Starting phenix.real_space_refine on Thu Sep 18 02:17:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itp_60874/09_2025/9itp_60874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itp_60874/09_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_60874/09_2025/9itp_60874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itp_60874/09_2025/9itp_60874.map" model { file = "/net/cci-nas-00/data/ceres_data/9itp_60874/09_2025/9itp_60874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itp_60874/09_2025/9itp_60874.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'GLN:plan1': 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: {'ASN:plan1': 4, 'PHE:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} 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: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 2} 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: {'ARG:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 74 Time building chain proxies: 3.51, per 1000 atoms: 0.26 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: 1.21 Conformation dependent library (CDL) restraints added in 620.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.34 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: 2.24 Time building geometry restraints manager: 1.56 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: 4.560 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- 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 : 12.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (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 ARG 0.003 0.000 ARG V 40 TYR 0.012 0.001 TYR Z 296 PHE 0.026 0.001 PHE Z 276 TRP 0.014 0.001 TRP T 208 HIS 0.004 0.001 HIS Y 149 Details of bonding type rmsd covalent geometry : bond 0.00418 (13606) covalent geometry : angle 0.57934 (18444) SS BOND : bond 0.69838 ( 2) SS BOND : angle 26.76995 ( 4) hydrogen bonds : bond 0.12909 ( 1200) hydrogen bonds : angle 5.55392 ( 3588) *********************** 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 : 0.538 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: 0.1058 time to fit residues: 80.5483 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 : 0.561 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0970 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 X 82 GLN X 112 GLN ** X 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN K 5 ASN K 33 GLN Z 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.084925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066444 restraints weight = 63091.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068113 restraints weight = 36013.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.069194 restraints weight = 24939.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.069936 restraints weight = 19485.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070449 restraints weight = 16436.322| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2291 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= 0.147 Angle : 0.612 9.732 18448 Z= 0.319 Chirality : 0.043 0.317 2239 Planarity : 0.005 0.064 2379 Dihedral : 3.929 19.527 1936 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.51 % Allowed : 30.92 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.20), residues: 1784 helix: 1.56 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -2.01 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 71 TYR 0.017 0.002 TYR Z 92 PHE 0.024 0.001 PHE J 62 TRP 0.014 0.001 TRP T 208 HIS 0.003 0.001 HIS Y 149 Details of bonding type rmsd covalent geometry : bond 0.00314 (13606) covalent geometry : angle 0.61224 (18444) SS BOND : bond 0.01603 ( 2) SS BOND : angle 0.94366 ( 4) hydrogen bonds : bond 0.04474 ( 1200) hydrogen bonds : angle 3.96276 ( 3588) *********************** 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 : 0.534 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: 0.8876 (tm-30) cc_final: 0.8574 (tm-30) REVERT: Y 88 LYS cc_start: 0.9104 (pptt) cc_final: 0.8745 (pptt) REVERT: Y 90 GLN cc_start: 0.8391 (tp40) cc_final: 0.8181 (tp40) REVERT: Y 127 GLN cc_start: 0.9080 (tp40) cc_final: 0.8736 (tp-100) REVERT: X 91 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9153 (mm-30) REVERT: X 99 ARG cc_start: 0.8709 (mmp-170) cc_final: 0.8334 (mmp80) REVERT: X 106 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8638 (tptm) REVERT: X 120 MET cc_start: 0.9472 (tpt) cc_final: 0.9038 (tmm) REVERT: U 101 GLU cc_start: 0.9342 (tp30) cc_final: 0.8689 (tp30) REVERT: U 105 LEU cc_start: 0.9350 (mt) cc_final: 0.8840 (mt) REVERT: U 119 ARG cc_start: 0.9105 (mmm-85) cc_final: 0.8894 (ttp80) REVERT: U 120 MET cc_start: 0.8969 (mmt) cc_final: 0.8523 (mmt) REVERT: U 123 GLU cc_start: 0.8851 (pp20) cc_final: 0.8498 (pp20) REVERT: H 49 MET cc_start: 0.9352 (ttt) cc_final: 0.8714 (tmm) REVERT: J 1 MET cc_start: 0.5028 (mmt) cc_final: 0.4717 (mmt) REVERT: J 26 ILE cc_start: 0.9674 (mm) cc_final: 0.9308 (tt) REVERT: K 1 MET cc_start: 0.7781 (mpt) cc_final: 0.7470 (mpt) REVERT: K 33 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8901 (tp40) REVERT: K 62 PHE cc_start: 0.9103 (m-10) cc_final: 0.8742 (m-10) REVERT: L 4 LEU cc_start: 0.9236 (tp) cc_final: 0.9018 (tp) REVERT: L 49 MET cc_start: 0.9017 (ppp) cc_final: 0.8757 (ppp) REVERT: M 1 MET cc_start: 0.6365 (mpp) cc_final: 0.4592 (mmt) REVERT: M 27 ILE cc_start: 0.9567 (mt) cc_final: 0.9279 (tt) REVERT: M 70 ILE cc_start: 0.8795 (mm) cc_final: 0.8448 (mm) REVERT: N 1 MET cc_start: 0.8259 (tpp) cc_final: 0.7667 (mmp) REVERT: N 49 MET cc_start: 0.9242 (ppp) cc_final: 0.8998 (ppp) REVERT: O 48 TYR cc_start: 0.8666 (m-80) cc_final: 0.8173 (m-80) REVERT: Z 78 ARG cc_start: 0.5012 (tmt170) cc_final: 0.4678 (tpt90) REVERT: Z 85 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8372 (tt0) REVERT: Z 113 ILE cc_start: 0.9387 (mt) cc_final: 0.9157 (mt) REVERT: Z 126 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8839 (mm) REVERT: Z 195 PHE cc_start: 0.8581 (m-80) cc_final: 0.8201 (m-80) REVERT: Z 280 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9022 (mm-30) REVERT: T 84 MET cc_start: 0.8922 (ttt) cc_final: 0.8594 (tmm) REVERT: T 85 GLU cc_start: 0.8962 (pt0) cc_final: 0.8640 (pt0) REVERT: T 115 LEU cc_start: 0.9215 (mt) cc_final: 0.8857 (pp) REVERT: T 277 TYR cc_start: 0.6042 (m-10) cc_final: 0.5397 (m-10) outliers start: 70 outliers final: 36 residues processed: 421 average time/residue: 0.1028 time to fit residues: 66.0005 Evaluate side-chains 385 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 347 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 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 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 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 174 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 60 ASN X 97 GLN X 115 GLN ** K 33 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 = 0.3780 r_free = 0.3780 target = 0.084851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.066366 restraints weight = 64149.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068050 restraints weight = 36388.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.069170 restraints weight = 24969.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069934 restraints weight = 19405.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.070386 restraints weight = 16269.111| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13608 Z= 0.143 Angle : 0.617 13.335 18448 Z= 0.318 Chirality : 0.043 0.281 2239 Planarity : 0.005 0.062 2379 Dihedral : 3.907 19.563 1933 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.51 % Allowed : 31.63 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.20), residues: 1784 helix: 1.56 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -1.93 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 37 TYR 0.024 0.002 TYR Z 92 PHE 0.024 0.001 PHE T 251 TRP 0.012 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00314 (13606) covalent geometry : angle 0.61726 (18444) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.72059 ( 4) hydrogen bonds : bond 0.04200 ( 1200) hydrogen bonds : angle 3.84005 ( 3588) *********************** 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 438 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 368 time to evaluate : 0.525 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: 0.8883 (tm-30) cc_final: 0.8575 (tm-30) REVERT: Y 88 LYS cc_start: 0.9088 (pptt) cc_final: 0.8766 (pptt) REVERT: Y 90 GLN cc_start: 0.8368 (tp40) cc_final: 0.8167 (tp40) REVERT: Y 127 GLN cc_start: 0.9106 (tp40) cc_final: 0.8751 (tp-100) REVERT: V 46 GLU cc_start: 0.9492 (OUTLIER) cc_final: 0.9286 (tp30) REVERT: X 99 ARG cc_start: 0.8670 (mmp-170) cc_final: 0.8320 (mmp80) REVERT: X 106 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8386 (tptm) REVERT: X 107 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: X 120 MET cc_start: 0.9435 (tpt) cc_final: 0.9017 (tmm) REVERT: U 88 LYS cc_start: 0.9458 (mmtt) cc_final: 0.9107 (mttp) REVERT: U 101 GLU cc_start: 0.9335 (tp30) cc_final: 0.8666 (tp30) REVERT: U 105 LEU cc_start: 0.9348 (mt) cc_final: 0.8748 (mt) REVERT: U 119 ARG cc_start: 0.9103 (mmm-85) cc_final: 0.8881 (ttp80) REVERT: U 120 MET cc_start: 0.8980 (mmt) cc_final: 0.8535 (mmt) REVERT: U 123 GLU cc_start: 0.8894 (pp20) cc_final: 0.8529 (pp20) REVERT: H 43 ASN cc_start: 0.9096 (t0) cc_final: 0.8612 (p0) REVERT: H 49 MET cc_start: 0.9307 (ttt) cc_final: 0.8728 (tmm) REVERT: K 1 MET cc_start: 0.7751 (mpt) cc_final: 0.7392 (mpt) REVERT: K 62 PHE cc_start: 0.9141 (m-10) cc_final: 0.8742 (m-10) REVERT: L 4 LEU cc_start: 0.9166 (tp) cc_final: 0.8834 (tp) REVERT: L 49 MET cc_start: 0.9079 (ppp) cc_final: 0.8829 (ppp) REVERT: M 27 ILE cc_start: 0.9589 (mt) cc_final: 0.9283 (tt) REVERT: M 70 ILE cc_start: 0.8895 (mm) cc_final: 0.8592 (mm) REVERT: N 1 MET cc_start: 0.8155 (tpp) cc_final: 0.7747 (mmm) REVERT: N 32 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9087 (p) REVERT: N 49 MET cc_start: 0.9250 (ppp) cc_final: 0.8970 (ppp) REVERT: P 7 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8789 (p) REVERT: Z 78 ARG cc_start: 0.5061 (tmt170) cc_final: 0.4720 (tpt90) REVERT: Z 85 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8373 (tt0) REVERT: Z 113 ILE cc_start: 0.9372 (mt) cc_final: 0.9163 (mt) REVERT: Z 126 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8881 (mm) REVERT: Z 195 PHE cc_start: 0.8678 (m-80) cc_final: 0.8324 (m-80) REVERT: Z 277 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8665 (m-80) REVERT: Z 280 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8993 (mm-30) REVERT: T 84 MET cc_start: 0.8941 (ttt) cc_final: 0.8532 (tmm) REVERT: T 85 GLU cc_start: 0.9012 (pt0) cc_final: 0.8536 (pt0) REVERT: T 115 LEU cc_start: 0.9217 (mt) cc_final: 0.8865 (pp) REVERT: T 277 TYR cc_start: 0.5632 (m-10) cc_final: 0.5224 (m-10) outliers start: 70 outliers final: 42 residues processed: 402 average time/residue: 0.0994 time to fit residues: 60.7902 Evaluate side-chains 397 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 349 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain 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 41 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 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 23 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN K 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.083679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.065220 restraints weight = 64669.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066875 restraints weight = 36721.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.067943 restraints weight = 25247.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.068655 restraints weight = 19647.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.069108 restraints weight = 16591.673| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3226 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= 0.161 Angle : 0.643 11.210 18448 Z= 0.330 Chirality : 0.043 0.211 2239 Planarity : 0.004 0.063 2379 Dihedral : 3.904 20.354 1933 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.37 % Allowed : 32.02 % Favored : 61.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.20), residues: 1784 helix: 1.51 (0.13), residues: 1449 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 37 TYR 0.026 0.002 TYR Z 92 PHE 0.024 0.001 PHE T 251 TRP 0.014 0.001 TRP T 208 HIS 0.003 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00364 (13606) covalent geometry : angle 0.64273 (18444) SS BOND : bond 0.00013 ( 2) SS BOND : angle 0.68328 ( 4) hydrogen bonds : bond 0.04181 ( 1200) hydrogen bonds : angle 3.85056 ( 3588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 351 time to evaluate : 0.521 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: 0.8898 (tm-30) cc_final: 0.8442 (tm-30) REVERT: Y 127 GLN cc_start: 0.9114 (tp40) cc_final: 0.8762 (tp-100) REVERT: V 46 GLU cc_start: 0.9485 (OUTLIER) cc_final: 0.9210 (tp30) REVERT: X 99 ARG cc_start: 0.8712 (mmp-170) cc_final: 0.8336 (mmp80) REVERT: X 106 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8402 (tptm) REVERT: X 107 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: X 143 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6527 (pp20) REVERT: U 88 LYS cc_start: 0.9453 (mmtt) cc_final: 0.9098 (mttp) REVERT: U 101 GLU cc_start: 0.9350 (tp30) cc_final: 0.8535 (tp30) REVERT: U 105 LEU cc_start: 0.9367 (mt) cc_final: 0.8588 (mt) REVERT: U 119 ARG cc_start: 0.9103 (mmm-85) cc_final: 0.8891 (ttp80) REVERT: U 120 MET cc_start: 0.8994 (mmt) cc_final: 0.8540 (mmt) REVERT: U 123 GLU cc_start: 0.8900 (pp20) cc_final: 0.8539 (pp20) REVERT: H 49 MET cc_start: 0.9311 (ttt) cc_final: 0.8782 (tmm) REVERT: K 62 PHE cc_start: 0.9203 (m-10) cc_final: 0.8802 (m-10) REVERT: L 4 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8769 (tp) REVERT: L 49 MET cc_start: 0.9174 (ppp) cc_final: 0.8834 (ppp) REVERT: M 1 MET cc_start: 0.6625 (mpp) cc_final: 0.5835 (tpp) REVERT: M 27 ILE cc_start: 0.9639 (mt) cc_final: 0.9339 (tt) REVERT: M 49 MET cc_start: 0.9105 (ttp) cc_final: 0.8621 (ppp) REVERT: M 70 ILE cc_start: 0.8974 (mm) cc_final: 0.8687 (mm) REVERT: N 49 MET cc_start: 0.9249 (ppp) cc_final: 0.8953 (ppp) REVERT: Q 43 ASN cc_start: 0.8199 (p0) cc_final: 0.7845 (m110) REVERT: Z 78 ARG cc_start: 0.5266 (tmt170) cc_final: 0.4950 (tpt90) REVERT: Z 85 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8416 (tt0) REVERT: Z 195 PHE cc_start: 0.8774 (m-80) cc_final: 0.8519 (t80) REVERT: Z 277 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: T 84 MET cc_start: 0.8945 (ttt) cc_final: 0.8536 (tmm) REVERT: T 85 GLU cc_start: 0.9039 (pt0) cc_final: 0.8626 (pt0) REVERT: T 97 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8401 (t0) REVERT: T 115 LEU cc_start: 0.9270 (mt) cc_final: 0.8968 (pp) REVERT: T 277 TYR cc_start: 0.5545 (m-10) cc_final: 0.5218 (m-10) outliers start: 81 outliers final: 49 residues processed: 399 average time/residue: 0.1031 time to fit residues: 62.4435 Evaluate side-chains 378 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 35 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 44 ARG Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 41 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 7 VAL Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 13 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 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 82 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 156 optimal weight: 0.0970 chunk 147 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** I 38 ASN K 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.083511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065379 restraints weight = 64079.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.066933 restraints weight = 37337.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.067968 restraints weight = 26112.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.068629 restraints weight = 20502.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.069114 restraints weight = 17450.264| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3466 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= 0.151 Angle : 0.661 15.093 18448 Z= 0.335 Chirality : 0.044 0.364 2239 Planarity : 0.004 0.064 2379 Dihedral : 3.964 19.999 1933 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.90 % Allowed : 34.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.20), residues: 1784 helix: 1.52 (0.13), residues: 1455 sheet: None (None), residues: 0 loop : -1.82 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 37 TYR 0.028 0.002 TYR Z 92 PHE 0.031 0.001 PHE P 62 TRP 0.021 0.002 TRP T 208 HIS 0.003 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00340 (13606) covalent geometry : angle 0.66146 (18444) SS BOND : bond 0.00025 ( 2) SS BOND : angle 0.61678 ( 4) hydrogen bonds : bond 0.04119 ( 1200) hydrogen bonds : angle 3.84642 ( 3588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 344 time to evaluate : 0.521 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: 0.8864 (tm-30) cc_final: 0.8359 (tm-30) REVERT: Y 88 LYS cc_start: 0.9132 (pptt) cc_final: 0.8763 (pptt) REVERT: Y 127 GLN cc_start: 0.9085 (tp40) cc_final: 0.8738 (tp-100) REVERT: V 46 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9264 (tp30) REVERT: X 99 ARG cc_start: 0.8696 (mmp-170) cc_final: 0.8302 (mmp80) REVERT: X 106 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8419 (tptm) REVERT: X 107 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: X 120 MET cc_start: 0.9434 (tpt) cc_final: 0.9064 (tmm) REVERT: X 143 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6551 (pp20) REVERT: U 88 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9133 (mttp) REVERT: U 120 MET cc_start: 0.8991 (mmt) cc_final: 0.8558 (mmt) REVERT: U 123 GLU cc_start: 0.8882 (pp20) cc_final: 0.8548 (pp20) REVERT: U 130 ASP cc_start: 0.9207 (m-30) cc_final: 0.8953 (m-30) REVERT: H 38 ASN cc_start: 0.8884 (t0) cc_final: 0.8610 (p0) REVERT: H 43 ASN cc_start: 0.9032 (t0) cc_final: 0.8566 (p0) REVERT: H 49 MET cc_start: 0.9310 (ttt) cc_final: 0.8779 (tmm) REVERT: K 55 PHE cc_start: 0.8615 (m-80) cc_final: 0.8293 (m-80) REVERT: K 62 PHE cc_start: 0.9202 (m-10) cc_final: 0.8846 (m-10) REVERT: L 4 LEU cc_start: 0.9156 (tp) cc_final: 0.8800 (tp) REVERT: L 49 MET cc_start: 0.9201 (ppp) cc_final: 0.8963 (ppp) REVERT: M 1 MET cc_start: 0.6569 (mpp) cc_final: 0.6093 (tpp) REVERT: M 27 ILE cc_start: 0.9655 (mt) cc_final: 0.9337 (tt) REVERT: M 62 PHE cc_start: 0.9101 (m-10) cc_final: 0.8827 (m-80) REVERT: M 70 ILE cc_start: 0.9004 (mm) cc_final: 0.8732 (mm) REVERT: N 49 MET cc_start: 0.9264 (ppp) cc_final: 0.8972 (ppp) REVERT: N 57 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8668 (mm-30) REVERT: N 70 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7756 (tt) REVERT: P 1 MET cc_start: 0.7072 (mpp) cc_final: 0.6616 (mtm) REVERT: Q 43 ASN cc_start: 0.8158 (p0) cc_final: 0.7851 (m110) REVERT: Z 78 ARG cc_start: 0.5329 (tmt170) cc_final: 0.5033 (tpt90) REVERT: Z 85 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8421 (tt0) REVERT: Z 195 PHE cc_start: 0.8767 (m-80) cc_final: 0.8485 (t80) REVERT: Z 277 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8754 (m-80) REVERT: Z 280 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8926 (mm-30) REVERT: T 65 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7797 (mm) REVERT: T 84 MET cc_start: 0.8915 (ttt) cc_final: 0.8512 (tmm) REVERT: T 85 GLU cc_start: 0.8993 (pt0) cc_final: 0.8591 (pt0) REVERT: T 97 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8379 (t0) REVERT: T 115 LEU cc_start: 0.9268 (mt) cc_final: 0.8979 (pp) REVERT: T 277 TYR cc_start: 0.5206 (m-80) cc_final: 0.4929 (m-10) outliers start: 75 outliers final: 43 residues processed: 384 average time/residue: 0.1039 time to fit residues: 60.4846 Evaluate side-chains 378 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 328 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 147 ARG 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 46 GLU Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain U residue 134 LEU Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain I residue 9 THR 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 13 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 41 ILE 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 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 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 85 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.083642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065571 restraints weight = 63937.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067125 restraints weight = 37020.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068139 restraints weight = 25868.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.068829 restraints weight = 20316.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069285 restraints weight = 17236.869| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13608 Z= 0.150 Angle : 0.668 13.675 18448 Z= 0.338 Chirality : 0.045 0.363 2239 Planarity : 0.005 0.064 2379 Dihedral : 3.958 19.848 1933 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.06 % Allowed : 35.25 % Favored : 58.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.20), residues: 1784 helix: 1.52 (0.13), residues: 1451 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 119 TYR 0.027 0.002 TYR Z 92 PHE 0.033 0.001 PHE P 62 TRP 0.022 0.002 TRP T 208 HIS 0.003 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00338 (13606) covalent geometry : angle 0.66836 (18444) SS BOND : bond 0.00033 ( 2) SS BOND : angle 0.60709 ( 4) hydrogen bonds : bond 0.04115 ( 1200) hydrogen bonds : angle 3.84578 ( 3588) *********************** 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 416 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 339 time to evaluate : 0.517 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: 0.8858 (tm-30) cc_final: 0.8417 (tm-30) REVERT: Y 127 GLN cc_start: 0.9086 (tp40) cc_final: 0.8741 (tp-100) REVERT: X 99 ARG cc_start: 0.8575 (mmp-170) cc_final: 0.8242 (mmp80) REVERT: X 106 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8422 (tptm) REVERT: X 107 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: X 120 MET cc_start: 0.9391 (tpt) cc_final: 0.9036 (tmm) REVERT: X 143 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6697 (pp20) REVERT: U 88 LYS cc_start: 0.9442 (mmtt) cc_final: 0.9133 (mttp) REVERT: U 123 GLU cc_start: 0.8822 (pp20) cc_final: 0.8522 (pp20) REVERT: U 130 ASP cc_start: 0.9215 (m-30) cc_final: 0.8957 (m-30) REVERT: H 43 ASN cc_start: 0.8957 (t0) cc_final: 0.8511 (p0) REVERT: H 49 MET cc_start: 0.9295 (ttt) cc_final: 0.8771 (tmm) REVERT: I 1 MET cc_start: 0.6636 (pmm) cc_final: 0.6414 (pmm) REVERT: K 55 PHE cc_start: 0.8663 (m-80) cc_final: 0.8310 (m-80) REVERT: K 62 PHE cc_start: 0.9195 (m-10) cc_final: 0.8855 (m-10) REVERT: L 49 MET cc_start: 0.9247 (ppp) cc_final: 0.8896 (ppp) REVERT: M 1 MET cc_start: 0.6710 (mpp) cc_final: 0.6305 (tpp) REVERT: M 27 ILE cc_start: 0.9663 (mt) cc_final: 0.9364 (tt) REVERT: M 49 MET cc_start: 0.9103 (ttp) cc_final: 0.8753 (ppp) REVERT: M 70 ILE cc_start: 0.9009 (mm) cc_final: 0.8754 (mm) REVERT: N 1 MET cc_start: 0.7445 (mmm) cc_final: 0.6845 (mmm) REVERT: N 49 MET cc_start: 0.9289 (ppp) cc_final: 0.8964 (ppp) REVERT: N 57 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8770 (mm-30) REVERT: N 70 ILE cc_start: 0.8161 (tp) cc_final: 0.7838 (tt) REVERT: P 1 MET cc_start: 0.7217 (mpp) cc_final: 0.6872 (mtm) REVERT: P 15 LEU cc_start: 0.9178 (mm) cc_final: 0.8961 (mm) REVERT: Q 43 ASN cc_start: 0.8208 (p0) cc_final: 0.7815 (m110) REVERT: Z 78 ARG cc_start: 0.5432 (tmt170) cc_final: 0.5124 (tpt90) REVERT: Z 194 THR cc_start: 0.8658 (p) cc_final: 0.8162 (t) REVERT: Z 195 PHE cc_start: 0.8810 (m-80) cc_final: 0.8492 (t80) REVERT: Z 264 MET cc_start: 0.9313 (mmm) cc_final: 0.9064 (tpp) REVERT: Z 277 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: Z 280 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8887 (mm-30) REVERT: T 65 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7840 (mm) REVERT: T 84 MET cc_start: 0.8838 (ttt) cc_final: 0.8459 (tmm) REVERT: T 85 GLU cc_start: 0.9019 (pt0) cc_final: 0.8547 (pt0) REVERT: T 97 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8393 (t0) REVERT: T 115 LEU cc_start: 0.9324 (mt) cc_final: 0.9036 (pp) REVERT: T 277 TYR cc_start: 0.5119 (m-80) cc_final: 0.4843 (m-80) outliers start: 77 outliers final: 54 residues processed: 379 average time/residue: 0.1052 time to fit residues: 59.9287 Evaluate side-chains 374 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 147 ARG 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 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 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 15 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 L residue 66 ILE 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 41 ILE Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 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 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 Z residue 271 LEU Chi-restraints excluded: chain Z residue 277 TYR Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 208 TRP 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 16 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** 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 = 0.3756 r_free = 0.3756 target = 0.083574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.065275 restraints weight = 64267.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066899 restraints weight = 36202.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067908 restraints weight = 24840.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068703 restraints weight = 19405.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.069217 restraints weight = 16220.642| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13608 Z= 0.149 Angle : 0.675 12.869 18448 Z= 0.343 Chirality : 0.045 0.395 2239 Planarity : 0.005 0.070 2379 Dihedral : 3.978 19.707 1933 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.43 % Allowed : 36.98 % Favored : 57.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.20), residues: 1784 helix: 1.42 (0.13), residues: 1459 sheet: None (None), residues: 0 loop : -1.92 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 37 TYR 0.029 0.002 TYR Z 92 PHE 0.036 0.001 PHE P 62 TRP 0.021 0.002 TRP T 208 HIS 0.003 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00334 (13606) covalent geometry : angle 0.67525 (18444) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.60087 ( 4) hydrogen bonds : bond 0.04114 ( 1200) hydrogen bonds : angle 3.90012 ( 3588) *********************** 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 414 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 345 time to evaluate : 0.511 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: 0.8875 (tm-30) cc_final: 0.8431 (tm-30) REVERT: Y 127 GLN cc_start: 0.9118 (tp40) cc_final: 0.8772 (tp-100) REVERT: X 89 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9046 (tp-100) REVERT: X 99 ARG cc_start: 0.8500 (mmp-170) cc_final: 0.8107 (mmp80) REVERT: X 103 GLU cc_start: 0.7959 (pp20) cc_final: 0.7607 (pp20) REVERT: X 106 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8442 (tptm) REVERT: X 107 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: X 120 MET cc_start: 0.9407 (tpt) cc_final: 0.9048 (tmm) REVERT: X 138 ARG cc_start: -0.0912 (OUTLIER) cc_final: -0.3563 (ttm170) REVERT: X 143 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: U 88 LYS cc_start: 0.9470 (mmtt) cc_final: 0.9179 (mttp) REVERT: U 119 ARG cc_start: 0.9374 (tpt90) cc_final: 0.9173 (tpt90) REVERT: U 130 ASP cc_start: 0.9232 (m-30) cc_final: 0.8972 (m-30) REVERT: H 43 ASN cc_start: 0.8937 (t0) cc_final: 0.8569 (p0) REVERT: H 46 VAL cc_start: 0.8746 (p) cc_final: 0.8475 (t) REVERT: H 49 MET cc_start: 0.9278 (ttt) cc_final: 0.8785 (tmm) REVERT: K 55 PHE cc_start: 0.8683 (m-80) cc_final: 0.8331 (m-80) REVERT: K 62 PHE cc_start: 0.9234 (m-10) cc_final: 0.8885 (m-10) REVERT: L 44 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7919 (tpt170) REVERT: L 49 MET cc_start: 0.9224 (ppp) cc_final: 0.8986 (ppp) REVERT: L 57 GLU cc_start: 0.9358 (tp30) cc_final: 0.9124 (tp30) REVERT: M 1 MET cc_start: 0.6801 (mpp) cc_final: 0.6359 (tpp) REVERT: M 27 ILE cc_start: 0.9674 (mt) cc_final: 0.9362 (tt) REVERT: M 62 PHE cc_start: 0.9124 (m-80) cc_final: 0.8787 (m-80) REVERT: N 49 MET cc_start: 0.9297 (ppp) cc_final: 0.8940 (ppp) REVERT: N 70 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7862 (tt) REVERT: Q 43 ASN cc_start: 0.8268 (p0) cc_final: 0.7944 (m-40) REVERT: Z 78 ARG cc_start: 0.5330 (tmt170) cc_final: 0.5062 (tpt90) REVERT: Z 89 GLU cc_start: 0.9175 (pt0) cc_final: 0.8866 (pt0) REVERT: Z 194 THR cc_start: 0.8664 (p) cc_final: 0.8206 (t) REVERT: Z 195 PHE cc_start: 0.8881 (m-80) cc_final: 0.8550 (t80) REVERT: Z 206 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8858 (mm-30) REVERT: Z 264 MET cc_start: 0.9322 (mmm) cc_final: 0.9063 (tpp) REVERT: Z 277 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8919 (m-80) REVERT: Z 294 LEU cc_start: 0.9680 (mt) cc_final: 0.9471 (mt) REVERT: T 65 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7856 (mm) REVERT: T 84 MET cc_start: 0.8843 (ttt) cc_final: 0.8458 (tmm) REVERT: T 85 GLU cc_start: 0.8952 (pt0) cc_final: 0.8541 (pt0) REVERT: T 97 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8463 (t0) REVERT: T 115 LEU cc_start: 0.9289 (mt) cc_final: 0.9017 (pp) REVERT: T 277 TYR cc_start: 0.5044 (m-80) cc_final: 0.4801 (m-10) outliers start: 69 outliers final: 53 residues processed: 381 average time/residue: 0.1006 time to fit residues: 58.3279 Evaluate side-chains 381 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 147 ARG 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 80 VAL Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain 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 15 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 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 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 41 ILE 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 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 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 208 TRP Chi-restraints excluded: chain T residue 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 287 GLN ** 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 = 0.3754 r_free = 0.3754 target = 0.083481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065411 restraints weight = 64008.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066958 restraints weight = 36136.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068012 restraints weight = 25033.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.068710 restraints weight = 19503.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069091 restraints weight = 16471.165| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13608 Z= 0.156 Angle : 0.716 12.328 18448 Z= 0.362 Chirality : 0.045 0.393 2239 Planarity : 0.005 0.064 2379 Dihedral : 3.992 20.349 1933 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.51 % Allowed : 37.21 % Favored : 57.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.20), residues: 1784 helix: 1.37 (0.13), residues: 1454 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 71 TYR 0.029 0.002 TYR Z 92 PHE 0.023 0.001 PHE H 62 TRP 0.021 0.002 TRP T 208 HIS 0.003 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00355 (13606) covalent geometry : angle 0.71581 (18444) SS BOND : bond 0.00356 ( 2) SS BOND : angle 1.32858 ( 4) hydrogen bonds : bond 0.04130 ( 1200) hydrogen bonds : angle 3.92781 ( 3588) *********************** 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 400 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 330 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 84 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8417 (tm-30) REVERT: Y 127 GLN cc_start: 0.9106 (tp40) cc_final: 0.8767 (tp-100) REVERT: Y 147 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7603 (ttp80) REVERT: X 99 ARG cc_start: 0.8494 (mmp-170) cc_final: 0.8108 (mmp80) REVERT: X 103 GLU cc_start: 0.7979 (pp20) cc_final: 0.7618 (pp20) REVERT: X 106 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8386 (tptm) REVERT: X 107 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: X 120 MET cc_start: 0.9370 (tpt) cc_final: 0.9025 (tmm) REVERT: X 138 ARG cc_start: -0.0848 (OUTLIER) cc_final: -0.3559 (ttm170) REVERT: X 143 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6620 (pp20) REVERT: U 88 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9190 (mttp) REVERT: U 130 ASP cc_start: 0.9240 (m-30) cc_final: 0.8979 (m-30) REVERT: K 55 PHE cc_start: 0.8695 (m-80) cc_final: 0.8363 (m-80) REVERT: K 62 PHE cc_start: 0.9211 (m-10) cc_final: 0.8896 (m-10) REVERT: L 44 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7963 (tpt170) REVERT: L 49 MET cc_start: 0.9236 (ppp) cc_final: 0.8987 (ppp) REVERT: L 57 GLU cc_start: 0.9347 (tp30) cc_final: 0.9125 (tp30) REVERT: M 1 MET cc_start: 0.6848 (mpp) cc_final: 0.6282 (tpp) REVERT: M 27 ILE cc_start: 0.9686 (mt) cc_final: 0.9359 (tt) REVERT: M 62 PHE cc_start: 0.9116 (m-10) cc_final: 0.8861 (m-80) REVERT: M 70 ILE cc_start: 0.8908 (mm) cc_final: 0.8618 (mm) REVERT: N 1 MET cc_start: 0.7593 (mmm) cc_final: 0.6574 (mmm) REVERT: N 49 MET cc_start: 0.9267 (ppp) cc_final: 0.8905 (ppp) REVERT: N 57 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8527 (mm-30) REVERT: N 70 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7885 (tt) REVERT: Q 43 ASN cc_start: 0.8323 (p0) cc_final: 0.7988 (m-40) REVERT: Z 78 ARG cc_start: 0.5342 (tmt170) cc_final: 0.5083 (tpt90) REVERT: Z 89 GLU cc_start: 0.9176 (pt0) cc_final: 0.8867 (pt0) REVERT: Z 126 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8979 (mm) REVERT: Z 194 THR cc_start: 0.8659 (p) cc_final: 0.8203 (t) REVERT: Z 195 PHE cc_start: 0.8870 (m-80) cc_final: 0.8580 (t80) REVERT: Z 264 MET cc_start: 0.9305 (mmm) cc_final: 0.9037 (tpp) REVERT: Z 294 LEU cc_start: 0.9694 (mt) cc_final: 0.9463 (mt) REVERT: T 65 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7798 (mm) REVERT: T 84 MET cc_start: 0.8822 (ttt) cc_final: 0.8491 (tmm) REVERT: T 85 GLU cc_start: 0.8940 (pt0) cc_final: 0.8520 (pt0) REVERT: T 97 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8421 (t0) REVERT: T 115 LEU cc_start: 0.9299 (mt) cc_final: 0.9047 (pp) REVERT: T 277 TYR cc_start: 0.4915 (m-80) cc_final: 0.4653 (m-80) outliers start: 70 outliers final: 44 residues processed: 368 average time/residue: 0.1040 time to fit residues: 57.9927 Evaluate side-chains 372 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 147 ARG 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 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 107 GLU Chi-restraints excluded: chain X residue 130 ASP Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 143 GLU Chi-restraints excluded: chain U residue 117 ARG Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 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 44 ARG Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 72 PHE Chi-restraints excluded: chain P residue 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 Q residue 45 VAL Chi-restraints excluded: chain Q residue 64 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 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 283 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 97 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 46 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.0020 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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** ** T 287 GLN ** 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 = 0.3751 r_free = 0.3751 target = 0.083144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.064674 restraints weight = 65058.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066251 restraints weight = 36895.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067274 restraints weight = 25603.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.067912 restraints weight = 20158.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068384 restraints weight = 17218.670| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4251 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= 0.156 Angle : 0.726 12.182 18448 Z= 0.369 Chirality : 0.045 0.414 2239 Planarity : 0.005 0.064 2379 Dihedral : 4.003 20.296 1933 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.80 % Allowed : 38.87 % Favored : 56.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.20), residues: 1784 helix: 1.37 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 71 TYR 0.032 0.002 TYR Z 92 PHE 0.018 0.001 PHE M 62 TRP 0.024 0.002 TRP T 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00350 (13606) covalent geometry : angle 0.72593 (18444) SS BOND : bond 0.00160 ( 2) SS BOND : angle 1.00156 ( 4) hydrogen bonds : bond 0.04138 ( 1200) hydrogen bonds : angle 3.93430 ( 3588) *********************** 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 395 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 0.538 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: 0.8897 (tm-30) cc_final: 0.8474 (tm-30) REVERT: Y 127 GLN cc_start: 0.9146 (tp40) cc_final: 0.8806 (tm-30) REVERT: Y 147 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7673 (ttp80) REVERT: X 89 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9056 (tp40) REVERT: X 99 ARG cc_start: 0.8520 (mmp-170) cc_final: 0.8160 (mmp80) REVERT: X 103 GLU cc_start: 0.8006 (pp20) cc_final: 0.7632 (pp20) REVERT: X 106 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8397 (tptm) REVERT: X 107 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: X 120 MET cc_start: 0.9408 (tpt) cc_final: 0.9049 (tmm) REVERT: X 143 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6718 (pp20) REVERT: U 88 LYS cc_start: 0.9502 (mmtt) cc_final: 0.9205 (mttp) REVERT: U 117 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7944 (ptm-80) REVERT: U 119 ARG cc_start: 0.9424 (tpt90) cc_final: 0.8916 (tpm170) REVERT: U 123 GLU cc_start: 0.8800 (pp20) cc_final: 0.8463 (pp20) REVERT: U 130 ASP cc_start: 0.9251 (m-30) cc_final: 0.8996 (m-30) REVERT: H 43 ASN cc_start: 0.8959 (t0) cc_final: 0.8575 (p0) REVERT: J 26 ILE cc_start: 0.9674 (mm) cc_final: 0.9420 (tt) REVERT: K 55 PHE cc_start: 0.8715 (m-80) cc_final: 0.8386 (m-80) REVERT: K 62 PHE cc_start: 0.9308 (m-10) cc_final: 0.8989 (m-10) REVERT: L 44 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8031 (tpt170) REVERT: L 49 MET cc_start: 0.9236 (ppp) cc_final: 0.8986 (ppp) REVERT: M 1 MET cc_start: 0.6844 (mpp) cc_final: 0.5928 (mmp) REVERT: M 27 ILE cc_start: 0.9693 (mt) cc_final: 0.9370 (tt) REVERT: M 62 PHE cc_start: 0.9194 (m-10) cc_final: 0.8885 (m-80) REVERT: M 70 ILE cc_start: 0.8955 (mm) cc_final: 0.8645 (mm) REVERT: N 1 MET cc_start: 0.7640 (mmm) cc_final: 0.7061 (mmm) REVERT: N 49 MET cc_start: 0.9279 (ppp) cc_final: 0.8897 (ppp) REVERT: N 57 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8520 (mm-30) REVERT: N 70 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7859 (tt) REVERT: Q 5 ASN cc_start: 0.8533 (p0) cc_final: 0.8312 (p0) REVERT: Q 43 ASN cc_start: 0.8382 (p0) cc_final: 0.8038 (m-40) REVERT: Z 78 ARG cc_start: 0.5512 (tmt170) cc_final: 0.5178 (tpt90) REVERT: Z 89 GLU cc_start: 0.9202 (pt0) cc_final: 0.8734 (pt0) REVERT: Z 126 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9018 (mm) REVERT: Z 194 THR cc_start: 0.8653 (p) cc_final: 0.8240 (t) REVERT: Z 195 PHE cc_start: 0.8921 (m-80) cc_final: 0.8564 (t80) REVERT: Z 264 MET cc_start: 0.9353 (mmm) cc_final: 0.9090 (tpp) REVERT: Z 280 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8824 (mm-30) REVERT: Z 294 LEU cc_start: 0.9671 (mt) cc_final: 0.9440 (mt) REVERT: T 65 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7828 (mm) REVERT: T 84 MET cc_start: 0.8827 (ttt) cc_final: 0.8510 (tmm) REVERT: T 85 GLU cc_start: 0.8904 (pt0) cc_final: 0.8491 (pt0) REVERT: T 97 ASN cc_start: 0.8797 (m-40) cc_final: 0.8529 (t0) REVERT: T 115 LEU cc_start: 0.9334 (mt) cc_final: 0.9124 (pp) REVERT: T 277 TYR cc_start: 0.4713 (m-80) cc_final: 0.4477 (m-80) REVERT: T 291 PHE cc_start: 0.9149 (t80) cc_final: 0.8688 (m-80) outliers start: 61 outliers final: 43 residues processed: 366 average time/residue: 0.1051 time to fit residues: 58.5631 Evaluate side-chains 370 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 22 ILE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 147 ARG 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 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 U residue 120 MET Chi-restraints excluded: chain H residue 27 ILE 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 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 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 41 ILE 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 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 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 T residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 115 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 115 GLN ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.083217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.064845 restraints weight = 64970.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066423 restraints weight = 36855.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.067460 restraints weight = 25559.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.068101 restraints weight = 20073.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.068585 restraints weight = 17126.693| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13608 Z= 0.156 Angle : 0.749 14.165 18448 Z= 0.375 Chirality : 0.046 0.424 2239 Planarity : 0.005 0.064 2379 Dihedral : 4.027 20.725 1933 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.72 % Allowed : 39.50 % Favored : 55.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 1784 helix: 1.33 (0.13), residues: 1451 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 37 TYR 0.033 0.002 TYR Z 92 PHE 0.021 0.001 PHE H 62 TRP 0.022 0.002 TRP T 208 HIS 0.001 0.000 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00356 (13606) covalent geometry : angle 0.74948 (18444) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.79899 ( 4) hydrogen bonds : bond 0.04147 ( 1200) hydrogen bonds : angle 3.94477 ( 3588) ********************** 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 393 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 333 time to evaluate : 0.424 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: 0.8900 (tm-30) cc_final: 0.8466 (tm-30) REVERT: Y 127 GLN cc_start: 0.9149 (tp40) cc_final: 0.8845 (tm-30) REVERT: V 21 LEU cc_start: 0.9396 (tp) cc_final: 0.9175 (tp) REVERT: X 89 GLN cc_start: 0.9346 (mm-40) cc_final: 0.9055 (tp40) REVERT: X 99 ARG cc_start: 0.8477 (mmp-170) cc_final: 0.8106 (mmp80) REVERT: X 103 GLU cc_start: 0.7988 (pp20) cc_final: 0.7618 (pp20) REVERT: X 106 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8391 (tptm) REVERT: X 107 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: X 120 MET cc_start: 0.9414 (tpt) cc_final: 0.9088 (tmm) REVERT: X 143 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6736 (pp20) REVERT: U 88 LYS cc_start: 0.9509 (mmtt) cc_final: 0.9216 (mttp) REVERT: U 117 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7958 (ptm-80) REVERT: U 119 ARG cc_start: 0.9443 (tpt90) cc_final: 0.8913 (tpm170) REVERT: U 123 GLU cc_start: 0.8832 (pp20) cc_final: 0.8483 (pp20) REVERT: U 130 ASP cc_start: 0.9258 (m-30) cc_final: 0.9003 (m-30) REVERT: H 57 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8930 (mm-30) REVERT: J 26 ILE cc_start: 0.9669 (mm) cc_final: 0.9431 (tt) REVERT: K 55 PHE cc_start: 0.8730 (m-80) cc_final: 0.8441 (m-80) REVERT: K 62 PHE cc_start: 0.9311 (m-10) cc_final: 0.8978 (m-10) REVERT: L 44 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8085 (tpt170) REVERT: M 1 MET cc_start: 0.6826 (mpp) cc_final: 0.6002 (mmp) REVERT: M 27 ILE cc_start: 0.9690 (mt) cc_final: 0.9362 (tt) REVERT: M 62 PHE cc_start: 0.9228 (m-10) cc_final: 0.8930 (m-80) REVERT: M 70 ILE cc_start: 0.8969 (mm) cc_final: 0.8686 (mm) REVERT: N 1 MET cc_start: 0.7637 (mmm) cc_final: 0.7147 (mmm) REVERT: N 49 MET cc_start: 0.9285 (ppp) cc_final: 0.8895 (ppp) REVERT: N 57 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8540 (mm-30) REVERT: N 70 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7831 (tt) REVERT: Q 5 ASN cc_start: 0.8558 (p0) cc_final: 0.8343 (p0) REVERT: Q 43 ASN cc_start: 0.8416 (p0) cc_final: 0.8013 (m-40) REVERT: Z 59 ASP cc_start: 0.8723 (t70) cc_final: 0.8488 (m-30) REVERT: Z 78 ARG cc_start: 0.5513 (tmt170) cc_final: 0.5176 (tpt90) REVERT: Z 89 GLU cc_start: 0.9206 (pt0) cc_final: 0.8726 (pt0) REVERT: Z 126 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9041 (mm) REVERT: Z 195 PHE cc_start: 0.8926 (m-80) cc_final: 0.8600 (t80) REVERT: Z 264 MET cc_start: 0.9396 (mmm) cc_final: 0.9096 (tpp) REVERT: Z 294 LEU cc_start: 0.9676 (mt) cc_final: 0.9438 (mt) REVERT: T 65 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7812 (mm) REVERT: T 84 MET cc_start: 0.8811 (ttt) cc_final: 0.8478 (tmm) REVERT: T 85 GLU cc_start: 0.8915 (pt0) cc_final: 0.8486 (pt0) REVERT: T 115 LEU cc_start: 0.9352 (mt) cc_final: 0.9114 (pp) REVERT: T 277 TYR cc_start: 0.4806 (m-80) cc_final: 0.4533 (m-80) REVERT: T 291 PHE cc_start: 0.9152 (t80) cc_final: 0.8683 (m-80) outliers start: 60 outliers final: 47 residues processed: 364 average time/residue: 0.0924 time to fit residues: 51.5798 Evaluate side-chains 369 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 U residue 120 MET Chi-restraints excluded: chain H residue 18 ILE 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 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 15 LEU Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 41 ILE 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 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 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 T residue 65 LEU Chi-restraints excluded: chain T residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN ** T 97 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 = 0.3691 r_free = 0.3691 target = 0.080688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.062524 restraints weight = 66061.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064012 restraints weight = 37385.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065008 restraints weight = 25952.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065615 restraints weight = 20374.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066133 restraints weight = 17412.611| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 13608 Z= 0.257 Angle : 0.807 12.606 18448 Z= 0.416 Chirality : 0.047 0.374 2239 Planarity : 0.005 0.067 2379 Dihedral : 4.132 22.406 1933 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.80 % Allowed : 39.81 % Favored : 55.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.19), residues: 1784 helix: 1.14 (0.13), residues: 1451 sheet: None (None), residues: 0 loop : -2.01 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 71 TYR 0.037 0.003 TYR Z 92 PHE 0.030 0.002 PHE H 62 TRP 0.025 0.002 TRP T 208 HIS 0.005 0.001 HIS V 149 Details of bonding type rmsd covalent geometry : bond 0.00574 (13606) covalent geometry : angle 0.80717 (18444) SS BOND : bond 0.00166 ( 2) SS BOND : angle 1.20354 ( 4) hydrogen bonds : bond 0.04466 ( 1200) hydrogen bonds : angle 4.15457 ( 3588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.91 seconds wall clock time: 49 minutes 36.34 seconds (2976.34 seconds total)