) REVERT: Y 127 GLN cc_start: 0.9104 (tp40) cc_final: 0.8760 (tp-100) REVERT: V 78 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9060 (ptmm) REVERT: X 91 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9145 (mm-30) REVERT: X 99 ARG cc_start: 0.8733 (mmp-170) cc_final: 0.8347 (mmp80) REVERT: X 106 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8487 (tptt) REVERT: X 120 MET cc_start: 0.9515 (tpt) cc_final: 0.9069 (tmm) REVERT: U 69 ILE cc_start: 0.9181 (mm) cc_final: 0.8976 (mm) REVERT: U 101 GLU cc_start: 0.9335 (tp30) cc_final: 0.8679 (tp30) REVERT: U 105 LEU cc_start: 0.9351 (mt) cc_final: 0.8846 (mt) REVERT: U 119 ARG cc_start: 0.9114 (mmm-85) cc_final: 0.8868 (ttp80) REVERT: U 120 MET cc_start: 0.8974 (mmt) cc_final: 0.8544 (mmt) REVERT: U 123 GLU cc_start: 0.8859 (pp20) cc_final: 0.8505 (pp20) REVERT: H 49 MET cc_start: 0.9360 (ttt) cc_final: 0.8691 (tmm) REVERT: J 1 MET cc_start: 0.5153 (mmt) cc_final: 0.4892 (mmt) REVERT: J 18 ILE cc_start: 0.9057 (mt) cc_final: 0.8842 (mt) REVERT: K 1 MET cc_start: 0.7878 (mpt) cc_final: 0.7494 (mpt) REVERT: K 33 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8938 (tp40) REVERT: K 62 PHE cc_start: 0.9169 (m-10) cc_final: 0.8809 (m-10) REVERT: L 4 LEU cc_start: 0.9243 (tp) cc_final: 0.9022 (tp) REVERT: M 1 MET cc_start: 0.6402 (mpp) cc_final: 0.4579 (mmt) REVERT: M 27 ILE cc_start: 0.9574 (mt) cc_final: 0.9288 (tt) REVERT: M 70 ILE cc_start: 0.8819 (mm) cc_final: 0.8465 (mm) REVERT: N 1 MET cc_start: 0.8353 (tpp) cc_final: 0.7588 (mmp) REVERT: N 49 MET cc_start: 0.9250 (ppp) cc_final: 0.8984 (ppp) REVERT: O 48 TYR cc_start: 0.8705 (m-80) cc_final: 0.8191 (m-80) REVERT: P 7 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8702 (p) REVERT: Z 78 ARG cc_start: 0.5081 (tmt170) cc_final: 0.4686 (tpt90) REVERT: Z 80 LEU cc_start: 0.8480 (mm) cc_final: 0.8272 (tp) REVERT: Z 85 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8430 (tt0) REVERT: Z 113 ILE cc_start: 0.9399 (mt) cc_final: 0.9181 (mt) REVERT: Z 195 PHE cc_start: 0.8676 (m-80) cc_final: 0.8282 (m-80) REVERT: Z 280 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9058 (mm-30) REVERT: T 84 MET cc_start: 0.8950 (ttt) cc_final: 0.8624 (tmm) REVERT: T 85 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8666 (pt0) REVERT: T 115 LEU cc_start: 0.9184 (mt) cc_final: 0.8840 (pp) REVERT: T 277 TYR cc_start: 0.6164 (m-10) cc_final: 0.5469 (m-10) outliers start: 70 outliers final: 35 residues processed: 420 average time/residue: 0.2145 time to fit residues: 135.0955 Evaluate side-chains 388 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 349 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 95 ILE Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain U residue 126 SER Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 299 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 106 optimal weight: 0.0050 chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 82 GLN ** V 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 GLN X 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.084595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.066098 restraints weight = 63852.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.067773 restraints weight = 36221.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068888 restraints weight = 24829.553| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13608 Z= 0.146 Angle : 0.616 12.611 18448 Z= 0.318 Chirality : 0.043 0.292 2239 Planarity : 0.004 0.063 2379 Dihedral : 3.895 19.622 1933 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.59 % Allowed : 31.71 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1784 helix: 1.54 (0.14), residues: 1451 sheet: None (None), residues: 0 loop : -1.97 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 31 PHE 0.024 0.001 PHE T 251 TYR 0.024 0.002 TYR Z 92 ARG 0.004 0.000 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 1200) hydrogen bonds : angle 3.85207 ( 3588) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.74652 ( 4) covalent geometry : bond 0.00326 (13606) covalent geometry : angle 0.61601 (18444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 370 time to evaluate : 1.429 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: Y 84 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8582 (tm-30) REVERT: Y 88 LYS cc_start: 0.9089 (pptt) cc_final: 0.8758 (pptt) REVERT: Y 90 GLN cc_start: 0.8358 (tp40) cc_final: 0.8150 (tp40) REVERT: Y 127 GLN cc_start: 0.9105 (tp40) cc_final: 0.8743 (tp-100) REVERT: V 46 GLU cc_start: 0.9508 (OUTLIER) cc_final: 0.9297 (tp30) REVERT: X 99 ARG cc_start: 0.8684 (mmp-170) cc_final: 0.8310 (mmp80) REVERT: X 106 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8400 (tptm) REVERT: X 107 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: X 120 MET cc_start: 0.9472 (tpt) cc_final: 0.9048 (tmm) REVERT: U 88 LYS cc_start: 0.9464 (mmtt) cc_final: 0.9098 (mttp) REVERT: U 101 GLU cc_start: 0.9333 (tp30) cc_final: 0.8672 (tp30) REVERT: U 105 LEU cc_start: 0.9350 (mt) cc_final: 0.8781 (mt) REVERT: U 119 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8881 (ttp80) REVERT: U 120 MET cc_start: 0.8992 (mmt) cc_final: 0.8541 (mmt) REVERT: U 123 GLU cc_start: 0.8886 (pp20) cc_final: 0.8508 (pp20) REVERT: H 43 ASN cc_start: 0.9119 (t0) cc_final: 0.8623 (p0) REVERT: H 49 MET cc_start: 0.9318 (ttt) cc_final: 0.8717 (tmm) REVERT: I 1 MET cc_start: 0.6784 (pmm) cc_final: 0.6483 (pmm) REVERT: K 1 MET cc_start: 0.7851 (mpt) cc_final: 0.7417 (mpt) REVERT: K 62 PHE cc_start: 0.9163 (m-10) cc_final: 0.8812 (m-10) REVERT: L 4 LEU cc_start: 0.9214 (tp) cc_final: 0.8888 (tp) REVERT: L 49 MET cc_start: 0.9074 (ppp) cc_final: 0.8819 (ppp) REVERT: M 27 ILE cc_start: 0.9598 (mt) cc_final: 0.9295 (tt) REVERT: M 48 TYR cc_start: 0.8881 (m-80) cc_final: 0.8642 (m-80) REVERT: M 70 ILE cc_start: 0.8895 (mm) cc_final: 0.8590 (mm) REVERT: N 1 MET cc_start: 0.8268 (tpp) cc_final: 0.7763 (mmm) REVERT: N 49 MET cc_start: 0.9234 (ppp) cc_final: 0.8947 (ppp) REVERT: P 7 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8842 (p) REVERT: Q 5 ASN cc_start: 0.8685 (p0) cc_final: 0.8455 (p0) REVERT: Z 78 ARG cc_start: 0.5102 (tmt170) cc_final: 0.4759 (tpt90) REVERT: Z 85 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8371 (tt0) REVERT: Z 126 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8874 (mm) REVERT: Z 195 PHE cc_start: 0.8709 (m-80) cc_final: 0.8344 (m-80) REVERT: Z 277 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: Z 280 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9012 (mm-30) REVERT: T 84 MET cc_start: 0.8963 (ttt) cc_final: 0.8557 (tmm) REVERT: T 85 GLU cc_start: 0.9050 (pt0) cc_final: 0.8547 (pt0) REVERT: T 115 LEU cc_start: 0.9207 (mt) cc_final: 0.8838 (pp) REVERT: T 277 TYR cc_start: 0.5643 (m-10) cc_final: 0.5208 (m-10) outliers start: 71 outliers final: 43 residues processed: 405 average time/residue: 0.2107 time to fit residues: 128.0155 Evaluate side-chains 391 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 343 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain T residue 97 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 135 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 127 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.084178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065862 restraints weight = 63562.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.067524 restraints weight = 36228.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.068613 restraints weight = 24898.849| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13608 Z= 0.147 Angle : 0.638 11.171 18448 Z= 0.327 Chirality : 0.044 0.240 2239 Planarity : 0.004 0.063 2379 Dihedral : 3.902 19.859 1933 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.98 % Allowed : 32.10 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1784 helix: 1.51 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.90 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 208 HIS 0.003 0.001 HIS Z 31 PHE 0.023 0.001 PHE T 251 TYR 0.026 0.002 TYR Z 92 ARG 0.009 0.000 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1200) hydrogen bonds : angle 3.82386 ( 3588) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.60299 ( 4) covalent geometry : bond 0.00332 (13606) covalent geometry : angle 0.63813 (18444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 356 time to evaluate : 1.406 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: Y 84 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8582 (tm-30) REVERT: Y 88 LYS cc_start: 0.9097 (pptt) cc_final: 0.8753 (pptt) REVERT: Y 90 GLN cc_start: 0.8363 (tp40) cc_final: 0.8157 (tp40) REVERT: Y 127 GLN cc_start: 0.9106 (tp40) cc_final: 0.8751 (tp-100) REVERT: V 46 GLU cc_start: 0.9498 (OUTLIER) cc_final: 0.9227 (tp30) REVERT: X 91 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9058 (mm-30) REVERT: X 99 ARG cc_start: 0.8645 (mmp-170) cc_final: 0.8284 (mmp80) REVERT: X 106 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8428 (tptm) REVERT: X 107 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: X 143 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6513 (pp20) REVERT: U 88 LYS cc_start: 0.9443 (mmtt) cc_final: 0.9071 (mtmm) REVERT: U 101 GLU cc_start: 0.9331 (tp30) cc_final: 0.8525 (tp30) REVERT: U 105 LEU cc_start: 0.9350 (mt) cc_final: 0.8555 (mt) REVERT: U 119 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8878 (ttp80) REVERT: U 120 MET cc_start: 0.8999 (mmt) cc_final: 0.8545 (mmt) REVERT: U 123 GLU cc_start: 0.8911 (pp20) cc_final: 0.8542 (pp20) REVERT: H 43 ASN cc_start: 0.9109 (t0) cc_final: 0.8593 (p0) REVERT: H 49 MET cc_start: 0.9307 (ttt) cc_final: 0.8783 (tmm) REVERT: K 62 PHE cc_start: 0.9178 (m-10) cc_final: 0.8789 (m-10) REVERT: L 1 MET cc_start: 0.5984 (mpp) cc_final: 0.5567 (mpp) REVERT: L 4 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8807 (tp) REVERT: L 49 MET cc_start: 0.9146 (ppp) cc_final: 0.8804 (ppp) REVERT: M 1 MET cc_start: 0.6576 (mpp) cc_final: 0.5464 (mmp) REVERT: M 27 ILE cc_start: 0.9633 (mt) cc_final: 0.9330 (tt) REVERT: M 49 MET cc_start: 0.9085 (ttp) cc_final: 0.8602 (ppp) REVERT: M 70 ILE cc_start: 0.8952 (mm) cc_final: 0.8671 (mm) REVERT: N 49 MET cc_start: 0.9220 (ppp) cc_final: 0.8913 (ppp) REVERT: P 7 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8869 (p) REVERT: Q 43 ASN cc_start: 0.8281 (p0) cc_final: 0.7871 (m110) REVERT: Z 78 ARG cc_start: 0.5225 (tmt170) cc_final: 0.4904 (tpt90) REVERT: Z 85 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8384 (tt0) REVERT: Z 126 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8930 (mm) REVERT: Z 195 PHE cc_start: 0.8787 (m-80) cc_final: 0.8524 (m-80) REVERT: Z 277 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: T 84 MET cc_start: 0.8958 (ttt) cc_final: 0.8545 (tmm) REVERT: T 85 GLU cc_start: 0.9054 (pt0) cc_final: 0.8620 (pt0) REVERT: T 97 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8370 (t0) REVERT: T 115 LEU cc_start: 0.9268 (mt) cc_final: 0.8965 (pp) REVERT: T 277 TYR cc_start: 0.5588 (m-10) cc_final: 0.5249 (m-10) outliers start: 76 outliers final: 45 residues processed: 399 average time/residue: 0.2151 time to fit residues: 128.1578 Evaluate side-chains 384 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 271 LEU Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 32 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.081542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.063222 restraints weight = 64671.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064724 restraints weight = 36691.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065791 restraints weight = 25650.011| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13608 Z= 0.203 Angle : 0.688 13.746 18448 Z= 0.356 Chirality : 0.045 0.364 2239 Planarity : 0.005 0.066 2379 Dihedral : 4.045 21.546 1933 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.92 % Allowed : 33.36 % Favored : 59.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1784 helix: 1.38 (0.13), residues: 1450 sheet: None (None), residues: 0 loop : -1.75 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 208 HIS 0.003 0.001 HIS X 149 PHE 0.031 0.002 PHE P 62 TYR 0.027 0.002 TYR Z 92 ARG 0.012 0.000 ARG J 44 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 1200) hydrogen bonds : angle 3.94544 ( 3588) SS BOND : bond 0.00037 ( 2) SS BOND : angle 0.86720 ( 4) covalent geometry : bond 0.00453 (13606) covalent geometry : angle 0.68808 (18444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 331 time to evaluate : 1.359 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: Y 84 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8438 (tm-30) REVERT: Y 127 GLN cc_start: 0.9161 (tp40) cc_final: 0.8840 (tp-100) REVERT: V 46 GLU cc_start: 0.9554 (OUTLIER) cc_final: 0.9296 (tp30) REVERT: X 106 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8381 (tptt) REVERT: X 107 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: X 120 MET cc_start: 0.9505 (tpt) cc_final: 0.9098 (tmm) REVERT: X 143 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6735 (pp20) REVERT: U 88 LYS cc_start: 0.9478 (mmtt) cc_final: 0.9169 (mttp) REVERT: U 119 ARG cc_start: 0.9132 (mmm-85) cc_final: 0.8866 (ttp80) REVERT: U 120 MET cc_start: 0.9034 (mmt) cc_final: 0.8617 (mmt) REVERT: U 123 GLU cc_start: 0.8878 (pp20) cc_final: 0.8553 (pp20) REVERT: U 130 ASP cc_start: 0.9227 (m-30) cc_final: 0.8981 (m-30) REVERT: H 49 MET cc_start: 0.9367 (ttt) cc_final: 0.8772 (tmm) REVERT: I 55 PHE cc_start: 0.9288 (m-80) cc_final: 0.9011 (m-80) REVERT: K 55 PHE cc_start: 0.8800 (m-80) cc_final: 0.8464 (m-80) REVERT: K 57 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8096 (tm-30) REVERT: K 62 PHE cc_start: 0.9293 (m-10) cc_final: 0.8933 (m-10) REVERT: L 49 MET cc_start: 0.9228 (ppp) cc_final: 0.8960 (ppp) REVERT: M 1 MET cc_start: 0.6691 (mpp) cc_final: 0.6020 (tpp) REVERT: M 27 ILE cc_start: 0.9679 (mt) cc_final: 0.9371 (tt) REVERT: M 48 TYR cc_start: 0.8978 (m-80) cc_final: 0.8656 (m-80) REVERT: M 62 PHE cc_start: 0.9211 (m-10) cc_final: 0.8932 (m-80) REVERT: M 70 ILE cc_start: 0.9085 (mm) cc_final: 0.8798 (mm) REVERT: N 1 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7105 (mmt) REVERT: N 49 MET cc_start: 0.9306 (ppp) cc_final: 0.8958 (ppp) REVERT: N 57 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8729 (mm-30) REVERT: P 1 MET cc_start: 0.7691 (mpp) cc_final: 0.7257 (pmm) REVERT: Q 43 ASN cc_start: 0.8436 (p0) cc_final: 0.7953 (m110) REVERT: Z 78 ARG cc_start: 0.5517 (tmt170) cc_final: 0.5045 (tpt90) REVERT: Z 85 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8536 (tt0) REVERT: Z 195 PHE cc_start: 0.8878 (m-80) cc_final: 0.8626 (t80) REVERT: Z 206 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8983 (mm-30) REVERT: Z 277 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8822 (m-80) REVERT: Z 280 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8956 (mm-30) REVERT: T 65 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7924 (mm) REVERT: T 84 MET cc_start: 0.8878 (ttt) cc_final: 0.8474 (tmm) REVERT: T 85 GLU cc_start: 0.9082 (pt0) cc_final: 0.8650 (pt0) REVERT: T 97 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8528 (t0) REVERT: T 115 LEU cc_start: 0.9284 (mt) cc_final: 0.9042 (pp) REVERT: T 277 TYR cc_start: 0.5311 (m-80) cc_final: 0.5090 (m-10) outliers start: 88 outliers final: 60 residues processed: 375 average time/residue: 0.2100 time to fit residues: 118.5661 Evaluate side-chains 379 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 312 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 107 GLU Chi-restraints excluded: chain Y residue 137 SER Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 202 PHE Chi-restraints excluded: chain T residue 208 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 55 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 82 GLN ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.082805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064658 restraints weight = 65007.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.066235 restraints weight = 36315.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.067294 restraints weight = 24976.231| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13608 Z= 0.154 Angle : 0.672 13.302 18448 Z= 0.342 Chirality : 0.045 0.344 2239 Planarity : 0.005 0.065 2379 Dihedral : 4.023 20.821 1933 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.61 % Allowed : 35.80 % Favored : 57.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1784 helix: 1.44 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 208 HIS 0.002 0.001 HIS Z 31 PHE 0.028 0.001 PHE P 62 TYR 0.030 0.002 TYR Z 92 ARG 0.005 0.000 ARG X 71 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1200) hydrogen bonds : angle 3.87144 ( 3588) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.74259 ( 4) covalent geometry : bond 0.00347 (13606) covalent geometry : angle 0.67182 (18444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 344 time to evaluate : 1.444 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: Y 34 MET cc_start: 0.9260 (mmm) cc_final: 0.9053 (mmm) REVERT: Y 84 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8432 (tm-30) REVERT: Y 90 GLN cc_start: 0.8400 (tp40) cc_final: 0.8189 (tp40) REVERT: Y 127 GLN cc_start: 0.9146 (tp40) cc_final: 0.8785 (tp-100) REVERT: V 46 GLU cc_start: 0.9511 (OUTLIER) cc_final: 0.9309 (tp30) REVERT: X 82 GLN cc_start: 0.8952 (tt0) cc_final: 0.8475 (mm-40) REVERT: X 99 ARG cc_start: 0.8604 (mmp-170) cc_final: 0.8251 (mmp80) REVERT: X 106 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8464 (tptm) REVERT: X 107 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: X 120 MET cc_start: 0.9431 (tpt) cc_final: 0.9070 (tmm) REVERT: X 138 ARG cc_start: -0.0846 (OUTLIER) cc_final: -0.3775 (ttm170) REVERT: X 143 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: U 88 LYS cc_start: 0.9469 (mmtt) cc_final: 0.8953 (mttp) REVERT: U 119 ARG cc_start: 0.9113 (mmm-85) cc_final: 0.8850 (ttp80) REVERT: U 120 MET cc_start: 0.9025 (mmt) cc_final: 0.8564 (mmt) REVERT: U 123 GLU cc_start: 0.8853 (pp20) cc_final: 0.8524 (pp20) REVERT: U 130 ASP cc_start: 0.9216 (m-30) cc_final: 0.8957 (m-30) REVERT: H 43 ASN cc_start: 0.8989 (t0) cc_final: 0.8557 (p0) REVERT: H 49 MET cc_start: 0.9325 (ttt) cc_final: 0.8748 (tmm) REVERT: K 55 PHE cc_start: 0.8716 (m-80) cc_final: 0.8381 (m-80) REVERT: K 62 PHE cc_start: 0.9271 (m-10) cc_final: 0.8927 (m-10) REVERT: L 44 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7765 (tpt170) REVERT: L 49 MET cc_start: 0.9241 (ppp) cc_final: 0.8900 (ppp) REVERT: L 57 GLU cc_start: 0.9403 (tp30) cc_final: 0.9057 (tp30) REVERT: M 1 MET cc_start: 0.6891 (mpp) cc_final: 0.6231 (tpp) REVERT: M 27 ILE cc_start: 0.9679 (mt) cc_final: 0.9370 (tt) REVERT: M 48 TYR cc_start: 0.8954 (m-80) cc_final: 0.8607 (m-80) REVERT: M 62 PHE cc_start: 0.9212 (m-10) cc_final: 0.9002 (m-80) REVERT: M 70 ILE cc_start: 0.9027 (mm) cc_final: 0.8745 (mm) REVERT: N 1 MET cc_start: 0.7271 (mmp) cc_final: 0.6909 (mmt) REVERT: N 49 MET cc_start: 0.9287 (ppp) cc_final: 0.8903 (ppp) REVERT: N 70 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7568 (tt) REVERT: Q 1 MET cc_start: 0.6856 (ttt) cc_final: 0.6605 (ppp) REVERT: Z 78 ARG cc_start: 0.5513 (tmt170) cc_final: 0.5031 (tpt90) REVERT: Z 85 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8472 (tt0) REVERT: Z 195 PHE cc_start: 0.8922 (m-80) cc_final: 0.8590 (t80) REVERT: Z 206 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8908 (mm-30) REVERT: Z 264 MET cc_start: 0.9328 (mmm) cc_final: 0.9068 (tpp) REVERT: Z 277 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8777 (m-80) REVERT: Z 280 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8949 (mm-30) REVERT: Z 294 LEU cc_start: 0.9702 (mt) cc_final: 0.9481 (mt) REVERT: T 65 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7795 (mm) REVERT: T 84 MET cc_start: 0.8867 (ttt) cc_final: 0.8497 (tmm) REVERT: T 85 GLU cc_start: 0.8981 (pt0) cc_final: 0.8491 (pt0) REVERT: T 97 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8515 (t0) REVERT: T 115 LEU cc_start: 0.9301 (mt) cc_final: 0.9029 (pp) REVERT: T 208 TRP cc_start: 0.7695 (OUTLIER) cc_final: 0.7483 (t60) REVERT: T 277 TYR cc_start: 0.5036 (m-80) cc_final: 0.4784 (m-10) outliers start: 84 outliers final: 52 residues processed: 386 average time/residue: 0.2209 time to fit residues: 127.3610 Evaluate side-chains 381 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 319 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 271 LEU Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 202 PHE Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 114 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 chunk 131 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN ** T 287 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 = 0.3748 r_free = 0.3748 target = 0.083320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.065065 restraints weight = 64956.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066671 restraints weight = 36525.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.067704 restraints weight = 25133.381| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13608 Z= 0.146 Angle : 0.678 12.948 18448 Z= 0.345 Chirality : 0.045 0.306 2239 Planarity : 0.005 0.128 2379 Dihedral : 4.034 20.271 1933 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.27 % Allowed : 37.53 % Favored : 57.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1784 helix: 1.43 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.93 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 208 HIS 0.002 0.001 HIS Z 31 PHE 0.023 0.001 PHE P 62 TYR 0.027 0.002 TYR Z 92 ARG 0.009 0.000 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 1200) hydrogen bonds : angle 3.89950 ( 3588) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.22513 ( 4) covalent geometry : bond 0.00323 (13606) covalent geometry : angle 0.67825 (18444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 345 time to evaluate : 1.353 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: Y 84 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8406 (tm-30) REVERT: Y 90 GLN cc_start: 0.8391 (tp40) cc_final: 0.8179 (tp40) REVERT: Y 127 GLN cc_start: 0.9138 (tp40) cc_final: 0.8779 (tp-100) REVERT: X 82 GLN cc_start: 0.8920 (tt0) cc_final: 0.8571 (mm-40) REVERT: X 99 ARG cc_start: 0.8480 (mmp-170) cc_final: 0.8132 (mmp80) REVERT: X 106 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8447 (tptm) REVERT: X 107 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8169 (pm20) REVERT: X 120 MET cc_start: 0.9401 (tpt) cc_final: 0.9052 (tmm) REVERT: X 138 ARG cc_start: -0.0789 (OUTLIER) cc_final: -0.3606 (ttp-170) REVERT: X 143 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6677 (pp20) REVERT: U 88 LYS cc_start: 0.9452 (mmtt) cc_final: 0.8971 (mttp) REVERT: U 119 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8861 (ttp80) REVERT: U 120 MET cc_start: 0.9016 (mmt) cc_final: 0.8551 (mmt) REVERT: U 123 GLU cc_start: 0.8848 (pp20) cc_final: 0.8518 (pp20) REVERT: U 130 ASP cc_start: 0.9214 (m-30) cc_final: 0.8952 (m-30) REVERT: H 49 MET cc_start: 0.9304 (ttt) cc_final: 0.8753 (tmm) REVERT: J 55 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8668 (m-10) REVERT: K 55 PHE cc_start: 0.8643 (m-80) cc_final: 0.8269 (m-80) REVERT: K 62 PHE cc_start: 0.9283 (m-10) cc_final: 0.8960 (m-10) REVERT: L 44 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7930 (tpt170) REVERT: L 49 MET cc_start: 0.9223 (ppp) cc_final: 0.8991 (ppp) REVERT: L 57 GLU cc_start: 0.9404 (tp30) cc_final: 0.9120 (tp30) REVERT: M 1 MET cc_start: 0.6863 (mpp) cc_final: 0.6260 (tpp) REVERT: M 27 ILE cc_start: 0.9686 (mt) cc_final: 0.9365 (tt) REVERT: M 48 TYR cc_start: 0.8969 (m-80) cc_final: 0.8626 (m-80) REVERT: M 62 PHE cc_start: 0.9201 (m-10) cc_final: 0.8934 (m-80) REVERT: N 1 MET cc_start: 0.7089 (mmp) cc_final: 0.6819 (mmt) REVERT: N 49 MET cc_start: 0.9249 (ppp) cc_final: 0.8869 (ppp) REVERT: N 57 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8558 (mm-30) REVERT: N 70 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7638 (tt) REVERT: Q 1 MET cc_start: 0.6947 (ttt) cc_final: 0.6717 (tmm) REVERT: Z 78 ARG cc_start: 0.5516 (tmt170) cc_final: 0.5057 (tpt90) REVERT: Z 89 GLU cc_start: 0.9206 (pt0) cc_final: 0.8832 (pt0) REVERT: Z 126 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8974 (mm) REVERT: Z 194 THR cc_start: 0.8695 (p) cc_final: 0.8272 (t) REVERT: Z 195 PHE cc_start: 0.8918 (m-80) cc_final: 0.8596 (t80) REVERT: Z 277 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8891 (m-80) REVERT: Z 283 VAL cc_start: 0.9586 (OUTLIER) cc_final: 0.9354 (p) REVERT: T 65 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7830 (mm) REVERT: T 84 MET cc_start: 0.8825 (ttt) cc_final: 0.8493 (tmm) REVERT: T 85 GLU cc_start: 0.8945 (pt0) cc_final: 0.8502 (pt0) REVERT: T 115 LEU cc_start: 0.9300 (mt) cc_final: 0.9042 (pp) REVERT: T 208 TRP cc_start: 0.7776 (OUTLIER) cc_final: 0.7548 (t60) REVERT: T 277 TYR cc_start: 0.4818 (m-80) cc_final: 0.4587 (m-10) outliers start: 67 outliers final: 44 residues processed: 380 average time/residue: 0.2183 time to fit residues: 123.6871 Evaluate side-chains 375 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 55 PHE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 202 PHE Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 299 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 173 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 287 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 = 0.3738 r_free = 0.3738 target = 0.082927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064765 restraints weight = 65013.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.066376 restraints weight = 36453.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067389 restraints weight = 25075.892| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13608 Z= 0.156 Angle : 0.710 12.731 18448 Z= 0.360 Chirality : 0.045 0.305 2239 Planarity : 0.005 0.065 2379 Dihedral : 4.018 20.291 1933 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.96 % Allowed : 38.79 % Favored : 56.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1784 helix: 1.35 (0.13), residues: 1455 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 170 PHE 0.030 0.001 PHE P 62 TYR 0.031 0.002 TYR Z 92 ARG 0.009 0.000 ARG X 71 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1200) hydrogen bonds : angle 3.96523 ( 3588) SS BOND : bond 0.00199 ( 2) SS BOND : angle 0.92842 ( 4) covalent geometry : bond 0.00354 (13606) covalent geometry : angle 0.70963 (18444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 334 time to evaluate : 1.344 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: Y 84 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8440 (tm-30) REVERT: Y 90 GLN cc_start: 0.8407 (tp40) cc_final: 0.8188 (tp40) REVERT: Y 127 GLN cc_start: 0.9156 (tp40) cc_final: 0.8800 (tp-100) REVERT: V 97 GLN cc_start: 0.8678 (mt0) cc_final: 0.8309 (mt0) REVERT: X 82 GLN cc_start: 0.8978 (tt0) cc_final: 0.8737 (mm-40) REVERT: X 99 ARG cc_start: 0.8489 (mmp-170) cc_final: 0.8091 (mmp80) REVERT: X 103 GLU cc_start: 0.8021 (pp20) cc_final: 0.7645 (pp20) REVERT: X 106 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8417 (tptm) REVERT: X 107 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: X 120 MET cc_start: 0.9377 (tpt) cc_final: 0.9035 (tmm) REVERT: X 138 ARG cc_start: -0.0728 (OUTLIER) cc_final: -0.3583 (ttp-170) REVERT: X 143 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6688 (pp20) REVERT: U 123 GLU cc_start: 0.8848 (pp20) cc_final: 0.8554 (pp20) REVERT: U 130 ASP cc_start: 0.9219 (m-30) cc_final: 0.8962 (m-30) REVERT: H 46 VAL cc_start: 0.8689 (p) cc_final: 0.8427 (t) REVERT: H 49 MET cc_start: 0.9313 (ttt) cc_final: 0.8795 (tmm) REVERT: K 55 PHE cc_start: 0.8683 (m-80) cc_final: 0.8367 (m-80) REVERT: K 62 PHE cc_start: 0.9322 (m-10) cc_final: 0.8986 (m-10) REVERT: L 44 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7979 (tpt170) REVERT: L 49 MET cc_start: 0.9242 (ppp) cc_final: 0.9011 (ppp) REVERT: L 57 GLU cc_start: 0.9382 (tp30) cc_final: 0.9062 (tp30) REVERT: M 1 MET cc_start: 0.6914 (mpp) cc_final: 0.6300 (tpp) REVERT: M 27 ILE cc_start: 0.9697 (mt) cc_final: 0.9372 (tt) REVERT: M 48 TYR cc_start: 0.8969 (m-80) cc_final: 0.8676 (m-80) REVERT: M 62 PHE cc_start: 0.9205 (m-10) cc_final: 0.9001 (m-80) REVERT: N 49 MET cc_start: 0.9271 (ppp) cc_final: 0.8881 (ppp) REVERT: N 57 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8589 (mm-30) REVERT: N 70 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7680 (tt) REVERT: Q 1 MET cc_start: 0.7193 (ttt) cc_final: 0.6875 (tmm) REVERT: Z 78 ARG cc_start: 0.5710 (tmt170) cc_final: 0.5206 (tpt90) REVERT: Z 89 GLU cc_start: 0.9220 (pt0) cc_final: 0.8854 (pt0) REVERT: Z 194 THR cc_start: 0.8727 (p) cc_final: 0.8304 (t) REVERT: Z 195 PHE cc_start: 0.8936 (m-80) cc_final: 0.8632 (t80) REVERT: Z 277 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.9058 (m-80) REVERT: Z 280 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8920 (mm-30) REVERT: Z 283 VAL cc_start: 0.9583 (OUTLIER) cc_final: 0.9240 (p) REVERT: T 65 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7837 (mm) REVERT: T 84 MET cc_start: 0.8830 (ttt) cc_final: 0.8515 (tmm) REVERT: T 85 GLU cc_start: 0.8929 (pt0) cc_final: 0.8483 (pt0) REVERT: T 97 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8295 (t0) REVERT: T 115 LEU cc_start: 0.9334 (mt) cc_final: 0.9101 (pp) REVERT: T 277 TYR cc_start: 0.4767 (m-80) cc_final: 0.4501 (m-80) outliers start: 63 outliers final: 45 residues processed: 368 average time/residue: 0.2196 time to fit residues: 120.3473 Evaluate side-chains 375 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 202 PHE Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 51 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 287 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 = 0.3739 r_free = 0.3739 target = 0.082889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064772 restraints weight = 65013.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066315 restraints weight = 36768.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067340 restraints weight = 25480.482| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13608 Z= 0.157 Angle : 0.739 14.454 18448 Z= 0.372 Chirality : 0.047 0.314 2239 Planarity : 0.005 0.065 2379 Dihedral : 4.032 21.106 1933 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.04 % Allowed : 38.95 % Favored : 56.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1784 helix: 1.33 (0.13), residues: 1449 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP T 208 HIS 0.001 0.000 HIS V 149 PHE 0.037 0.001 PHE P 62 TYR 0.031 0.002 TYR Z 92 ARG 0.010 0.000 ARG X 71 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 1200) hydrogen bonds : angle 3.97072 ( 3588) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.77665 ( 4) covalent geometry : bond 0.00355 (13606) covalent geometry : angle 0.73919 (18444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 326 time to evaluate : 1.423 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: Y 84 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8467 (tm-30) REVERT: Y 90 GLN cc_start: 0.8397 (tp40) cc_final: 0.8174 (tp40) REVERT: Y 127 GLN cc_start: 0.9184 (tp40) cc_final: 0.8828 (tp-100) REVERT: X 82 GLN cc_start: 0.8998 (tt0) cc_final: 0.8662 (mm-40) REVERT: X 89 GLN cc_start: 0.9356 (mm-40) cc_final: 0.9073 (tp-100) REVERT: X 99 ARG cc_start: 0.8490 (mmp-170) cc_final: 0.8110 (mmp80) REVERT: X 103 GLU cc_start: 0.8002 (pp20) cc_final: 0.7667 (pp20) REVERT: X 106 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8360 (tptm) REVERT: X 107 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: X 120 MET cc_start: 0.9407 (tpt) cc_final: 0.9083 (tmm) REVERT: X 138 ARG cc_start: -0.1032 (OUTLIER) cc_final: -0.3731 (ttm170) REVERT: X 143 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6707 (pp20) REVERT: U 88 LYS cc_start: 0.9480 (mmtt) cc_final: 0.9005 (mttp) REVERT: U 123 GLU cc_start: 0.8831 (pp20) cc_final: 0.8615 (pp20) REVERT: U 130 ASP cc_start: 0.9226 (m-30) cc_final: 0.8959 (m-30) REVERT: H 46 VAL cc_start: 0.8634 (p) cc_final: 0.8422 (t) REVERT: H 49 MET cc_start: 0.9332 (ttt) cc_final: 0.8817 (tmm) REVERT: J 26 ILE cc_start: 0.9664 (mm) cc_final: 0.9447 (tt) REVERT: K 55 PHE cc_start: 0.8703 (m-80) cc_final: 0.8378 (m-80) REVERT: K 62 PHE cc_start: 0.9332 (m-10) cc_final: 0.8980 (m-10) REVERT: L 44 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8084 (tpt170) REVERT: L 49 MET cc_start: 0.9241 (ppp) cc_final: 0.8995 (ppp) REVERT: L 57 GLU cc_start: 0.9398 (tp30) cc_final: 0.9078 (tp30) REVERT: M 1 MET cc_start: 0.6791 (mpp) cc_final: 0.5620 (mmp) REVERT: M 27 ILE cc_start: 0.9699 (mt) cc_final: 0.9373 (tt) REVERT: M 48 TYR cc_start: 0.9010 (m-80) cc_final: 0.8730 (m-80) REVERT: M 62 PHE cc_start: 0.9244 (m-10) cc_final: 0.9011 (m-80) REVERT: M 70 ILE cc_start: 0.8920 (mm) cc_final: 0.8610 (mm) REVERT: N 49 MET cc_start: 0.9278 (ppp) cc_final: 0.8873 (ppp) REVERT: N 57 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8568 (mm-30) REVERT: N 70 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7683 (tt) REVERT: O 15 LEU cc_start: 0.9200 (mp) cc_final: 0.8974 (mp) REVERT: Z 78 ARG cc_start: 0.5765 (tmt170) cc_final: 0.5236 (tpt90) REVERT: Z 89 GLU cc_start: 0.9232 (pt0) cc_final: 0.8754 (pt0) REVERT: Z 194 THR cc_start: 0.8700 (p) cc_final: 0.8294 (t) REVERT: Z 195 PHE cc_start: 0.8973 (m-80) cc_final: 0.8677 (t80) REVERT: Z 264 MET cc_start: 0.9466 (mmp) cc_final: 0.8998 (tpp) REVERT: Z 277 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.9059 (m-80) REVERT: Z 280 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8951 (mm-30) REVERT: Z 283 VAL cc_start: 0.9556 (OUTLIER) cc_final: 0.9242 (p) REVERT: T 65 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7822 (mm) REVERT: T 84 MET cc_start: 0.8837 (ttt) cc_final: 0.8531 (tmm) REVERT: T 85 GLU cc_start: 0.8918 (pt0) cc_final: 0.8481 (pt0) REVERT: T 97 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8461 (t0) REVERT: T 115 LEU cc_start: 0.9334 (mt) cc_final: 0.9123 (pp) REVERT: T 277 TYR cc_start: 0.4725 (m-80) cc_final: 0.4458 (m-80) outliers start: 64 outliers final: 45 residues processed: 361 average time/residue: 0.2170 time to fit residues: 117.8870 Evaluate side-chains 372 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 318 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 120 MET Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 202 PHE Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 144 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN T 97 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.082559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064637 restraints weight = 65495.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.066175 restraints weight = 37273.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.067189 restraints weight = 25876.290| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13608 Z= 0.168 Angle : 0.752 13.597 18448 Z= 0.380 Chirality : 0.048 0.384 2239 Planarity : 0.005 0.065 2379 Dihedral : 4.059 20.147 1933 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.72 % Allowed : 39.26 % Favored : 56.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1784 helix: 1.30 (0.13), residues: 1449 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP T 208 HIS 0.002 0.000 HIS V 149 PHE 0.034 0.001 PHE P 62 TYR 0.038 0.002 TYR Z 92 ARG 0.010 0.000 ARG T 96 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1200) hydrogen bonds : angle 4.00942 ( 3588) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.77417 ( 4) covalent geometry : bond 0.00385 (13606) covalent geometry : angle 0.75196 (18444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 1.557 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: Y 84 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8448 (tm-30) REVERT: Y 90 GLN cc_start: 0.8435 (tp40) cc_final: 0.8196 (tp40) REVERT: Y 127 GLN cc_start: 0.9140 (tp40) cc_final: 0.8785 (tp-100) REVERT: X 82 GLN cc_start: 0.8944 (tt0) cc_final: 0.8640 (mm-40) REVERT: X 89 GLN cc_start: 0.9352 (mm-40) cc_final: 0.9062 (tp-100) REVERT: X 99 ARG cc_start: 0.8486 (mmp-170) cc_final: 0.8087 (mmp80) REVERT: X 103 GLU cc_start: 0.8026 (pp20) cc_final: 0.7671 (pp20) REVERT: X 106 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8459 (tptm) REVERT: X 107 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: X 120 MET cc_start: 0.9347 (tpt) cc_final: 0.9041 (tmm) REVERT: X 138 ARG cc_start: -0.0599 (OUTLIER) cc_final: -0.3457 (ttp-170) REVERT: X 143 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6691 (pp20) REVERT: U 88 LYS cc_start: 0.9477 (mmtt) cc_final: 0.8981 (mttp) REVERT: U 130 ASP cc_start: 0.9216 (m-30) cc_final: 0.8958 (m-30) REVERT: H 57 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8917 (mm-30) REVERT: K 55 PHE cc_start: 0.8676 (m-80) cc_final: 0.8401 (m-80) REVERT: K 62 PHE cc_start: 0.9291 (m-10) cc_final: 0.8974 (m-10) REVERT: L 44 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8029 (tpt170) REVERT: L 49 MET cc_start: 0.9255 (ppp) cc_final: 0.9031 (ppp) REVERT: L 57 GLU cc_start: 0.9332 (tp30) cc_final: 0.9026 (tp30) REVERT: M 1 MET cc_start: 0.6882 (mpp) cc_final: 0.6323 (tpp) REVERT: M 27 ILE cc_start: 0.9702 (mt) cc_final: 0.9363 (tt) REVERT: M 48 TYR cc_start: 0.8940 (m-80) cc_final: 0.8645 (m-80) REVERT: M 70 ILE cc_start: 0.8941 (mm) cc_final: 0.8640 (mm) REVERT: N 15 LEU cc_start: 0.9180 (mp) cc_final: 0.8893 (tp) REVERT: N 57 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8582 (mm-30) REVERT: N 70 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7778 (tt) REVERT: Q 1 MET cc_start: 0.7613 (ppp) cc_final: 0.7120 (ppp) REVERT: Z 78 ARG cc_start: 0.5780 (tmt170) cc_final: 0.5155 (tpt90) REVERT: Z 89 GLU cc_start: 0.9207 (pt0) cc_final: 0.8746 (pt0) REVERT: Z 194 THR cc_start: 0.8743 (p) cc_final: 0.8337 (t) REVERT: Z 195 PHE cc_start: 0.8882 (m-80) cc_final: 0.8624 (t80) REVERT: Z 277 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.9016 (m-80) REVERT: Z 280 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8912 (tp30) REVERT: T 65 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7756 (mm) REVERT: T 84 MET cc_start: 0.8786 (ttt) cc_final: 0.8458 (tmm) REVERT: T 85 GLU cc_start: 0.8929 (pt0) cc_final: 0.8468 (pt0) REVERT: T 97 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8490 (t0) REVERT: T 115 LEU cc_start: 0.9339 (mt) cc_final: 0.9107 (pp) REVERT: T 277 TYR cc_start: 0.4679 (m-80) cc_final: 0.4412 (m-80) outliers start: 60 outliers final: 41 residues processed: 359 average time/residue: 0.2250 time to fit residues: 120.5235 Evaluate side-chains 364 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 315 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 181 VAL Chi-restraints excluded: chain Z residue 241 VAL Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 202 PHE Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 94 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 175 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.083071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065064 restraints weight = 65738.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066619 restraints weight = 37372.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.067486 restraints weight = 25891.971| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13608 Z= 0.156 Angle : 0.750 14.874 18448 Z= 0.380 Chirality : 0.047 0.302 2239 Planarity : 0.005 0.065 2379 Dihedral : 4.068 20.584 1933 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.25 % Allowed : 40.28 % Favored : 55.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1784 helix: 1.27 (0.13), residues: 1454 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 208 HIS 0.001 0.000 HIS V 149 PHE 0.034 0.001 PHE H 62 TYR 0.032 0.002 TYR Z 92 ARG 0.009 0.000 ARG X 71 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1200) hydrogen bonds : angle 4.02088 ( 3588) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.70145 ( 4) covalent geometry : bond 0.00354 (13606) covalent geometry : angle 0.75013 (18444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5045.13 seconds wall clock time: 88 minutes 54.21 seconds (5334.21 seconds total)