Starting phenix.real_space_refine on Wed Jun 11 21:36:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itp_60874/06_2025/9itp_60874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itp_60874/06_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_60874/06_2025/9itp_60874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itp_60874/06_2025/9itp_60874.map" model { file = "/net/cci-nas-00/data/ceres_data/9itp_60874/06_2025/9itp_60874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itp_60874/06_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-5710/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: 8.62, per 1000 atoms: 0.64 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 1.7 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: 3.78 Time building geometry restraints manager: 3.78 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: 5.070 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.070 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- 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 : 1.336 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: 0.2188 time to fit residues: 164.1224 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 : 1.327 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066330 restraints weight = 62836.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067994 restraints weight = 35408.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069088 restraints weight = 24316.439| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 1.352 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: 0.9098 (pptt) cc_final: 0.8731 (pptt) REVERT: Y 90 GLN cc_start: 0.8366 (tp40) cc_final: 0.8163 (tp40) REVERT: Y 127 GLN cc_start: 0.9103 (tp40) cc_final: 0.8758 (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: 0.9070 (tmm) REVERT: U 69 ILE cc_start: 0.9181 (mm) cc_final: 0.8976 (mm) REVERT: U 101 GLU cc_start: 0.9334 (tp30) cc_final: 0.8678 (tp30) REVERT: U 105 LEU cc_start: 0.9351 (mt) cc_final: 0.8845 (mt) REVERT: U 119 ARG cc_start: 0.9113 (mmm-85) cc_final: 0.8869 (ttp80) REVERT: U 120 MET cc_start: 0.8972 (mmt) cc_final: 0.8542 (mmt) REVERT: U 123 GLU cc_start: 0.8857 (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: 0.4893 (mmt) REVERT: J 18 ILE cc_start: 0.9056 (mt) cc_final: 0.8840 (mt) REVERT: K 1 MET cc_start: 0.7877 (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: 0.9173 (m-10) cc_final: 0.8814 (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: 0.4580 (mmt) REVERT: M 27 ILE cc_start: 0.9575 (mt) cc_final: 0.9288 (tt) REVERT: M 70 ILE cc_start: 0.8820 (mm) cc_final: 0.8465 (mm) REVERT: N 1 MET cc_start: 0.8352 (tpp) cc_final: 0.7589 (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: 0.8190 (m-80) REVERT: P 7 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8703 (p) REVERT: Z 78 ARG cc_start: 0.5083 (tmt170) cc_final: 0.4687 (tpt90) REVERT: Z 80 LEU cc_start: 0.8480 (mm) cc_final: 0.8273 (tp) REVERT: Z 85 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8429 (tt0) REVERT: Z 113 ILE cc_start: 0.9399 (mt) cc_final: 0.9182 (mt) REVERT: Z 195 PHE cc_start: 0.8677 (m-80) cc_final: 0.8283 (m-80) REVERT: Z 280 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9059 (mm-30) REVERT: T 84 MET cc_start: 0.8951 (ttt) cc_final: 0.8626 (tmm) REVERT: T 85 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8665 (pt0) REVERT: T 115 LEU cc_start: 0.9184 (mt) cc_final: 0.8840 (pp) REVERT: T 277 TYR cc_start: 0.6171 (m-10) cc_final: 0.5473 (m-10) outliers start: 70 outliers final: 35 residues processed: 420 average time/residue: 0.2136 time to fit residues: 134.6512 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 : 1.544 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 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 ** X 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.084639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.066164 restraints weight = 63859.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.067827 restraints weight = 36190.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068944 restraints weight = 24904.199| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2733 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= 0.143 Angle : 0.617 12.666 18448 Z= 0.318 Chirality : 0.043 0.283 2239 Planarity : 0.005 0.063 2379 Dihedral : 3.905 19.610 1933 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.57 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 0.013 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 31 PHE 0.025 0.001 PHE T 251 TYR 0.024 0.002 TYR Z 92 ARG 0.005 0.000 ARG Y 147 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 1200) hydrogen bonds : angle 3.85034 ( 3588) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.77119 ( 4) covalent geometry : bond 0.00316 (13606) covalent geometry : angle 0.61673 (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 : 1.384 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: 0.8581 (tm-30) REVERT: Y 88 LYS cc_start: 0.9090 (pptt) cc_final: 0.8758 (pptt) REVERT: Y 90 GLN cc_start: 0.8359 (tp40) cc_final: 0.8151 (tp40) REVERT: Y 127 GLN cc_start: 0.9106 (tp40) cc_final: 0.8744 (tp-100) REVERT: V 46 GLU cc_start: 0.9509 (OUTLIER) cc_final: 0.9297 (tp30) REVERT: X 99 ARG cc_start: 0.8682 (mmp-170) cc_final: 0.8307 (mmp80) REVERT: X 106 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8401 (tptm) REVERT: X 107 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: X 120 MET cc_start: 0.9470 (tpt) cc_final: 0.9046 (tmm) REVERT: U 88 LYS cc_start: 0.9452 (mmtt) cc_final: 0.9074 (mttp) REVERT: U 101 GLU cc_start: 0.9332 (tp30) cc_final: 0.8670 (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: 0.8880 (ttp80) REVERT: U 120 MET cc_start: 0.8993 (mmt) cc_final: 0.8538 (mmt) REVERT: U 123 GLU cc_start: 0.8886 (pp20) cc_final: 0.8507 (pp20) REVERT: H 43 ASN cc_start: 0.9123 (t0) cc_final: 0.8633 (p0) REVERT: H 49 MET cc_start: 0.9325 (ttt) cc_final: 0.8726 (tmm) REVERT: I 1 MET cc_start: 0.6789 (pmm) cc_final: 0.6484 (pmm) REVERT: K 1 MET cc_start: 0.7845 (mpt) cc_final: 0.7412 (mpt) REVERT: K 62 PHE cc_start: 0.9163 (m-10) cc_final: 0.8811 (m-10) REVERT: L 4 LEU cc_start: 0.9221 (tp) cc_final: 0.8892 (tp) REVERT: L 49 MET cc_start: 0.9064 (ppp) cc_final: 0.8807 (ppp) REVERT: M 27 ILE cc_start: 0.9598 (mt) cc_final: 0.9295 (tt) REVERT: M 48 TYR cc_start: 0.8887 (m-80) cc_final: 0.8645 (m-80) REVERT: M 70 ILE cc_start: 0.8895 (mm) cc_final: 0.8590 (mm) REVERT: N 1 MET cc_start: 0.8230 (tpp) cc_final: 0.7764 (mmm) REVERT: N 49 MET cc_start: 0.9235 (ppp) cc_final: 0.8946 (ppp) REVERT: P 7 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8844 (p) REVERT: Q 5 ASN cc_start: 0.8685 (p0) cc_final: 0.8457 (p0) REVERT: Z 78 ARG cc_start: 0.5107 (tmt170) cc_final: 0.4775 (tpt90) REVERT: Z 85 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8374 (tt0) REVERT: Z 126 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8887 (mm) REVERT: Z 195 PHE cc_start: 0.8714 (m-80) cc_final: 0.8350 (m-80) REVERT: Z 277 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: Z 280 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9010 (mm-30) REVERT: T 84 MET cc_start: 0.8960 (ttt) cc_final: 0.8552 (tmm) REVERT: T 85 GLU cc_start: 0.9048 (pt0) cc_final: 0.8545 (pt0) REVERT: T 115 LEU cc_start: 0.9210 (mt) cc_final: 0.8848 (pp) outliers start: 71 outliers final: 43 residues processed: 405 average time/residue: 0.2202 time to fit residues: 133.8364 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 : 1.370 ------------------------------------------------------------------------------- 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 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 56 THR 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 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: 0.7980 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 127 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.084186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.065911 restraints weight = 63597.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067574 restraints weight = 36186.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068654 restraints weight = 24797.430| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3163 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= 0.147 Angle : 0.639 11.236 18448 Z= 0.326 Chirality : 0.044 0.276 2239 Planarity : 0.004 0.063 2379 Dihedral : 3.911 19.841 1933 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.74 % Allowed : 32.34 % 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: 1.31 (0.20), residues: 1784 helix: 1.51 (0.13), residues: 1445 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 339 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 0.026 0.001 PHE T 251 TYR 0.027 0.002 TYR Z 92 ARG 0.010 0.000 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1200) hydrogen bonds : angle 3.82183 ( 3588) SS BOND : bond 0.00038 ( 2) SS BOND : angle 0.59838 ( 4) covalent geometry : bond 0.00332 (13606) covalent geometry : angle 0.63867 (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 431 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 358 time to evaluate : 1.506 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 78 LYS cc_start: 0.9157 (pttt) cc_final: 0.8898 (ptpp) REVERT: Y 84 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8583 (tm-30) REVERT: Y 88 LYS cc_start: 0.9096 (pptt) cc_final: 0.8753 (pptt) REVERT: Y 90 GLN cc_start: 0.8364 (tp40) cc_final: 0.8156 (tp40) REVERT: Y 127 GLN cc_start: 0.9106 (tp40) cc_final: 0.8750 (tp-100) REVERT: V 46 GLU cc_start: 0.9493 (OUTLIER) cc_final: 0.9218 (tp30) REVERT: X 91 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9057 (mm-30) REVERT: X 99 ARG cc_start: 0.8640 (mmp-170) cc_final: 0.8281 (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: 0.8208 (pm20) REVERT: X 143 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6547 (pp20) REVERT: U 88 LYS cc_start: 0.9437 (mmtt) cc_final: 0.9093 (mttp) REVERT: U 101 GLU cc_start: 0.9328 (tp30) cc_final: 0.8519 (tp30) REVERT: U 105 LEU cc_start: 0.9348 (mt) cc_final: 0.8551 (mt) REVERT: U 119 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8878 (ttp80) REVERT: U 120 MET cc_start: 0.8995 (mmt) cc_final: 0.8540 (mmt) REVERT: U 123 GLU cc_start: 0.8894 (pp20) cc_final: 0.8528 (pp20) REVERT: H 43 ASN cc_start: 0.9106 (t0) cc_final: 0.8594 (p0) REVERT: H 49 MET cc_start: 0.9306 (ttt) cc_final: 0.8786 (tmm) REVERT: K 62 PHE cc_start: 0.9183 (m-10) cc_final: 0.8799 (m-10) REVERT: L 1 MET cc_start: 0.5964 (mpp) cc_final: 0.5519 (mpp) REVERT: L 4 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8813 (tp) REVERT: L 49 MET cc_start: 0.9144 (ppp) cc_final: 0.8806 (ppp) REVERT: M 1 MET cc_start: 0.6599 (mpp) cc_final: 0.5538 (mmp) REVERT: M 27 ILE cc_start: 0.9630 (mt) cc_final: 0.9298 (tt) REVERT: M 48 TYR cc_start: 0.8889 (m-80) cc_final: 0.8619 (m-80) REVERT: M 70 ILE cc_start: 0.8947 (mm) cc_final: 0.8664 (mm) REVERT: N 32 VAL cc_start: 0.9415 (p) cc_final: 0.9197 (p) REVERT: N 49 MET cc_start: 0.9209 (ppp) cc_final: 0.8901 (ppp) REVERT: P 7 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8869 (p) REVERT: Q 43 ASN cc_start: 0.8269 (p0) cc_final: 0.7862 (m110) REVERT: Z 78 ARG cc_start: 0.5220 (tmt170) cc_final: 0.4903 (tpt90) REVERT: Z 85 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8383 (tt0) REVERT: Z 126 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8931 (mm) REVERT: Z 195 PHE cc_start: 0.8779 (m-80) cc_final: 0.8521 (m-80) REVERT: Z 277 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8759 (m-80) REVERT: T 84 MET cc_start: 0.8962 (ttt) cc_final: 0.8551 (tmm) REVERT: T 85 GLU cc_start: 0.9055 (pt0) cc_final: 0.8625 (pt0) REVERT: T 97 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8371 (t0) REVERT: T 115 LEU cc_start: 0.9267 (mt) cc_final: 0.8958 (pp) REVERT: T 277 TYR cc_start: 0.5279 (m-10) cc_final: 0.4050 (m-80) outliers start: 73 outliers final: 42 residues processed: 398 average time/residue: 0.2187 time to fit residues: 130.6649 Evaluate side-chains 384 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU 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 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 18 ILE 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 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: 7.9990 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.083942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065559 restraints weight = 64055.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.067168 restraints weight = 36266.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068253 restraints weight = 25031.620| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13608 Z= 0.146 Angle : 0.654 14.481 18448 Z= 0.331 Chirality : 0.044 0.388 2239 Planarity : 0.004 0.063 2379 Dihedral : 3.951 19.751 1933 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.51 % Allowed : 34.78 % 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: 1.30 (0.20), residues: 1784 helix: 1.49 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -1.84 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 208 HIS 0.003 0.001 HIS Z 31 PHE 0.032 0.001 PHE P 62 TYR 0.026 0.002 TYR Z 92 ARG 0.006 0.000 ARG X 71 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 1200) hydrogen bonds : angle 3.81135 ( 3588) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.56713 ( 4) covalent geometry : bond 0.00328 (13606) covalent geometry : angle 0.65364 (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 421 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 351 time to evaluate : 1.361 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: Y 84 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8576 (tm-30) REVERT: Y 88 LYS cc_start: 0.9105 (pptt) cc_final: 0.8766 (pptt) REVERT: Y 90 GLN cc_start: 0.8382 (tp40) cc_final: 0.8173 (tp40) REVERT: Y 127 GLN cc_start: 0.9110 (tp40) cc_final: 0.8760 (tp-100) REVERT: V 46 GLU cc_start: 0.9512 (OUTLIER) cc_final: 0.9278 (tp30) REVERT: X 99 ARG cc_start: 0.8661 (mmp-170) cc_final: 0.8299 (mmp80) REVERT: X 106 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8447 (tptm) REVERT: X 107 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: X 120 MET cc_start: 0.9485 (tpt) cc_final: 0.9088 (tmm) REVERT: X 143 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6546 (pp20) REVERT: U 88 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9129 (mttp) REVERT: U 101 GLU cc_start: 0.9291 (tp30) cc_final: 0.8546 (tp30) REVERT: U 105 LEU cc_start: 0.9322 (mt) cc_final: 0.8702 (mt) REVERT: U 120 MET cc_start: 0.9000 (mmt) cc_final: 0.8559 (mmt) REVERT: U 123 GLU cc_start: 0.8904 (pp20) cc_final: 0.8559 (pp20) REVERT: H 38 ASN cc_start: 0.8986 (t0) cc_final: 0.8691 (p0) REVERT: H 43 ASN cc_start: 0.9086 (t0) cc_final: 0.8557 (p0) REVERT: H 49 MET cc_start: 0.9271 (ttt) cc_final: 0.8754 (tmm) REVERT: K 62 PHE cc_start: 0.9209 (m-10) cc_final: 0.8811 (m-10) REVERT: L 1 MET cc_start: 0.6049 (mpp) cc_final: 0.5807 (mpp) REVERT: L 4 LEU cc_start: 0.9194 (tp) cc_final: 0.8820 (tp) REVERT: L 49 MET cc_start: 0.9176 (ppp) cc_final: 0.8951 (ppp) REVERT: M 1 MET cc_start: 0.6657 (mpp) cc_final: 0.6133 (tpp) REVERT: M 27 ILE cc_start: 0.9642 (mt) cc_final: 0.9321 (tt) REVERT: M 49 MET cc_start: 0.9059 (ttp) cc_final: 0.8718 (ppp) REVERT: M 70 ILE cc_start: 0.8975 (mm) cc_final: 0.8696 (mm) REVERT: N 1 MET cc_start: 0.7411 (mmm) cc_final: 0.6590 (mmm) REVERT: N 49 MET cc_start: 0.9235 (ppp) cc_final: 0.8924 (ppp) REVERT: N 57 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8717 (mm-30) REVERT: N 70 ILE cc_start: 0.8026 (tp) cc_final: 0.7705 (tt) REVERT: P 1 MET cc_start: 0.6965 (mpp) cc_final: 0.6684 (pmm) REVERT: Q 43 ASN cc_start: 0.8299 (p0) cc_final: 0.7912 (m110) REVERT: Z 78 ARG cc_start: 0.5455 (tmt170) cc_final: 0.5053 (tpt90) REVERT: Z 85 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8413 (tt0) REVERT: Z 126 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8924 (mm) REVERT: Z 195 PHE cc_start: 0.8799 (m-80) cc_final: 0.8503 (t80) REVERT: Z 277 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8780 (m-80) REVERT: Z 280 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8949 (mm-30) REVERT: T 65 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7833 (mm) REVERT: T 84 MET cc_start: 0.8946 (ttt) cc_final: 0.8533 (tmm) REVERT: T 85 GLU cc_start: 0.9070 (pt0) cc_final: 0.8632 (pt0) REVERT: T 97 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8396 (t0) REVERT: T 115 LEU cc_start: 0.9296 (mt) cc_final: 0.9028 (pp) REVERT: T 277 TYR cc_start: 0.5160 (m-10) cc_final: 0.4864 (m-10) outliers start: 70 outliers final: 43 residues processed: 386 average time/residue: 0.2206 time to fit residues: 127.2339 Evaluate side-chains 380 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 22 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 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 H residue 13 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 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 33 GLN Chi-restraints excluded: chain L residue 44 ARG 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 7 VAL Chi-restraints excluded: chain O residue 72 PHE 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 45 VAL Chi-restraints excluded: chain Q residue 49 MET 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 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 97 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 55 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** K 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.083751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.065300 restraints weight = 65194.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066953 restraints weight = 36957.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068004 restraints weight = 25407.056| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13608 Z= 0.151 Angle : 0.669 13.594 18448 Z= 0.338 Chirality : 0.045 0.361 2239 Planarity : 0.004 0.063 2379 Dihedral : 3.934 19.768 1933 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.59 % Allowed : 36.19 % Favored : 58.22 % 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: 1453 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 208 HIS 0.003 0.001 HIS Z 31 PHE 0.033 0.001 PHE P 62 TYR 0.028 0.002 TYR Z 92 ARG 0.006 0.000 ARG U 119 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1200) hydrogen bonds : angle 3.81917 ( 3588) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.59206 ( 4) covalent geometry : bond 0.00343 (13606) covalent geometry : angle 0.66905 (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 414 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 343 time to evaluate : 1.351 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: 0.8902 (tm-30) cc_final: 0.8378 (tm-30) REVERT: Y 88 LYS cc_start: 0.9113 (pptt) cc_final: 0.8731 (pptt) REVERT: Y 90 GLN cc_start: 0.8401 (tp40) cc_final: 0.8193 (tp40) REVERT: Y 127 GLN cc_start: 0.9120 (tp40) cc_final: 0.8775 (tp-100) REVERT: V 46 GLU cc_start: 0.9497 (OUTLIER) cc_final: 0.9295 (tp30) REVERT: X 106 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8447 (tptm) REVERT: X 107 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: X 120 MET cc_start: 0.9462 (tpt) cc_final: 0.9069 (tmm) REVERT: X 143 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6656 (pp20) REVERT: U 88 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9124 (mttp) REVERT: U 123 GLU cc_start: 0.8833 (pp20) cc_final: 0.8529 (pp20) REVERT: U 130 ASP cc_start: 0.9207 (m-30) cc_final: 0.8950 (m-30) REVERT: H 43 ASN cc_start: 0.9009 (t0) cc_final: 0.8531 (p0) REVERT: H 49 MET cc_start: 0.9271 (ttt) cc_final: 0.8742 (tmm) REVERT: K 1 MET cc_start: 0.7827 (mpt) cc_final: 0.7598 (mpt) REVERT: K 33 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8931 (tp40) REVERT: K 55 PHE cc_start: 0.8609 (m-80) cc_final: 0.8315 (m-80) REVERT: K 62 PHE cc_start: 0.9241 (m-10) cc_final: 0.8891 (m-10) REVERT: L 49 MET cc_start: 0.9223 (ppp) cc_final: 0.8892 (ppp) REVERT: L 57 GLU cc_start: 0.9375 (tp30) cc_final: 0.9073 (tp30) REVERT: M 1 MET cc_start: 0.6703 (mpp) cc_final: 0.6117 (tpp) REVERT: M 27 ILE cc_start: 0.9657 (mt) cc_final: 0.9325 (tt) REVERT: M 62 PHE cc_start: 0.9194 (m-10) cc_final: 0.8991 (m-80) REVERT: M 70 ILE cc_start: 0.9032 (mm) cc_final: 0.8763 (mm) REVERT: N 1 MET cc_start: 0.7542 (mmm) cc_final: 0.6726 (mmm) REVERT: N 49 MET cc_start: 0.9278 (ppp) cc_final: 0.8945 (ppp) REVERT: N 57 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8780 (mm-30) REVERT: N 70 ILE cc_start: 0.8055 (tp) cc_final: 0.7767 (tt) REVERT: Q 1 MET cc_start: 0.6882 (ptm) cc_final: 0.6501 (ppp) REVERT: Q 43 ASN cc_start: 0.8319 (p0) cc_final: 0.7886 (m110) REVERT: Z 78 ARG cc_start: 0.5484 (tmt170) cc_final: 0.5071 (tpt90) REVERT: Z 126 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8936 (mm) REVERT: Z 194 THR cc_start: 0.8653 (p) cc_final: 0.8146 (t) REVERT: Z 195 PHE cc_start: 0.8870 (m-80) cc_final: 0.8538 (t80) REVERT: Z 264 MET cc_start: 0.9364 (mmm) cc_final: 0.9116 (tpp) REVERT: Z 277 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8712 (m-80) REVERT: Z 280 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8921 (mm-30) REVERT: T 65 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7869 (mm) REVERT: T 84 MET cc_start: 0.8894 (ttt) cc_final: 0.8509 (tmm) REVERT: T 85 GLU cc_start: 0.9046 (pt0) cc_final: 0.8554 (pt0) REVERT: T 97 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8423 (t0) REVERT: T 115 LEU cc_start: 0.9308 (mt) cc_final: 0.9048 (pp) REVERT: T 277 TYR cc_start: 0.5206 (m-10) cc_final: 0.3944 (m-80) outliers start: 71 outliers final: 49 residues processed: 378 average time/residue: 0.2151 time to fit residues: 123.5167 Evaluate side-chains 385 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 328 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU 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 22 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 143 GLU 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 57 GLU 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 33 GLN 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 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 7 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 61 ILE 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 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 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 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.0470 chunk 114 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3765 r_free = 0.3765 target = 0.084219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.066291 restraints weight = 64623.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067852 restraints weight = 37456.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.068865 restraints weight = 26123.930| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13608 Z= 0.146 Angle : 0.672 12.688 18448 Z= 0.340 Chirality : 0.045 0.381 2239 Planarity : 0.005 0.063 2379 Dihedral : 3.961 19.359 1933 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.43 % Allowed : 36.43 % Favored : 58.14 % 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: 1.53 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 208 HIS 0.003 0.001 HIS Z 31 PHE 0.034 0.001 PHE P 62 TYR 0.028 0.002 TYR Z 92 ARG 0.008 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 1200) hydrogen bonds : angle 3.84562 ( 3588) SS BOND : bond 0.00103 ( 2) SS BOND : angle 1.39516 ( 4) covalent geometry : bond 0.00327 (13606) covalent geometry : angle 0.67129 (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 419 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 350 time to evaluate : 1.389 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: 0.8884 (tm-30) cc_final: 0.8570 (tm-30) REVERT: Y 88 LYS cc_start: 0.9119 (pptt) cc_final: 0.8793 (pptt) REVERT: Y 90 GLN cc_start: 0.8387 (tp40) cc_final: 0.8156 (tp40) REVERT: Y 127 GLN cc_start: 0.9090 (tp40) cc_final: 0.8746 (tp-100) REVERT: X 89 GLN cc_start: 0.9334 (mm-40) cc_final: 0.9044 (tp-100) REVERT: X 99 ARG cc_start: 0.8487 (mmp-170) cc_final: 0.8106 (mmp80) REVERT: X 103 GLU cc_start: 0.7972 (pp20) cc_final: 0.7619 (pp20) REVERT: X 106 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8449 (tptm) REVERT: X 107 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: X 120 MET cc_start: 0.9396 (tpt) cc_final: 0.9025 (tmm) REVERT: X 143 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6689 (pp20) REVERT: U 88 LYS cc_start: 0.9441 (mmtt) cc_final: 0.9140 (mttp) REVERT: U 119 ARG cc_start: 0.9356 (tpt90) cc_final: 0.9152 (tpt90) REVERT: U 130 ASP cc_start: 0.9198 (m-30) cc_final: 0.8937 (m-30) REVERT: H 43 ASN cc_start: 0.8920 (t0) cc_final: 0.8506 (p0) REVERT: H 46 VAL cc_start: 0.8757 (p) cc_final: 0.8518 (t) REVERT: H 49 MET cc_start: 0.9238 (ttt) cc_final: 0.8797 (tmm) REVERT: K 1 MET cc_start: 0.7852 (mpt) cc_final: 0.7510 (mpt) REVERT: K 55 PHE cc_start: 0.8565 (m-80) cc_final: 0.8315 (m-80) REVERT: K 62 PHE cc_start: 0.9194 (m-10) cc_final: 0.8853 (m-10) REVERT: L 44 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7797 (tpt170) REVERT: L 49 MET cc_start: 0.9217 (ppp) cc_final: 0.9002 (ppp) REVERT: L 57 GLU cc_start: 0.9372 (tp30) cc_final: 0.9076 (tp30) REVERT: M 1 MET cc_start: 0.6685 (mpp) cc_final: 0.5721 (mmp) REVERT: M 27 ILE cc_start: 0.9662 (mt) cc_final: 0.9324 (tt) REVERT: M 62 PHE cc_start: 0.9158 (m-10) cc_final: 0.8854 (m-80) REVERT: M 70 ILE cc_start: 0.9024 (mm) cc_final: 0.8767 (mm) REVERT: N 49 MET cc_start: 0.9276 (ppp) cc_final: 0.8933 (ppp) REVERT: N 57 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8721 (mm-30) REVERT: N 70 ILE cc_start: 0.8046 (tp) cc_final: 0.7730 (tt) REVERT: Q 1 MET cc_start: 0.7265 (ptm) cc_final: 0.6633 (ppp) REVERT: Q 43 ASN cc_start: 0.8254 (p0) cc_final: 0.7895 (m-40) REVERT: Z 78 ARG cc_start: 0.5441 (tmt170) cc_final: 0.5029 (tpt90) REVERT: Z 89 GLU cc_start: 0.9163 (pt0) cc_final: 0.8858 (pt0) REVERT: Z 126 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8951 (mm) REVERT: Z 194 THR cc_start: 0.8660 (p) cc_final: 0.8205 (t) REVERT: Z 195 PHE cc_start: 0.8861 (m-80) cc_final: 0.8512 (t80) REVERT: Z 264 MET cc_start: 0.9311 (mmm) cc_final: 0.9076 (tpp) REVERT: Z 277 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: T 65 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7857 (mm) REVERT: T 84 MET cc_start: 0.8841 (ttt) cc_final: 0.8469 (tmm) REVERT: T 85 GLU cc_start: 0.8960 (pt0) cc_final: 0.8503 (pt0) REVERT: T 97 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8434 (t0) REVERT: T 115 LEU cc_start: 0.9316 (mt) cc_final: 0.9032 (pp) REVERT: T 277 TYR cc_start: 0.5041 (m-10) cc_final: 0.4714 (m-80) outliers start: 69 outliers final: 46 residues processed: 386 average time/residue: 0.2169 time to fit residues: 126.0924 Evaluate side-chains 382 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 329 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain V residue 22 ILE 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 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 45 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 57 GLU 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 O residue 1 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 PHE 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 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 T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 208 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 173 optimal weight: 1.9990 chunk 170 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 127 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 = 0.3743 r_free = 0.3743 target = 0.083065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.064950 restraints weight = 64902.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066560 restraints weight = 36506.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067576 restraints weight = 25039.727| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13608 Z= 0.165 Angle : 0.714 12.000 18448 Z= 0.363 Chirality : 0.046 0.385 2239 Planarity : 0.005 0.065 2379 Dihedral : 3.973 19.897 1933 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.27 % Allowed : 37.92 % Favored : 56.81 % 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: 1.11 (0.20), residues: 1784 helix: 1.35 (0.13), residues: 1455 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 208 HIS 0.002 0.001 HIS V 149 PHE 0.033 0.001 PHE P 62 TYR 0.028 0.002 TYR Z 92 ARG 0.009 0.000 ARG X 71 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 1200) hydrogen bonds : angle 3.91621 ( 3588) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.98913 ( 4) covalent geometry : bond 0.00377 (13606) covalent geometry : angle 0.71378 (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: 67 poor density : 330 time to evaluate : 1.381 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: 0.8857 (tm-30) cc_final: 0.8392 (tm-30) REVERT: Y 90 GLN cc_start: 0.8402 (tp40) cc_final: 0.8191 (tp40) REVERT: Y 127 GLN cc_start: 0.9135 (tp40) cc_final: 0.8797 (tp-100) REVERT: X 99 ARG cc_start: 0.8523 (mmp-170) cc_final: 0.8133 (mmp80) REVERT: X 103 GLU cc_start: 0.8023 (pp20) cc_final: 0.7647 (pp20) REVERT: X 106 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8385 (tptm) REVERT: X 107 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: X 120 MET cc_start: 0.9373 (tpt) cc_final: 0.8997 (tmm) REVERT: X 143 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6735 (pp20) REVERT: U 88 LYS cc_start: 0.9463 (mmtt) cc_final: 0.9156 (mttp) REVERT: U 130 ASP cc_start: 0.9241 (m-30) cc_final: 0.8986 (m-30) REVERT: H 46 VAL cc_start: 0.8685 (p) cc_final: 0.8442 (t) REVERT: H 49 MET cc_start: 0.9301 (ttt) cc_final: 0.8794 (tmm) REVERT: K 1 MET cc_start: 0.7905 (mpt) cc_final: 0.7510 (mpt) REVERT: K 55 PHE cc_start: 0.8675 (m-80) cc_final: 0.8339 (m-80) REVERT: K 62 PHE cc_start: 0.9270 (m-10) cc_final: 0.8924 (m-10) REVERT: L 44 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7871 (tpt170) REVERT: L 49 MET cc_start: 0.9233 (ppp) cc_final: 0.8987 (ppp) REVERT: L 57 GLU cc_start: 0.9403 (tp30) cc_final: 0.9116 (tp30) REVERT: M 1 MET cc_start: 0.6701 (mpp) cc_final: 0.5587 (mmp) REVERT: M 27 ILE cc_start: 0.9682 (mt) cc_final: 0.9360 (tt) REVERT: M 62 PHE cc_start: 0.9198 (m-10) cc_final: 0.8966 (m-80) REVERT: N 1 MET cc_start: 0.7591 (mmm) cc_final: 0.6860 (mmm) REVERT: N 49 MET cc_start: 0.9303 (ppp) cc_final: 0.8926 (ppp) REVERT: N 70 ILE cc_start: 0.7993 (tp) cc_final: 0.7653 (tt) REVERT: Q 1 MET cc_start: 0.7484 (ptm) cc_final: 0.6536 (ppp) REVERT: Q 43 ASN cc_start: 0.8400 (p0) cc_final: 0.8058 (m-40) REVERT: Z 78 ARG cc_start: 0.5540 (tmt170) cc_final: 0.5099 (tpt90) REVERT: Z 194 THR cc_start: 0.8718 (p) cc_final: 0.8285 (t) REVERT: Z 195 PHE cc_start: 0.8968 (m-80) cc_final: 0.8699 (t80) REVERT: Z 264 MET cc_start: 0.9328 (mmm) cc_final: 0.9080 (tpp) REVERT: Z 277 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.8897 (m-80) REVERT: T 65 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7815 (mm) REVERT: T 84 MET cc_start: 0.8858 (ttt) cc_final: 0.8526 (tmm) REVERT: T 85 GLU cc_start: 0.8956 (pt0) cc_final: 0.8501 (pt0) REVERT: T 115 LEU cc_start: 0.9311 (mt) cc_final: 0.9082 (pp) REVERT: T 277 TYR cc_start: 0.5018 (m-10) cc_final: 0.4702 (m-80) outliers start: 67 outliers final: 43 residues processed: 363 average time/residue: 0.2167 time to fit residues: 118.8362 Evaluate side-chains 364 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 316 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 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 78 LYS Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 45 GLU 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 H residue 27 ILE Chi-restraints excluded: chain H residue 45 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 26 ILE Chi-restraints excluded: chain J residue 49 MET 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 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 O residue 1 MET Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 72 PHE 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 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 271 LEU Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain T residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 51 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 117 optimal weight: 0.4980 chunk 145 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** 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 = 0.3748 r_free = 0.3748 target = 0.083200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064972 restraints weight = 64941.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.066532 restraints weight = 37184.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.067545 restraints weight = 25824.557| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4203 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= 0.155 Angle : 0.726 13.701 18448 Z= 0.369 Chirality : 0.046 0.405 2239 Planarity : 0.005 0.064 2379 Dihedral : 3.998 20.532 1933 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.48 % Allowed : 39.02 % Favored : 56.49 % 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: 1.11 (0.20), residues: 1784 helix: 1.36 (0.13), residues: 1450 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 208 HIS 0.001 0.000 HIS V 149 PHE 0.035 0.001 PHE P 62 TYR 0.029 0.002 TYR Z 92 ARG 0.009 0.000 ARG U 119 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 1200) hydrogen bonds : angle 3.92537 ( 3588) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.80274 ( 4) covalent geometry : bond 0.00350 (13606) covalent geometry : angle 0.72624 (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 389 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 332 time to evaluate : 2.265 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: Y 84 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8359 (tm-30) REVERT: Y 88 LYS cc_start: 0.9121 (pptt) cc_final: 0.8714 (pptt) REVERT: Y 90 GLN cc_start: 0.8386 (tp40) cc_final: 0.8182 (tp40) REVERT: Y 127 GLN cc_start: 0.9157 (tp40) cc_final: 0.8814 (tm-30) REVERT: X 89 GLN cc_start: 0.9352 (mm-40) cc_final: 0.9067 (tp40) REVERT: X 99 ARG cc_start: 0.8507 (mmp-170) cc_final: 0.8121 (mmp80) REVERT: X 103 GLU cc_start: 0.8028 (pp20) cc_final: 0.7663 (pp20) REVERT: X 106 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8363 (tptm) REVERT: X 107 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: X 120 MET cc_start: 0.9401 (tpt) cc_final: 0.9035 (tmm) REVERT: U 88 LYS cc_start: 0.9488 (mmtt) cc_final: 0.9184 (mttp) REVERT: U 123 GLU cc_start: 0.8796 (pp20) cc_final: 0.8467 (pp20) REVERT: U 130 ASP cc_start: 0.9247 (m-30) cc_final: 0.8989 (m-30) REVERT: H 43 ASN cc_start: 0.8956 (t0) cc_final: 0.8576 (p0) REVERT: J 15 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8834 (mp) REVERT: K 1 MET cc_start: 0.7870 (mpt) cc_final: 0.7543 (mpt) REVERT: K 55 PHE cc_start: 0.8687 (m-80) cc_final: 0.8355 (m-80) REVERT: K 62 PHE cc_start: 0.9284 (m-10) cc_final: 0.8961 (m-10) REVERT: L 44 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7985 (tpt170) REVERT: L 49 MET cc_start: 0.9245 (ppp) cc_final: 0.9002 (ppp) REVERT: L 57 GLU cc_start: 0.9413 (tp30) cc_final: 0.9105 (tp30) REVERT: M 1 MET cc_start: 0.6578 (mpp) cc_final: 0.5455 (mmp) REVERT: M 27 ILE cc_start: 0.9690 (mt) cc_final: 0.9359 (tt) REVERT: M 62 PHE cc_start: 0.9252 (m-10) cc_final: 0.8981 (m-80) REVERT: M 70 ILE cc_start: 0.8937 (mm) cc_final: 0.8624 (mm) REVERT: N 1 MET cc_start: 0.7690 (mmm) cc_final: 0.6946 (mmm) REVERT: N 49 MET cc_start: 0.9267 (ppp) cc_final: 0.8879 (ppp) REVERT: N 57 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8519 (mm-30) REVERT: N 70 ILE cc_start: 0.7998 (tp) cc_final: 0.7651 (tt) REVERT: Q 1 MET cc_start: 0.7572 (ptm) cc_final: 0.6245 (ppp) REVERT: Q 43 ASN cc_start: 0.8441 (p0) cc_final: 0.8080 (m-40) REVERT: Z 78 ARG cc_start: 0.5640 (tmt170) cc_final: 0.5121 (tpt90) REVERT: Z 89 GLU cc_start: 0.9211 (pt0) cc_final: 0.8846 (pt0) REVERT: Z 194 THR cc_start: 0.8682 (p) cc_final: 0.8268 (t) REVERT: Z 195 PHE cc_start: 0.8980 (m-80) cc_final: 0.8660 (t80) REVERT: Z 264 MET cc_start: 0.9358 (mmm) cc_final: 0.8987 (tpp) REVERT: Z 277 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.9040 (m-80) REVERT: T 65 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7845 (mm) REVERT: T 84 MET cc_start: 0.8858 (ttt) cc_final: 0.8540 (tmm) REVERT: T 85 GLU cc_start: 0.8917 (pt0) cc_final: 0.8493 (pt0) REVERT: T 97 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8412 (t0) REVERT: T 115 LEU cc_start: 0.9333 (mt) cc_final: 0.9101 (pp) REVERT: T 277 TYR cc_start: 0.4709 (m-10) cc_final: 0.4408 (m-80) outliers start: 57 outliers final: 45 residues processed: 358 average time/residue: 0.2375 time to fit residues: 127.9905 Evaluate side-chains 373 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 322 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 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 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 H residue 27 ILE Chi-restraints excluded: chain H residue 45 VAL 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 32 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 15 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 N residue 32 VAL Chi-restraints excluded: chain O residue 1 MET 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 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 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 271 LEU 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 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 144 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 131 optimal weight: 0.0030 chunk 126 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.083768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065604 restraints weight = 64978.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067157 restraints weight = 36814.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068205 restraints weight = 25444.794| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4315 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= 0.151 Angle : 0.752 14.015 18448 Z= 0.379 Chirality : 0.047 0.407 2239 Planarity : 0.005 0.064 2379 Dihedral : 4.024 20.509 1933 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 1.10 (0.20), residues: 1784 helix: 1.36 (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 0.022 0.002 TRP T 208 HIS 0.001 0.000 HIS U 149 PHE 0.033 0.001 PHE P 62 TYR 0.040 0.002 TYR Z 92 ARG 0.013 0.000 ARG U 119 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1200) hydrogen bonds : angle 3.93187 ( 3588) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.71117 ( 4) covalent geometry : bond 0.00337 (13606) covalent geometry : angle 0.75237 (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: 54 poor density : 331 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: Y 84 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8448 (tm-30) REVERT: Y 88 LYS cc_start: 0.9119 (pptt) cc_final: 0.8719 (pptt) REVERT: Y 90 GLN cc_start: 0.8370 (tp40) cc_final: 0.8162 (tp40) REVERT: Y 127 GLN cc_start: 0.9141 (tp40) cc_final: 0.8802 (tm-30) REVERT: X 71 ARG cc_start: 0.8367 (ptp-170) cc_final: 0.8137 (ptp-170) REVERT: X 89 GLN cc_start: 0.9340 (mm-40) cc_final: 0.9052 (tp40) REVERT: X 99 ARG cc_start: 0.8465 (mmp-170) cc_final: 0.8093 (mmp80) REVERT: X 103 GLU cc_start: 0.8001 (pp20) cc_final: 0.7639 (pp20) REVERT: X 106 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8362 (tptm) REVERT: X 107 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: X 120 MET cc_start: 0.9406 (tpt) cc_final: 0.9073 (tmm) REVERT: U 123 GLU cc_start: 0.8770 (pp20) cc_final: 0.8568 (pp20) REVERT: U 130 ASP cc_start: 0.9255 (m-30) cc_final: 0.8998 (m-30) REVERT: H 43 ASN cc_start: 0.8975 (t0) cc_final: 0.8572 (p0) REVERT: H 57 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8922 (mm-30) REVERT: J 26 ILE cc_start: 0.9645 (mm) cc_final: 0.9370 (tt) REVERT: K 1 MET cc_start: 0.7893 (mpt) cc_final: 0.7526 (mpt) REVERT: K 55 PHE cc_start: 0.8664 (m-80) cc_final: 0.8351 (m-80) REVERT: K 62 PHE cc_start: 0.9292 (m-10) cc_final: 0.8955 (m-10) REVERT: L 44 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8021 (tpt170) REVERT: L 49 MET cc_start: 0.9229 (ppp) cc_final: 0.8981 (ppp) REVERT: L 57 GLU cc_start: 0.9398 (tp30) cc_final: 0.9103 (tp30) REVERT: M 1 MET cc_start: 0.6576 (mpp) cc_final: 0.5464 (mmp) REVERT: M 27 ILE cc_start: 0.9690 (mt) cc_final: 0.9362 (tt) REVERT: M 62 PHE cc_start: 0.9245 (m-10) cc_final: 0.8999 (m-80) REVERT: M 70 ILE cc_start: 0.8967 (mm) cc_final: 0.8679 (mm) REVERT: N 1 MET cc_start: 0.7647 (mmm) cc_final: 0.7016 (mmm) REVERT: N 49 MET cc_start: 0.9280 (ppp) cc_final: 0.8891 (ppp) REVERT: N 57 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8481 (mm-30) REVERT: N 70 ILE cc_start: 0.8062 (tp) cc_final: 0.7706 (tt) REVERT: P 7 VAL cc_start: 0.9000 (t) cc_final: 0.8779 (p) REVERT: Q 1 MET cc_start: 0.7208 (ptm) cc_final: 0.6320 (ppp) REVERT: Q 5 ASN cc_start: 0.8582 (p0) cc_final: 0.8260 (p0) REVERT: Q 43 ASN cc_start: 0.8453 (p0) cc_final: 0.8126 (m-40) REVERT: Z 78 ARG cc_start: 0.5619 (tmt170) cc_final: 0.5109 (tpt90) REVERT: Z 89 GLU cc_start: 0.9199 (pt0) cc_final: 0.8679 (pt0) REVERT: Z 194 THR cc_start: 0.8668 (p) cc_final: 0.8282 (t) REVERT: Z 195 PHE cc_start: 0.8959 (m-80) cc_final: 0.8659 (t80) REVERT: Z 264 MET cc_start: 0.9339 (mmm) cc_final: 0.8942 (tpp) REVERT: Z 277 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.9027 (m-80) REVERT: T 65 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7850 (mm) REVERT: T 84 MET cc_start: 0.8836 (ttt) cc_final: 0.8469 (tmm) REVERT: T 85 GLU cc_start: 0.8907 (pt0) cc_final: 0.8564 (pt0) REVERT: T 97 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8342 (t0) REVERT: T 115 LEU cc_start: 0.9328 (mt) cc_final: 0.9116 (pp) REVERT: T 277 TYR cc_start: 0.4743 (m-10) cc_final: 0.4426 (m-80) outliers start: 54 outliers final: 43 residues processed: 355 average time/residue: 0.2160 time to fit residues: 115.4246 Evaluate side-chains 370 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 322 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 LEU 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 94 ILE Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain U residue 120 MET Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 65 VAL 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 49 MET 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 O residue 1 MET 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 45 VAL Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain Q residue 11 LEU 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 271 LEU 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 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 94 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 115 GLN ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.083627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.065636 restraints weight = 65245.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.067187 restraints weight = 36881.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068151 restraints weight = 25564.761| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4398 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 : 0.757 14.282 18448 Z= 0.381 Chirality : 0.046 0.396 2239 Planarity : 0.005 0.064 2379 Dihedral : 4.017 20.037 1933 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.01 % Allowed : 40.44 % Favored : 55.55 % 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: 1.13 (0.20), residues: 1784 helix: 1.36 (0.13), residues: 1454 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 208 HIS 0.001 0.000 HIS U 149 PHE 0.033 0.001 PHE H 62 TYR 0.033 0.002 TYR Z 92 ARG 0.015 0.000 ARG U 119 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 1200) hydrogen bonds : angle 3.94149 ( 3588) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.69220 ( 4) covalent geometry : bond 0.00357 (13606) covalent geometry : angle 0.75746 (18444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6756.04 seconds wall clock time: 120 minutes 2.68 seconds (7202.68 seconds total)