Starting phenix.real_space_refine on Wed Apr 30 08:45:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itq_60875/04_2025/9itq_60875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itq_60875/04_2025/9itq_60875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itq_60875/04_2025/9itq_60875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itq_60875/04_2025/9itq_60875.map" model { file = "/net/cci-nas-00/data/ceres_data/9itq_60875/04_2025/9itq_60875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itq_60875/04_2025/9itq_60875.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.009 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 19 5.16 5 C 6236 2.51 5 N 1526 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9411 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "O" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "P" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Q" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Y" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "V" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 197 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "U" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "T" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1777 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 Chain: "Z" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1877 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 239} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 7.27, per 1000 atoms: 0.77 Number of scatterers: 9411 At special positions: 0 Unit cell: (89.28, 129.27, 80.91, 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 19 16.00 O 1630 8.00 N 1526 7.00 C 6236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS T 135 " - pdb=" SG CYS T 173 " distance=2.91 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 1 sheets defined 85.5% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.888A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 4.190A pdb=" N GLY H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 72 removed outlier: 3.838A pdb=" N VAL H 46 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET H 49 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 37 removed outlier: 4.586A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 3.512A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 72 Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix removed outlier: 4.426A pdb=" N GLY J 23 " --> pdb=" O GLY J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 72 removed outlier: 3.571A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 38 removed outlier: 3.653A pdb=" N VAL K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.760A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 3.587A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 71 removed outlier: 3.786A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE L 55 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.594A pdb=" N VAL M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix removed outlier: 4.042A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 3.607A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.556A pdb=" N ALA N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 38 Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.662A pdb=" N MET N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 4.057A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix removed outlier: 3.999A pdb=" N GLY O 23 " --> pdb=" O GLY O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 71 removed outlier: 3.589A pdb=" N ALA O 58 " --> pdb=" O ALA O 54 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 17 through 38 removed outlier: 4.117A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 3.734A pdb=" N GLY P 52 " --> pdb=" O TYR P 48 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.671A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.618A pdb=" N ASN Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 72 removed outlier: 3.691A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 48 removed outlier: 3.654A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 24 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix Processing helix chain 'V' and resid 8 through 45 removed outlier: 3.609A pdb=" N LEU V 28 " --> pdb=" O ILE V 24 " (cutoff:3.500A) Proline residue: V 32 - end of helix Processing helix chain 'X' and resid 11 through 41 Proline residue: X 32 - end of helix Processing helix chain 'U' and resid 10 through 42 removed outlier: 5.579A pdb=" N ARG U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Proline residue: U 32 - end of helix Processing helix chain 'T' and resid 50 through 71 removed outlier: 3.649A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE T 56 " --> pdb=" O PHE T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 3.533A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.674A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.526A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 212 removed outlier: 3.913A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 220 removed outlier: 4.273A pdb=" N TYR T 217 " --> pdb=" O GLY T 214 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU T 218 " --> pdb=" O PRO T 215 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS T 220 " --> pdb=" O TYR T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 268 removed outlier: 3.981A pdb=" N PHE T 230 " --> pdb=" O GLY T 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE T 233 " --> pdb=" O SER T 229 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE T 234 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Proline residue: T 243 - end of helix removed outlier: 3.632A pdb=" N ILE T 254 " --> pdb=" O LEU T 250 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.857A pdb=" N PHE T 285 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 70 removed outlier: 3.893A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 removed outlier: 3.593A pdb=" N ILE Z 87 " --> pdb=" O VAL Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 125 Proline residue: Z 108 - end of helix removed outlier: 4.211A pdb=" N VAL Z 117 " --> pdb=" O ILE Z 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY Z 120 " --> pdb=" O PHE Z 116 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.548A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Z 212 " --> pdb=" O TRP Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 220 removed outlier: 3.536A pdb=" N LYS Z 219 " --> pdb=" O PRO Z 215 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 225 removed outlier: 4.036A pdb=" N ASN Z 225 " --> pdb=" O PHE Z 222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 268 Proline residue: Z 243 - end of helix removed outlier: 3.511A pdb=" N ILE Z 254 " --> pdb=" O LEU Z 250 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 304 removed outlier: 4.577A pdb=" N PHE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 39 through 41 removed outlier: 7.273A pdb=" N ILE Z 48 " --> pdb=" O PHE Z 40 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2607 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: 2.68 Time building geometry restraints manager: 2.82 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: 2845 1.34 - 1.46: 1325 1.46 - 1.58: 5361 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9567 Sorted by residual: bond pdb=" N ILE T 39 " pdb=" CA ILE T 39 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.65e+00 bond pdb=" N ILE J 18 " pdb=" CA ILE J 18 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.56e+00 bond pdb=" N ILE P 41 " pdb=" CA ILE P 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N VAL T 134 " pdb=" CA VAL T 134 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.79e+00 bond pdb=" N VAL T 38 " pdb=" CA VAL T 38 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.63e+00 ... (remaining 9562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12812 1.94 - 3.88: 209 3.88 - 5.82: 35 5.82 - 7.76: 2 7.76 - 9.70: 2 Bond angle restraints: 13060 Sorted by residual: angle pdb=" N ILE L 41 " pdb=" CA ILE L 41 " pdb=" C ILE L 41 " ideal model delta sigma weight residual 112.29 107.86 4.43 9.40e-01 1.13e+00 2.22e+01 angle pdb=" N ALA N 17 " pdb=" CA ALA N 17 " pdb=" C ALA N 17 " ideal model delta sigma weight residual 114.04 109.09 4.95 1.24e+00 6.50e-01 1.59e+01 angle pdb=" N LYS T 219 " pdb=" CA LYS T 219 " pdb=" C LYS T 219 " ideal model delta sigma weight residual 114.04 109.44 4.60 1.24e+00 6.50e-01 1.37e+01 angle pdb=" CA CYS T 173 " pdb=" C CYS T 173 " pdb=" O CYS T 173 " ideal model delta sigma weight residual 122.64 118.02 4.62 1.25e+00 6.40e-01 1.37e+01 angle pdb=" N ALA T 175 " pdb=" CA ALA T 175 " pdb=" C ALA T 175 " ideal model delta sigma weight residual 111.71 108.06 3.65 1.15e+00 7.56e-01 1.01e+01 ... (remaining 13055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4830 17.75 - 35.50: 456 35.50 - 53.26: 111 53.26 - 71.01: 14 71.01 - 88.76: 7 Dihedral angle restraints: 5418 sinusoidal: 1648 harmonic: 3770 Sorted by residual: dihedral pdb=" CA PHE T 52 " pdb=" C PHE T 52 " pdb=" N VAL T 53 " pdb=" CA VAL T 53 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA MET P 49 " pdb=" C MET P 49 " pdb=" N PHE P 50 " pdb=" CA PHE P 50 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LEU P 64 " pdb=" C LEU P 64 " pdb=" N VAL P 65 " pdb=" CA VAL P 65 " ideal model delta harmonic sigma weight residual -180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1218 0.044 - 0.088: 310 0.088 - 0.132: 94 0.132 - 0.176: 15 0.176 - 0.220: 5 Chirality restraints: 1642 Sorted by residual: chirality pdb=" CG LEU M 15 " pdb=" CB LEU M 15 " pdb=" CD1 LEU M 15 " pdb=" CD2 LEU M 15 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL T 134 " pdb=" N VAL T 134 " pdb=" C VAL T 134 " pdb=" CB VAL T 134 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CB ILE P 18 " pdb=" CA ILE P 18 " pdb=" CG1 ILE P 18 " pdb=" CG2 ILE P 18 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 1639 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO Q 20 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET N 49 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET N 49 " -0.030 2.00e-02 2.50e+03 pdb=" O MET N 49 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE N 50 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY L 19 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO L 20 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 20 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 20 " 0.024 5.00e-02 4.00e+02 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 121 2.68 - 3.24: 10373 3.24 - 3.79: 16032 3.79 - 4.35: 19402 4.35 - 4.90: 31511 Nonbonded interactions: 77439 Sorted by model distance: nonbonded pdb=" O VAL T 134 " pdb=" SG CYS T 135 " model vdw 2.128 3.400 nonbonded pdb=" O GLY T 226 " pdb=" OG SER T 229 " model vdw 2.200 3.040 nonbonded pdb=" O ARG P 44 " pdb=" OG1 THR P 47 " model vdw 2.247 3.040 nonbonded pdb=" O ARG J 44 " pdb=" OG1 THR J 47 " model vdw 2.278 3.040 nonbonded pdb=" O ASN T 99 " pdb=" OH TYR T 296 " model vdw 2.291 3.040 ... (remaining 77434 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' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'J' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'K' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'L' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'M' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'N' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'O' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'P' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'Q' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) } ncs_group { reference = (chain 'T' and (resid 19 through 134 or (resid 135 through 176 and (name N or na \ me CA or name C or name O or name CB )) or resid 177 through 304)) selection = (chain 'Z' and ((resid 19 through 32 and (name N or name CA or name C or name O \ or name CB )) or resid 33 or (resid 34 through 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 72 or (resid 73 through 78 and (n \ ame N or name CA or name C or name O or name CB )) or resid 79 or (resid 80 and \ (name N or name CA or name C or name O or name CB )) or resid 81 through 136 or \ resid 172 through 182 or (resid 183 through 189 and (name N or name CA or name C \ or name O or name CB )) or resid 190 through 216 or (resid 217 through 225 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 304)) } ncs_group { reference = (chain 'U' and resid 10 through 41) selection = (chain 'V' and resid 10 through 41) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.120 Find NCS groups from input model: 0.420 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.010 0.878 9568 Z= 0.492 Angle : 0.661 26.411 13062 Z= 0.385 Chirality : 0.044 0.220 1642 Planarity : 0.005 0.048 1666 Dihedral : 15.126 88.762 3009 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.50 % Allowed : 26.64 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1325 helix: 1.19 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 31 PHE 0.015 0.001 PHE N 68 TYR 0.009 0.001 TYR T 277 ARG 0.001 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.13857 ( 874) hydrogen bonds : angle 5.57961 ( 2607) SS BOND : bond 0.87785 ( 1) SS BOND : angle 19.67063 ( 2) covalent geometry : bond 0.00333 ( 9567) covalent geometry : angle 0.61449 (13060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 464 time to evaluate : 0.955 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: H 37 ARG cc_start: 0.9329 (ttm110) cc_final: 0.8958 (ttm110) REVERT: H 62 PHE cc_start: 0.9265 (m-80) cc_final: 0.8966 (m-80) REVERT: I 15 LEU cc_start: 0.9087 (tp) cc_final: 0.8493 (tp) REVERT: I 46 VAL cc_start: 0.9275 (t) cc_final: 0.8978 (p) REVERT: I 49 MET cc_start: 0.9619 (ttt) cc_final: 0.8931 (tmm) REVERT: I 53 ILE cc_start: 0.9600 (pt) cc_final: 0.9252 (pt) REVERT: I 59 LEU cc_start: 0.9600 (mp) cc_final: 0.9253 (mp) REVERT: I 62 PHE cc_start: 0.8877 (m-10) cc_final: 0.8522 (m-80) REVERT: I 68 PHE cc_start: 0.9015 (m-80) cc_final: 0.8806 (m-80) REVERT: J 40 GLU cc_start: 0.8709 (mm-30) cc_final: 0.7948 (mp0) REVERT: J 48 TYR cc_start: 0.9254 (m-80) cc_final: 0.8636 (m-80) REVERT: J 49 MET cc_start: 0.9579 (ppp) cc_final: 0.9357 (ppp) REVERT: K 33 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8962 (mm110) REVERT: K 49 MET cc_start: 0.9582 (tmm) cc_final: 0.9083 (tmm) REVERT: K 53 ILE cc_start: 0.9611 (mm) cc_final: 0.9384 (mt) REVERT: K 62 PHE cc_start: 0.9436 (m-10) cc_final: 0.9235 (m-80) REVERT: L 48 TYR cc_start: 0.9323 (m-80) cc_final: 0.9097 (m-80) REVERT: M 32 VAL cc_start: 0.9877 (t) cc_final: 0.9600 (p) REVERT: M 33 GLN cc_start: 0.9098 (mm110) cc_final: 0.8645 (mm110) REVERT: M 46 VAL cc_start: 0.9567 (t) cc_final: 0.9156 (t) REVERT: M 49 MET cc_start: 0.9359 (ttp) cc_final: 0.8963 (tmm) REVERT: M 50 PHE cc_start: 0.9066 (m-80) cc_final: 0.8539 (m-80) REVERT: M 66 ILE cc_start: 0.9692 (mm) cc_final: 0.9375 (tt) REVERT: N 48 TYR cc_start: 0.9151 (m-80) cc_final: 0.8875 (m-80) REVERT: N 51 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8694 (pt) REVERT: N 55 PHE cc_start: 0.9376 (m-80) cc_final: 0.9075 (m-80) REVERT: N 57 GLU cc_start: 0.9583 (mm-30) cc_final: 0.9242 (tm-30) REVERT: O 29 SER cc_start: 0.9706 (t) cc_final: 0.9356 (p) REVERT: O 48 TYR cc_start: 0.8919 (m-80) cc_final: 0.8555 (m-80) REVERT: O 49 MET cc_start: 0.9497 (ttp) cc_final: 0.9267 (ptm) REVERT: O 62 PHE cc_start: 0.9012 (m-80) cc_final: 0.8712 (m-80) REVERT: O 66 ILE cc_start: 0.9385 (mm) cc_final: 0.8999 (mm) REVERT: P 29 SER cc_start: 0.9455 (t) cc_final: 0.9139 (t) REVERT: P 38 ASN cc_start: 0.9291 (t0) cc_final: 0.8844 (t0) REVERT: P 61 ILE cc_start: 0.9648 (mm) cc_final: 0.9443 (mm) REVERT: Q 28 VAL cc_start: 0.9713 (t) cc_final: 0.9501 (m) REVERT: Q 37 ARG cc_start: 0.8697 (mmp80) cc_final: 0.8104 (mmm160) REVERT: Q 43 ASN cc_start: 0.9252 (p0) cc_final: 0.8464 (t0) REVERT: Q 49 MET cc_start: 0.9553 (ttp) cc_final: 0.9137 (tmm) REVERT: T 102 TYR cc_start: 0.8850 (m-80) cc_final: 0.8637 (m-80) REVERT: T 122 TRP cc_start: 0.8812 (m-10) cc_final: 0.8513 (m-10) REVERT: T 200 ILE cc_start: 0.9436 (tt) cc_final: 0.9234 (pt) REVERT: T 206 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8456 (mm-30) REVERT: T 240 LEU cc_start: 0.9552 (mt) cc_final: 0.9263 (mt) REVERT: T 244 PHE cc_start: 0.9457 (m-80) cc_final: 0.9063 (m-80) REVERT: T 260 LEU cc_start: 0.9610 (tp) cc_final: 0.9367 (tp) REVERT: T 261 LEU cc_start: 0.9165 (mt) cc_final: 0.8816 (mt) REVERT: T 277 TYR cc_start: 0.8908 (m-80) cc_final: 0.8413 (m-80) REVERT: T 287 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9195 (tp40) REVERT: Z 75 MET cc_start: 0.9190 (tpt) cc_final: 0.8936 (mpp) REVERT: Z 93 ASN cc_start: 0.9078 (m-40) cc_final: 0.8838 (t0) REVERT: Z 95 PHE cc_start: 0.9424 (m-10) cc_final: 0.9031 (m-80) REVERT: Z 114 PHE cc_start: 0.9172 (t80) cc_final: 0.8838 (t80) REVERT: Z 190 ASP cc_start: 0.7796 (t0) cc_final: 0.7496 (p0) REVERT: Z 206 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8804 (mm-30) REVERT: Z 264 MET cc_start: 0.9396 (mmt) cc_final: 0.8860 (tpp) REVERT: Z 277 TYR cc_start: 0.8806 (m-80) cc_final: 0.8495 (m-80) REVERT: Z 282 PHE cc_start: 0.9357 (t80) cc_final: 0.9010 (t80) REVERT: Z 296 TYR cc_start: 0.9124 (t80) cc_final: 0.8682 (t80) REVERT: Z 298 PHE cc_start: 0.9283 (m-10) cc_final: 0.9046 (m-10) outliers start: 4 outliers final: 1 residues processed: 466 average time/residue: 0.1620 time to fit residues: 111.5898 Evaluate side-chains 375 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain N residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN H 38 ASN J 33 GLN Z 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.070064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.057459 restraints weight = 44892.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058815 restraints weight = 30758.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059890 restraints weight = 23152.929| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9568 Z= 0.168 Angle : 0.696 11.005 13062 Z= 0.363 Chirality : 0.047 0.299 1642 Planarity : 0.005 0.068 1666 Dihedral : 4.140 31.009 1397 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.83 % Allowed : 29.37 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1325 helix: 1.29 (0.15), residues: 1061 sheet: None (None), residues: 0 loop : -1.98 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 208 HIS 0.001 0.000 HIS Z 31 PHE 0.024 0.001 PHE Z 202 TYR 0.021 0.002 TYR M 48 ARG 0.006 0.001 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 874) hydrogen bonds : angle 4.48184 ( 2607) SS BOND : bond 0.00165 ( 1) SS BOND : angle 1.66533 ( 2) covalent geometry : bond 0.00358 ( 9567) covalent geometry : angle 0.69608 (13060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 409 time to evaluate : 0.940 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: H 37 ARG cc_start: 0.9322 (ttm110) cc_final: 0.9043 (ttm110) REVERT: H 57 GLU cc_start: 0.9161 (tp30) cc_final: 0.8723 (tp30) REVERT: H 59 LEU cc_start: 0.9762 (mm) cc_final: 0.9550 (mp) REVERT: H 61 ILE cc_start: 0.9723 (mm) cc_final: 0.9396 (mm) REVERT: H 62 PHE cc_start: 0.9265 (m-80) cc_final: 0.8761 (m-80) REVERT: I 15 LEU cc_start: 0.9174 (tp) cc_final: 0.8547 (tp) REVERT: I 46 VAL cc_start: 0.9343 (t) cc_final: 0.9099 (p) REVERT: I 49 MET cc_start: 0.9618 (ttt) cc_final: 0.8951 (tmm) REVERT: I 59 LEU cc_start: 0.9627 (mp) cc_final: 0.9182 (mp) REVERT: I 68 PHE cc_start: 0.9053 (m-80) cc_final: 0.8590 (m-80) REVERT: J 40 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7947 (mp0) REVERT: J 48 TYR cc_start: 0.9284 (m-80) cc_final: 0.8594 (m-80) REVERT: J 49 MET cc_start: 0.9615 (ppp) cc_final: 0.9077 (ppp) REVERT: J 57 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8766 (mt-10) REVERT: K 33 GLN cc_start: 0.9308 (mm-40) cc_final: 0.9071 (mm-40) REVERT: K 48 TYR cc_start: 0.9288 (m-80) cc_final: 0.8395 (m-80) REVERT: K 49 MET cc_start: 0.9569 (tmm) cc_final: 0.9272 (tmm) REVERT: M 32 VAL cc_start: 0.9873 (t) cc_final: 0.9636 (p) REVERT: M 33 GLN cc_start: 0.9125 (mm110) cc_final: 0.8743 (mm110) REVERT: M 46 VAL cc_start: 0.9522 (t) cc_final: 0.9193 (t) REVERT: M 49 MET cc_start: 0.9347 (ttp) cc_final: 0.9136 (ppp) REVERT: M 50 PHE cc_start: 0.9074 (m-80) cc_final: 0.8559 (m-80) REVERT: M 66 ILE cc_start: 0.9663 (mm) cc_final: 0.9386 (tt) REVERT: N 48 TYR cc_start: 0.9312 (m-80) cc_final: 0.8697 (m-80) REVERT: N 55 PHE cc_start: 0.9433 (m-80) cc_final: 0.9231 (m-80) REVERT: N 57 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9051 (tm-30) REVERT: N 68 PHE cc_start: 0.8957 (m-10) cc_final: 0.8746 (m-10) REVERT: O 29 SER cc_start: 0.9656 (t) cc_final: 0.9310 (p) REVERT: O 49 MET cc_start: 0.9459 (ttp) cc_final: 0.8804 (tmm) REVERT: O 62 PHE cc_start: 0.9032 (m-80) cc_final: 0.8684 (m-80) REVERT: O 66 ILE cc_start: 0.9479 (mm) cc_final: 0.9270 (mm) REVERT: P 43 ASN cc_start: 0.9365 (p0) cc_final: 0.9158 (p0) REVERT: P 57 GLU cc_start: 0.9554 (tp30) cc_final: 0.8972 (mm-30) REVERT: Q 28 VAL cc_start: 0.9859 (t) cc_final: 0.9654 (m) REVERT: Q 37 ARG cc_start: 0.8500 (mmp80) cc_final: 0.7974 (mmm160) REVERT: Q 38 ASN cc_start: 0.9019 (p0) cc_final: 0.8768 (p0) REVERT: Q 43 ASN cc_start: 0.8899 (p0) cc_final: 0.8691 (t0) REVERT: Q 57 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8398 (tm-30) REVERT: T 89 GLU cc_start: 0.9304 (pt0) cc_final: 0.8999 (pp20) REVERT: T 122 TRP cc_start: 0.8895 (m-10) cc_final: 0.8468 (m-10) REVERT: T 200 ILE cc_start: 0.9442 (tt) cc_final: 0.9237 (pt) REVERT: T 206 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8404 (mm-30) REVERT: T 240 LEU cc_start: 0.9613 (mt) cc_final: 0.9398 (mt) REVERT: T 253 ASN cc_start: 0.9427 (m-40) cc_final: 0.8947 (m110) REVERT: T 264 MET cc_start: 0.9616 (mmm) cc_final: 0.9310 (mmm) REVERT: T 277 TYR cc_start: 0.8997 (m-80) cc_final: 0.8340 (m-80) REVERT: Z 85 GLU cc_start: 0.9261 (tt0) cc_final: 0.8534 (tm-30) REVERT: Z 89 GLU cc_start: 0.8812 (pt0) cc_final: 0.8054 (pt0) REVERT: Z 95 PHE cc_start: 0.9409 (m-10) cc_final: 0.8989 (m-80) REVERT: Z 114 PHE cc_start: 0.9361 (t80) cc_final: 0.9150 (t80) REVERT: Z 190 ASP cc_start: 0.7843 (t0) cc_final: 0.7556 (p0) REVERT: Z 202 PHE cc_start: 0.9205 (t80) cc_final: 0.8933 (t80) REVERT: Z 228 MET cc_start: 0.7102 (ttt) cc_final: 0.6870 (ttt) REVERT: Z 239 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9190 (mm-30) REVERT: Z 264 MET cc_start: 0.9443 (mmt) cc_final: 0.8929 (tpp) REVERT: Z 277 TYR cc_start: 0.8818 (m-80) cc_final: 0.8568 (m-80) REVERT: Z 282 PHE cc_start: 0.9403 (t80) cc_final: 0.9070 (t80) REVERT: Z 296 TYR cc_start: 0.9086 (t80) cc_final: 0.8673 (t80) outliers start: 39 outliers final: 23 residues processed: 427 average time/residue: 0.1531 time to fit residues: 98.4475 Evaluate side-chains 405 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 381 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 39 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Z 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058022 restraints weight = 44989.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059339 restraints weight = 31433.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060327 restraints weight = 24164.203| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9568 Z= 0.159 Angle : 0.690 10.015 13062 Z= 0.355 Chirality : 0.048 0.383 1642 Planarity : 0.005 0.063 1666 Dihedral : 4.058 25.391 1393 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 6.20 % Allowed : 29.74 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1325 helix: 1.19 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 31 PHE 0.036 0.001 PHE I 62 TYR 0.034 0.002 TYR M 48 ARG 0.008 0.001 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 874) hydrogen bonds : angle 4.37250 ( 2607) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.63026 ( 2) covalent geometry : bond 0.00348 ( 9567) covalent geometry : angle 0.68999 (13060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 401 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9328 (ttm110) cc_final: 0.8914 (ttm110) REVERT: H 59 LEU cc_start: 0.9758 (mm) cc_final: 0.9512 (mp) REVERT: H 62 PHE cc_start: 0.9184 (m-80) cc_final: 0.8717 (m-80) REVERT: I 15 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8662 (tp) REVERT: I 49 MET cc_start: 0.9616 (ttt) cc_final: 0.9019 (tmm) REVERT: I 55 PHE cc_start: 0.9485 (m-80) cc_final: 0.9263 (m-80) REVERT: I 59 LEU cc_start: 0.9658 (mp) cc_final: 0.9443 (mp) REVERT: I 68 PHE cc_start: 0.9107 (m-80) cc_final: 0.8648 (m-80) REVERT: J 40 GLU cc_start: 0.8686 (mm-30) cc_final: 0.7947 (mp0) REVERT: J 44 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7405 (ttt90) REVERT: J 48 TYR cc_start: 0.9254 (m-80) cc_final: 0.8599 (m-80) REVERT: J 49 MET cc_start: 0.9633 (ppp) cc_final: 0.9103 (ppp) REVERT: J 57 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8757 (mt-10) REVERT: K 33 GLN cc_start: 0.9291 (mm-40) cc_final: 0.9037 (mm-40) REVERT: L 43 ASN cc_start: 0.8813 (t0) cc_final: 0.8457 (m110) REVERT: L 48 TYR cc_start: 0.9390 (m-80) cc_final: 0.8680 (m-80) REVERT: M 32 VAL cc_start: 0.9868 (t) cc_final: 0.9622 (p) REVERT: M 46 VAL cc_start: 0.9479 (t) cc_final: 0.9132 (t) REVERT: M 50 PHE cc_start: 0.9062 (m-80) cc_final: 0.8596 (m-80) REVERT: N 41 ILE cc_start: 0.9618 (OUTLIER) cc_final: 0.9110 (tp) REVERT: N 48 TYR cc_start: 0.9308 (m-80) cc_final: 0.8709 (m-80) REVERT: N 55 PHE cc_start: 0.9445 (m-80) cc_final: 0.9125 (m-80) REVERT: O 29 SER cc_start: 0.9615 (t) cc_final: 0.9266 (p) REVERT: O 37 ARG cc_start: 0.9120 (mmt90) cc_final: 0.8669 (mtm180) REVERT: O 44 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.7591 (mmm-85) REVERT: O 48 TYR cc_start: 0.8929 (m-80) cc_final: 0.8408 (m-80) REVERT: O 49 MET cc_start: 0.9449 (ttp) cc_final: 0.8785 (tmm) REVERT: O 57 GLU cc_start: 0.9202 (pt0) cc_final: 0.8978 (pp20) REVERT: O 62 PHE cc_start: 0.9074 (m-80) cc_final: 0.8741 (m-80) REVERT: O 66 ILE cc_start: 0.9531 (mm) cc_final: 0.9227 (mm) REVERT: O 70 ILE cc_start: 0.8699 (mm) cc_final: 0.8474 (mm) REVERT: P 37 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7943 (ttm170) REVERT: P 43 ASN cc_start: 0.9407 (p0) cc_final: 0.9185 (p0) REVERT: P 57 GLU cc_start: 0.9482 (tp30) cc_final: 0.8921 (mm-30) REVERT: Q 28 VAL cc_start: 0.9795 (t) cc_final: 0.9586 (m) REVERT: Q 37 ARG cc_start: 0.8779 (mmp80) cc_final: 0.8193 (mmm160) REVERT: Q 38 ASN cc_start: 0.8976 (p0) cc_final: 0.8762 (p0) REVERT: Q 43 ASN cc_start: 0.8972 (p0) cc_final: 0.8771 (t0) REVERT: Q 49 MET cc_start: 0.9183 (tmm) cc_final: 0.8929 (tmm) REVERT: Q 57 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: T 89 GLU cc_start: 0.9261 (pt0) cc_final: 0.8985 (pp20) REVERT: T 122 TRP cc_start: 0.8900 (m-10) cc_final: 0.8582 (m-10) REVERT: T 206 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8411 (mm-30) REVERT: T 228 MET cc_start: 0.9040 (ppp) cc_final: 0.8766 (ppp) REVERT: T 240 LEU cc_start: 0.9610 (mt) cc_final: 0.9354 (mt) REVERT: T 253 ASN cc_start: 0.9331 (m-40) cc_final: 0.8999 (m-40) REVERT: T 264 MET cc_start: 0.9695 (mmm) cc_final: 0.9420 (mmm) REVERT: T 277 TYR cc_start: 0.8854 (m-80) cc_final: 0.8414 (m-80) REVERT: Z 85 GLU cc_start: 0.9264 (tt0) cc_final: 0.8615 (tm-30) REVERT: Z 95 PHE cc_start: 0.9399 (m-10) cc_final: 0.8970 (m-80) REVERT: Z 206 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8964 (mm-30) REVERT: Z 228 MET cc_start: 0.7162 (ttt) cc_final: 0.6788 (ttt) REVERT: Z 239 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9241 (mm-30) REVERT: Z 264 MET cc_start: 0.9448 (mmt) cc_final: 0.8932 (tpp) REVERT: Z 277 TYR cc_start: 0.8873 (m-80) cc_final: 0.8540 (m-80) REVERT: Z 282 PHE cc_start: 0.9348 (t80) cc_final: 0.9011 (t80) REVERT: Z 286 ILE cc_start: 0.9607 (pt) cc_final: 0.9311 (pt) REVERT: Z 296 TYR cc_start: 0.9074 (t80) cc_final: 0.8769 (t80) outliers start: 50 outliers final: 33 residues processed: 426 average time/residue: 0.1637 time to fit residues: 104.8810 Evaluate side-chains 409 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 372 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 80 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Z 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.057547 restraints weight = 45336.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.058613 restraints weight = 31634.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.059623 restraints weight = 25103.353| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9568 Z= 0.163 Angle : 0.718 10.147 13062 Z= 0.371 Chirality : 0.048 0.247 1642 Planarity : 0.004 0.055 1666 Dihedral : 4.100 25.026 1393 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.32 % Allowed : 32.22 % Favored : 61.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1325 helix: 1.15 (0.16), residues: 1055 sheet: None (None), residues: 0 loop : -2.09 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 208 HIS 0.000 0.000 HIS Z 31 PHE 0.036 0.001 PHE P 62 TYR 0.021 0.002 TYR K 48 ARG 0.005 0.000 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04792 ( 874) hydrogen bonds : angle 4.39232 ( 2607) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.45182 ( 2) covalent geometry : bond 0.00356 ( 9567) covalent geometry : angle 0.71846 (13060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 394 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9312 (ttm110) cc_final: 0.8926 (ttm110) REVERT: H 48 TYR cc_start: 0.9165 (m-80) cc_final: 0.8964 (m-80) REVERT: H 59 LEU cc_start: 0.9766 (mm) cc_final: 0.9520 (mp) REVERT: H 62 PHE cc_start: 0.9203 (m-80) cc_final: 0.8738 (m-80) REVERT: I 49 MET cc_start: 0.9577 (ttt) cc_final: 0.8986 (tmm) REVERT: I 55 PHE cc_start: 0.9482 (m-80) cc_final: 0.9240 (m-80) REVERT: I 57 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: I 68 PHE cc_start: 0.9137 (m-80) cc_final: 0.8675 (m-80) REVERT: J 40 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8011 (mp0) REVERT: J 44 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7831 (mmm-85) REVERT: J 48 TYR cc_start: 0.9297 (m-80) cc_final: 0.8643 (m-80) REVERT: J 49 MET cc_start: 0.9630 (ppp) cc_final: 0.9126 (ppp) REVERT: J 57 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8807 (mt-10) REVERT: K 33 GLN cc_start: 0.9303 (mm-40) cc_final: 0.9076 (mm-40) REVERT: K 57 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9214 (mm-30) REVERT: L 43 ASN cc_start: 0.8711 (t0) cc_final: 0.8296 (m-40) REVERT: M 33 GLN cc_start: 0.9342 (mm110) cc_final: 0.9000 (mm110) REVERT: M 46 VAL cc_start: 0.9515 (t) cc_final: 0.9226 (t) REVERT: M 50 PHE cc_start: 0.9221 (m-80) cc_final: 0.8604 (m-80) REVERT: N 48 TYR cc_start: 0.9352 (m-80) cc_final: 0.8708 (m-80) REVERT: N 55 PHE cc_start: 0.9444 (m-80) cc_final: 0.9167 (m-80) REVERT: N 64 LEU cc_start: 0.9775 (tp) cc_final: 0.9437 (tp) REVERT: O 29 SER cc_start: 0.9582 (t) cc_final: 0.9242 (p) REVERT: O 37 ARG cc_start: 0.9083 (mmt90) cc_final: 0.8672 (mtm180) REVERT: O 44 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.7515 (mmm-85) REVERT: O 48 TYR cc_start: 0.8931 (m-80) cc_final: 0.8307 (m-80) REVERT: O 49 MET cc_start: 0.9477 (ttp) cc_final: 0.8813 (tmm) REVERT: O 57 GLU cc_start: 0.9173 (pt0) cc_final: 0.8919 (pp20) REVERT: O 62 PHE cc_start: 0.9118 (m-80) cc_final: 0.8770 (m-80) REVERT: O 66 ILE cc_start: 0.9554 (mm) cc_final: 0.9227 (mm) REVERT: P 37 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7875 (ttm170) REVERT: P 42 GLU cc_start: 0.9261 (mt-10) cc_final: 0.9016 (tt0) REVERT: P 43 ASN cc_start: 0.9409 (p0) cc_final: 0.9185 (p0) REVERT: P 48 TYR cc_start: 0.9221 (m-80) cc_final: 0.8969 (m-80) REVERT: Q 28 VAL cc_start: 0.9792 (t) cc_final: 0.9574 (m) REVERT: Q 37 ARG cc_start: 0.8819 (mmp80) cc_final: 0.8221 (mmm160) REVERT: Q 57 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: T 84 MET cc_start: 0.9064 (mmm) cc_final: 0.8432 (mpp) REVERT: T 89 GLU cc_start: 0.9116 (pt0) cc_final: 0.8912 (pp20) REVERT: T 122 TRP cc_start: 0.8963 (m-10) cc_final: 0.8615 (m-10) REVERT: T 206 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8412 (mm-30) REVERT: T 228 MET cc_start: 0.9039 (ppp) cc_final: 0.8500 (ppp) REVERT: T 253 ASN cc_start: 0.9579 (m-40) cc_final: 0.9213 (m110) REVERT: T 264 MET cc_start: 0.9688 (mmm) cc_final: 0.9365 (mmm) REVERT: T 277 TYR cc_start: 0.8829 (m-80) cc_final: 0.8427 (m-80) REVERT: Z 85 GLU cc_start: 0.9267 (tt0) cc_final: 0.8577 (tm-30) REVERT: Z 95 PHE cc_start: 0.9418 (m-10) cc_final: 0.8982 (m-80) REVERT: Z 228 MET cc_start: 0.7196 (ttt) cc_final: 0.6788 (ttt) REVERT: Z 264 MET cc_start: 0.9431 (mmt) cc_final: 0.8930 (tpp) REVERT: Z 277 TYR cc_start: 0.8875 (m-80) cc_final: 0.8564 (m-80) REVERT: Z 282 PHE cc_start: 0.9344 (t80) cc_final: 0.8987 (t80) REVERT: Z 286 ILE cc_start: 0.9634 (pt) cc_final: 0.9315 (pt) REVERT: Z 296 TYR cc_start: 0.9050 (t80) cc_final: 0.8837 (t80) outliers start: 51 outliers final: 31 residues processed: 420 average time/residue: 0.1624 time to fit residues: 102.1832 Evaluate side-chains 398 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 364 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 37 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 109 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN J 33 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.070537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057918 restraints weight = 45013.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058948 restraints weight = 32159.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059958 restraints weight = 25607.241| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9568 Z= 0.160 Angle : 0.731 9.562 13062 Z= 0.374 Chirality : 0.049 0.268 1642 Planarity : 0.004 0.049 1666 Dihedral : 4.152 25.091 1393 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.95 % Allowed : 36.93 % Favored : 57.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1325 helix: 1.15 (0.16), residues: 1055 sheet: None (None), residues: 0 loop : -1.84 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.025 0.001 PHE Z 202 TYR 0.016 0.002 TYR L 48 ARG 0.004 0.000 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 874) hydrogen bonds : angle 4.40103 ( 2607) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.39054 ( 2) covalent geometry : bond 0.00353 ( 9567) covalent geometry : angle 0.73094 (13060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 386 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9313 (ttm110) cc_final: 0.8940 (ttm110) REVERT: H 62 PHE cc_start: 0.9177 (m-80) cc_final: 0.8834 (m-80) REVERT: I 15 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8356 (tp) REVERT: I 49 MET cc_start: 0.9552 (ttt) cc_final: 0.9127 (ppp) REVERT: I 55 PHE cc_start: 0.9454 (m-80) cc_final: 0.9247 (m-80) REVERT: I 57 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8833 (mp0) REVERT: I 68 PHE cc_start: 0.9145 (m-80) cc_final: 0.8655 (m-80) REVERT: J 40 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8021 (mp0) REVERT: J 44 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7499 (ttt90) REVERT: J 48 TYR cc_start: 0.9286 (m-80) cc_final: 0.8708 (m-80) REVERT: J 49 MET cc_start: 0.9617 (ppp) cc_final: 0.9102 (ppp) REVERT: J 57 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8774 (mt-10) REVERT: K 33 GLN cc_start: 0.9315 (mm-40) cc_final: 0.9090 (mm-40) REVERT: K 48 TYR cc_start: 0.9257 (m-80) cc_final: 0.8215 (m-80) REVERT: K 57 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9173 (mm-30) REVERT: K 62 PHE cc_start: 0.9447 (m-80) cc_final: 0.9029 (m-80) REVERT: L 43 ASN cc_start: 0.8680 (t0) cc_final: 0.8232 (m-40) REVERT: M 33 GLN cc_start: 0.9363 (mm110) cc_final: 0.9136 (mm110) REVERT: M 46 VAL cc_start: 0.9424 (t) cc_final: 0.9176 (t) REVERT: M 49 MET cc_start: 0.9387 (ppp) cc_final: 0.9089 (ppp) REVERT: M 50 PHE cc_start: 0.9219 (m-80) cc_final: 0.8628 (m-80) REVERT: N 48 TYR cc_start: 0.9323 (m-80) cc_final: 0.8696 (m-80) REVERT: N 55 PHE cc_start: 0.9444 (m-80) cc_final: 0.9150 (m-80) REVERT: N 64 LEU cc_start: 0.9782 (tp) cc_final: 0.9582 (tt) REVERT: O 29 SER cc_start: 0.9545 (t) cc_final: 0.9206 (p) REVERT: O 37 ARG cc_start: 0.9052 (mmt90) cc_final: 0.8676 (mtm180) REVERT: O 44 ARG cc_start: 0.8383 (mmm-85) cc_final: 0.7461 (mmm-85) REVERT: O 48 TYR cc_start: 0.8941 (m-80) cc_final: 0.8315 (m-80) REVERT: O 49 MET cc_start: 0.9479 (ttp) cc_final: 0.8796 (tmm) REVERT: O 57 GLU cc_start: 0.9196 (pt0) cc_final: 0.8926 (pp20) REVERT: O 62 PHE cc_start: 0.9097 (m-80) cc_final: 0.8749 (m-80) REVERT: O 66 ILE cc_start: 0.9557 (mm) cc_final: 0.9251 (mm) REVERT: P 37 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7886 (ttm170) REVERT: P 42 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9023 (tt0) REVERT: P 43 ASN cc_start: 0.9424 (p0) cc_final: 0.9207 (p0) REVERT: P 48 TYR cc_start: 0.9218 (m-80) cc_final: 0.8960 (m-80) REVERT: P 57 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8652 (pt0) REVERT: Q 28 VAL cc_start: 0.9791 (t) cc_final: 0.9587 (m) REVERT: Q 37 ARG cc_start: 0.8720 (mmp80) cc_final: 0.8154 (mmm160) REVERT: Q 57 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: T 84 MET cc_start: 0.9064 (mmm) cc_final: 0.8435 (mpp) REVERT: T 122 TRP cc_start: 0.8945 (m-10) cc_final: 0.8600 (m-10) REVERT: T 206 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8436 (mm-30) REVERT: T 228 MET cc_start: 0.9058 (ppp) cc_final: 0.8798 (ppp) REVERT: T 239 GLU cc_start: 0.9733 (tp30) cc_final: 0.9380 (tp30) REVERT: T 253 ASN cc_start: 0.9527 (m-40) cc_final: 0.9280 (m110) REVERT: T 264 MET cc_start: 0.9697 (mmm) cc_final: 0.9402 (mmm) REVERT: T 277 TYR cc_start: 0.8808 (m-80) cc_final: 0.8428 (m-80) REVERT: Z 85 GLU cc_start: 0.9271 (tt0) cc_final: 0.8586 (tm-30) REVERT: Z 95 PHE cc_start: 0.9402 (m-10) cc_final: 0.8967 (m-80) REVERT: Z 228 MET cc_start: 0.7271 (ttt) cc_final: 0.6849 (ttt) REVERT: Z 264 MET cc_start: 0.9454 (mmt) cc_final: 0.8982 (tpp) REVERT: Z 277 TYR cc_start: 0.8917 (m-80) cc_final: 0.8564 (m-80) REVERT: Z 282 PHE cc_start: 0.9355 (t80) cc_final: 0.9034 (t80) REVERT: Z 286 ILE cc_start: 0.9652 (pt) cc_final: 0.9307 (pt) REVERT: Z 296 TYR cc_start: 0.8987 (t80) cc_final: 0.8766 (t80) outliers start: 48 outliers final: 39 residues processed: 411 average time/residue: 0.1692 time to fit residues: 104.3099 Evaluate side-chains 405 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 362 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.070662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057942 restraints weight = 45305.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059172 restraints weight = 32351.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059909 restraints weight = 25262.176| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9568 Z= 0.163 Angle : 0.753 11.985 13062 Z= 0.385 Chirality : 0.051 0.490 1642 Planarity : 0.004 0.049 1666 Dihedral : 4.201 24.936 1393 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.95 % Allowed : 38.91 % Favored : 55.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1325 helix: 1.11 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -1.63 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.035 0.001 PHE Z 202 TYR 0.016 0.001 TYR T 102 ARG 0.003 0.000 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 874) hydrogen bonds : angle 4.42999 ( 2607) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.33572 ( 2) covalent geometry : bond 0.00359 ( 9567) covalent geometry : angle 0.75323 (13060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 389 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9289 (ttm110) cc_final: 0.9062 (ttm110) REVERT: H 48 TYR cc_start: 0.9028 (m-80) cc_final: 0.8768 (m-80) REVERT: H 62 PHE cc_start: 0.9250 (m-80) cc_final: 0.8881 (m-80) REVERT: I 15 LEU cc_start: 0.9276 (mm) cc_final: 0.8262 (tp) REVERT: I 48 TYR cc_start: 0.9363 (m-80) cc_final: 0.9085 (m-80) REVERT: I 49 MET cc_start: 0.9565 (OUTLIER) cc_final: 0.9016 (tmm) REVERT: I 55 PHE cc_start: 0.9452 (m-80) cc_final: 0.9252 (m-80) REVERT: I 57 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.8814 (mp0) REVERT: I 68 PHE cc_start: 0.9161 (m-80) cc_final: 0.8730 (m-80) REVERT: J 40 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8000 (mp0) REVERT: J 44 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7655 (mmm-85) REVERT: J 48 TYR cc_start: 0.9289 (m-80) cc_final: 0.8676 (m-80) REVERT: J 49 MET cc_start: 0.9615 (ppp) cc_final: 0.9092 (ppp) REVERT: J 57 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8903 (mt-10) REVERT: K 42 GLU cc_start: 0.9201 (pm20) cc_final: 0.8957 (pm20) REVERT: K 48 TYR cc_start: 0.9244 (m-80) cc_final: 0.8191 (m-80) REVERT: K 49 MET cc_start: 0.9579 (ppp) cc_final: 0.9187 (ppp) REVERT: K 53 ILE cc_start: 0.9689 (mt) cc_final: 0.9428 (mt) REVERT: K 57 GLU cc_start: 0.9601 (mm-30) cc_final: 0.9104 (mm-30) REVERT: L 29 SER cc_start: 0.9435 (t) cc_final: 0.9182 (p) REVERT: L 43 ASN cc_start: 0.8643 (t0) cc_final: 0.8245 (m-40) REVERT: M 33 GLN cc_start: 0.9352 (mm110) cc_final: 0.8877 (mm-40) REVERT: M 46 VAL cc_start: 0.9377 (t) cc_final: 0.9170 (t) REVERT: M 48 TYR cc_start: 0.9411 (m-80) cc_final: 0.9156 (m-80) REVERT: M 49 MET cc_start: 0.9358 (ppp) cc_final: 0.9001 (ppp) REVERT: M 50 PHE cc_start: 0.9233 (m-80) cc_final: 0.8624 (m-80) REVERT: N 48 TYR cc_start: 0.9379 (m-80) cc_final: 0.8761 (m-80) REVERT: N 55 PHE cc_start: 0.9464 (m-80) cc_final: 0.9115 (m-80) REVERT: O 29 SER cc_start: 0.9542 (t) cc_final: 0.9211 (p) REVERT: O 37 ARG cc_start: 0.9014 (mmt90) cc_final: 0.8611 (mtm180) REVERT: O 44 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.7426 (mmm-85) REVERT: O 48 TYR cc_start: 0.8950 (m-80) cc_final: 0.8357 (m-80) REVERT: O 49 MET cc_start: 0.9482 (ttp) cc_final: 0.8776 (tmm) REVERT: O 57 GLU cc_start: 0.9215 (pt0) cc_final: 0.8932 (pp20) REVERT: O 62 PHE cc_start: 0.9116 (m-80) cc_final: 0.8764 (m-80) REVERT: O 66 ILE cc_start: 0.9533 (mm) cc_final: 0.9218 (mm) REVERT: P 37 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7723 (ttm170) REVERT: P 43 ASN cc_start: 0.9445 (p0) cc_final: 0.9190 (p0) REVERT: Q 28 VAL cc_start: 0.9814 (t) cc_final: 0.9591 (m) REVERT: Q 37 ARG cc_start: 0.8701 (mmp80) cc_final: 0.8230 (mmm160) REVERT: Q 57 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: Q 61 ILE cc_start: 0.9076 (pt) cc_final: 0.8803 (pt) REVERT: T 84 MET cc_start: 0.9052 (mmm) cc_final: 0.8429 (mpp) REVERT: T 85 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7957 (pp20) REVERT: T 122 TRP cc_start: 0.8953 (m-10) cc_final: 0.8616 (m-10) REVERT: T 206 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8433 (mm-30) REVERT: T 228 MET cc_start: 0.9021 (ppp) cc_final: 0.8763 (ppp) REVERT: T 253 ASN cc_start: 0.9583 (m-40) cc_final: 0.9222 (m110) REVERT: T 264 MET cc_start: 0.9689 (mmm) cc_final: 0.9417 (mmm) REVERT: T 277 TYR cc_start: 0.8811 (m-80) cc_final: 0.8431 (m-80) REVERT: Z 85 GLU cc_start: 0.9277 (tt0) cc_final: 0.8602 (tm-30) REVERT: Z 95 PHE cc_start: 0.9398 (m-10) cc_final: 0.8949 (m-80) REVERT: Z 228 MET cc_start: 0.7334 (ttt) cc_final: 0.6879 (ttt) REVERT: Z 242 LYS cc_start: 0.9441 (mttt) cc_final: 0.9184 (mtpp) REVERT: Z 264 MET cc_start: 0.9431 (mmt) cc_final: 0.8917 (tpp) REVERT: Z 277 TYR cc_start: 0.8918 (m-80) cc_final: 0.8552 (m-80) REVERT: Z 282 PHE cc_start: 0.9356 (t80) cc_final: 0.9047 (t80) REVERT: Z 286 ILE cc_start: 0.9658 (pt) cc_final: 0.9289 (pt) REVERT: Z 296 TYR cc_start: 0.8961 (t80) cc_final: 0.8738 (t80) outliers start: 48 outliers final: 38 residues processed: 412 average time/residue: 0.1572 time to fit residues: 96.2481 Evaluate side-chains 413 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 370 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.070556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057722 restraints weight = 45725.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058823 restraints weight = 32314.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059854 restraints weight = 25348.407| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9568 Z= 0.166 Angle : 0.791 14.812 13062 Z= 0.399 Chirality : 0.051 0.295 1642 Planarity : 0.004 0.049 1666 Dihedral : 4.239 24.983 1393 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.70 % Allowed : 42.38 % Favored : 51.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1325 helix: 1.21 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.62 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.031 0.001 PHE Z 202 TYR 0.014 0.001 TYR N 48 ARG 0.008 0.001 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 874) hydrogen bonds : angle 4.41613 ( 2607) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.32190 ( 2) covalent geometry : bond 0.00377 ( 9567) covalent geometry : angle 0.79060 (13060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 384 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9300 (ttm110) cc_final: 0.9077 (ttm110) REVERT: H 48 TYR cc_start: 0.9115 (m-80) cc_final: 0.8799 (m-80) REVERT: H 62 PHE cc_start: 0.9213 (m-10) cc_final: 0.8960 (m-80) REVERT: I 15 LEU cc_start: 0.9230 (mm) cc_final: 0.8282 (tp) REVERT: I 48 TYR cc_start: 0.9374 (m-80) cc_final: 0.8990 (m-80) REVERT: I 49 MET cc_start: 0.9567 (OUTLIER) cc_final: 0.9032 (tmm) REVERT: I 55 PHE cc_start: 0.9431 (m-80) cc_final: 0.9180 (m-80) REVERT: I 57 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8865 (mp0) REVERT: I 68 PHE cc_start: 0.9201 (m-80) cc_final: 0.8725 (m-80) REVERT: J 40 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8159 (mp0) REVERT: J 44 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7362 (ttt90) REVERT: J 48 TYR cc_start: 0.9279 (m-80) cc_final: 0.8744 (m-80) REVERT: J 49 MET cc_start: 0.9613 (ppp) cc_final: 0.9111 (ppp) REVERT: J 57 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8816 (mt-10) REVERT: K 15 LEU cc_start: 0.9168 (mm) cc_final: 0.8924 (mm) REVERT: K 48 TYR cc_start: 0.9274 (m-80) cc_final: 0.8155 (m-80) REVERT: K 49 MET cc_start: 0.9574 (ppp) cc_final: 0.9354 (ppp) REVERT: K 57 GLU cc_start: 0.9630 (mm-30) cc_final: 0.9095 (mm-30) REVERT: L 29 SER cc_start: 0.9539 (t) cc_final: 0.9206 (p) REVERT: L 43 ASN cc_start: 0.8656 (t0) cc_final: 0.8243 (m110) REVERT: M 33 GLN cc_start: 0.9409 (mm110) cc_final: 0.8883 (mm110) REVERT: M 48 TYR cc_start: 0.9407 (m-80) cc_final: 0.9097 (m-80) REVERT: M 49 MET cc_start: 0.9371 (ppp) cc_final: 0.9054 (ppp) REVERT: M 50 PHE cc_start: 0.9220 (m-80) cc_final: 0.8659 (m-80) REVERT: N 18 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7815 (tt) REVERT: N 24 ILE cc_start: 0.9594 (mt) cc_final: 0.9343 (mm) REVERT: N 48 TYR cc_start: 0.9385 (m-80) cc_final: 0.8812 (m-80) REVERT: N 55 PHE cc_start: 0.9485 (m-80) cc_final: 0.9111 (m-80) REVERT: O 29 SER cc_start: 0.9584 (t) cc_final: 0.9217 (p) REVERT: O 37 ARG cc_start: 0.8975 (mmt90) cc_final: 0.8654 (mtm180) REVERT: O 44 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7355 (mmm-85) REVERT: O 48 TYR cc_start: 0.8960 (m-80) cc_final: 0.8308 (m-80) REVERT: O 49 MET cc_start: 0.9498 (ttp) cc_final: 0.8824 (tmm) REVERT: O 57 GLU cc_start: 0.9183 (pt0) cc_final: 0.8898 (pp20) REVERT: O 62 PHE cc_start: 0.9132 (m-80) cc_final: 0.8760 (m-80) REVERT: O 66 ILE cc_start: 0.9534 (mm) cc_final: 0.9222 (mm) REVERT: P 37 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7682 (ttm170) REVERT: P 42 GLU cc_start: 0.9254 (mt-10) cc_final: 0.9002 (tt0) REVERT: P 43 ASN cc_start: 0.9447 (p0) cc_final: 0.9216 (p0) REVERT: P 48 TYR cc_start: 0.9179 (m-80) cc_final: 0.8877 (m-80) REVERT: P 57 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8666 (pt0) REVERT: Q 28 VAL cc_start: 0.9793 (t) cc_final: 0.9582 (m) REVERT: Q 37 ARG cc_start: 0.8686 (mmp80) cc_final: 0.8021 (mmm160) REVERT: Q 57 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: Q 61 ILE cc_start: 0.9064 (pt) cc_final: 0.8776 (pt) REVERT: T 122 TRP cc_start: 0.8949 (m-10) cc_final: 0.8743 (m-10) REVERT: T 206 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8442 (mm-30) REVERT: T 228 MET cc_start: 0.9048 (ppp) cc_final: 0.8801 (ppp) REVERT: T 253 ASN cc_start: 0.9562 (m-40) cc_final: 0.9285 (m110) REVERT: T 264 MET cc_start: 0.9693 (mmm) cc_final: 0.9417 (mmm) REVERT: T 277 TYR cc_start: 0.8825 (m-80) cc_final: 0.8423 (m-80) REVERT: Z 95 PHE cc_start: 0.9407 (m-10) cc_final: 0.8958 (m-80) REVERT: Z 228 MET cc_start: 0.7338 (ttt) cc_final: 0.6899 (ttt) REVERT: Z 242 LYS cc_start: 0.9420 (mttt) cc_final: 0.9179 (mtpp) REVERT: Z 249 ARG cc_start: 0.9348 (ttm110) cc_final: 0.8983 (ptp-110) REVERT: Z 264 MET cc_start: 0.9460 (mmt) cc_final: 0.8939 (tpp) REVERT: Z 277 TYR cc_start: 0.8921 (m-80) cc_final: 0.8587 (m-80) REVERT: Z 282 PHE cc_start: 0.9366 (t80) cc_final: 0.8866 (t80) REVERT: Z 286 ILE cc_start: 0.9655 (pt) cc_final: 0.9205 (pt) outliers start: 46 outliers final: 35 residues processed: 405 average time/residue: 0.1563 time to fit residues: 94.0715 Evaluate side-chains 408 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 368 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN K 33 GLN ** Z 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057818 restraints weight = 46188.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059051 restraints weight = 32344.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059986 restraints weight = 25003.235| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9568 Z= 0.167 Angle : 0.801 13.374 13062 Z= 0.408 Chirality : 0.052 0.275 1642 Planarity : 0.005 0.049 1666 Dihedral : 4.267 25.018 1393 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.58 % Allowed : 43.25 % Favored : 51.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1325 helix: 1.12 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.55 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.031 0.001 PHE Z 202 TYR 0.022 0.001 TYR N 48 ARG 0.006 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 874) hydrogen bonds : angle 4.44803 ( 2607) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.29655 ( 2) covalent geometry : bond 0.00376 ( 9567) covalent geometry : angle 0.80124 (13060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 386 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9292 (ttm110) cc_final: 0.9064 (ttm110) REVERT: H 48 TYR cc_start: 0.9110 (m-80) cc_final: 0.8790 (m-80) REVERT: H 62 PHE cc_start: 0.9269 (m-10) cc_final: 0.9026 (m-80) REVERT: I 15 LEU cc_start: 0.9307 (mm) cc_final: 0.8373 (tp) REVERT: I 48 TYR cc_start: 0.9373 (m-80) cc_final: 0.8971 (m-80) REVERT: I 49 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9060 (tmm) REVERT: I 55 PHE cc_start: 0.9420 (m-80) cc_final: 0.9149 (m-80) REVERT: I 57 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8812 (mp0) REVERT: I 68 PHE cc_start: 0.9197 (m-80) cc_final: 0.8719 (m-80) REVERT: J 18 ILE cc_start: 0.8396 (tp) cc_final: 0.8040 (tp) REVERT: J 40 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8173 (mp0) REVERT: J 44 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7164 (ttt-90) REVERT: J 48 TYR cc_start: 0.9305 (m-80) cc_final: 0.8732 (m-80) REVERT: J 49 MET cc_start: 0.9615 (ppp) cc_final: 0.9122 (ppp) REVERT: J 57 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8698 (mt-10) REVERT: K 15 LEU cc_start: 0.9134 (mm) cc_final: 0.8890 (mm) REVERT: K 48 TYR cc_start: 0.9261 (m-80) cc_final: 0.8157 (m-80) REVERT: K 57 GLU cc_start: 0.9644 (mm-30) cc_final: 0.9072 (mm-30) REVERT: L 43 ASN cc_start: 0.8665 (t0) cc_final: 0.8297 (m110) REVERT: M 33 GLN cc_start: 0.9408 (mm110) cc_final: 0.8895 (mm110) REVERT: M 48 TYR cc_start: 0.9429 (m-80) cc_final: 0.9062 (m-80) REVERT: M 49 MET cc_start: 0.9364 (ppp) cc_final: 0.8992 (ppp) REVERT: M 50 PHE cc_start: 0.9213 (m-80) cc_final: 0.8521 (m-80) REVERT: N 18 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7822 (tt) REVERT: N 24 ILE cc_start: 0.9616 (mt) cc_final: 0.9367 (mm) REVERT: N 48 TYR cc_start: 0.9431 (m-80) cc_final: 0.8753 (m-80) REVERT: N 55 PHE cc_start: 0.9461 (m-80) cc_final: 0.9112 (m-80) REVERT: O 29 SER cc_start: 0.9547 (t) cc_final: 0.9212 (p) REVERT: O 37 ARG cc_start: 0.8979 (mmt90) cc_final: 0.8637 (mtm180) REVERT: O 44 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7330 (mmm-85) REVERT: O 48 TYR cc_start: 0.8954 (m-80) cc_final: 0.8311 (m-80) REVERT: O 57 GLU cc_start: 0.9162 (pt0) cc_final: 0.8774 (pp20) REVERT: O 62 PHE cc_start: 0.9137 (m-80) cc_final: 0.8767 (m-80) REVERT: O 66 ILE cc_start: 0.9538 (mm) cc_final: 0.9232 (mm) REVERT: P 37 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7724 (ttm170) REVERT: P 42 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9019 (tt0) REVERT: P 43 ASN cc_start: 0.9455 (p0) cc_final: 0.9218 (p0) REVERT: P 57 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8625 (pt0) REVERT: Q 28 VAL cc_start: 0.9780 (t) cc_final: 0.9579 (m) REVERT: Q 37 ARG cc_start: 0.8686 (mmp80) cc_final: 0.7998 (mmm160) REVERT: Q 57 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: Q 61 ILE cc_start: 0.9089 (pt) cc_final: 0.8777 (pt) REVERT: T 122 TRP cc_start: 0.8974 (m-10) cc_final: 0.8750 (m-10) REVERT: T 206 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8485 (mm-30) REVERT: T 228 MET cc_start: 0.9044 (ppp) cc_final: 0.8802 (ppp) REVERT: T 253 ASN cc_start: 0.9571 (m-40) cc_final: 0.9188 (m110) REVERT: T 264 MET cc_start: 0.9687 (mmm) cc_final: 0.9440 (mmm) REVERT: T 277 TYR cc_start: 0.8830 (m-80) cc_final: 0.8434 (m-80) REVERT: Z 74 GLN cc_start: 0.9072 (tp40) cc_final: 0.8718 (mp10) REVERT: Z 85 GLU cc_start: 0.9201 (tt0) cc_final: 0.8631 (tm-30) REVERT: Z 95 PHE cc_start: 0.9418 (m-10) cc_final: 0.9000 (m-80) REVERT: Z 202 PHE cc_start: 0.9139 (t80) cc_final: 0.8832 (m-80) REVERT: Z 228 MET cc_start: 0.7330 (ttt) cc_final: 0.6889 (ttt) REVERT: Z 242 LYS cc_start: 0.9429 (mttt) cc_final: 0.9177 (mtpp) REVERT: Z 249 ARG cc_start: 0.9309 (ttm110) cc_final: 0.8854 (ptp-110) REVERT: Z 264 MET cc_start: 0.9446 (mmt) cc_final: 0.8935 (tpp) REVERT: Z 277 TYR cc_start: 0.8925 (m-80) cc_final: 0.8536 (m-80) REVERT: Z 282 PHE cc_start: 0.9345 (t80) cc_final: 0.8903 (t80) outliers start: 45 outliers final: 35 residues processed: 406 average time/residue: 0.1663 time to fit residues: 99.5652 Evaluate side-chains 412 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 372 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain Q residue 40 GLU Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 74 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 = 0.3448 r_free = 0.3448 target = 0.071058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058144 restraints weight = 45600.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059344 restraints weight = 32736.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060124 restraints weight = 25602.541| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9568 Z= 0.176 Angle : 0.849 13.168 13062 Z= 0.429 Chirality : 0.054 0.343 1642 Planarity : 0.005 0.049 1666 Dihedral : 4.303 24.920 1393 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.95 % Allowed : 44.24 % Favored : 49.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1325 helix: 1.04 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.030 0.001 PHE Z 202 TYR 0.017 0.001 TYR P 48 ARG 0.009 0.001 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 874) hydrogen bonds : angle 4.52246 ( 2607) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.28186 ( 2) covalent geometry : bond 0.00410 ( 9567) covalent geometry : angle 0.84865 (13060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 380 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9281 (ttm110) cc_final: 0.9064 (ttm110) REVERT: H 48 TYR cc_start: 0.9115 (m-80) cc_final: 0.8760 (m-80) REVERT: I 15 LEU cc_start: 0.9318 (mm) cc_final: 0.8388 (tp) REVERT: I 48 TYR cc_start: 0.9362 (m-80) cc_final: 0.9107 (m-80) REVERT: I 49 MET cc_start: 0.9560 (OUTLIER) cc_final: 0.9073 (tmm) REVERT: I 57 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.8845 (mp0) REVERT: I 68 PHE cc_start: 0.9145 (m-80) cc_final: 0.8660 (m-80) REVERT: J 18 ILE cc_start: 0.8469 (tp) cc_final: 0.8130 (tp) REVERT: J 40 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8235 (mp0) REVERT: J 44 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6597 (ttt-90) REVERT: J 48 TYR cc_start: 0.9299 (m-80) cc_final: 0.8547 (m-80) REVERT: J 49 MET cc_start: 0.9599 (ppp) cc_final: 0.9122 (ppp) REVERT: K 48 TYR cc_start: 0.9247 (m-80) cc_final: 0.8178 (m-80) REVERT: K 49 MET cc_start: 0.9472 (ppp) cc_final: 0.9035 (ppp) REVERT: K 57 GLU cc_start: 0.9667 (mm-30) cc_final: 0.9106 (mm-30) REVERT: L 43 ASN cc_start: 0.8604 (t0) cc_final: 0.8247 (m110) REVERT: M 33 GLN cc_start: 0.9459 (mm110) cc_final: 0.8934 (mm110) REVERT: M 48 TYR cc_start: 0.9407 (m-80) cc_final: 0.9011 (m-80) REVERT: M 49 MET cc_start: 0.9349 (ppp) cc_final: 0.8946 (ppp) REVERT: M 50 PHE cc_start: 0.9167 (m-80) cc_final: 0.8458 (m-80) REVERT: N 24 ILE cc_start: 0.9606 (mt) cc_final: 0.9381 (mm) REVERT: N 48 TYR cc_start: 0.9417 (m-80) cc_final: 0.8764 (m-80) REVERT: N 55 PHE cc_start: 0.9469 (m-80) cc_final: 0.9139 (m-80) REVERT: O 29 SER cc_start: 0.9541 (t) cc_final: 0.9198 (p) REVERT: O 37 ARG cc_start: 0.8932 (mmt90) cc_final: 0.8623 (mtm180) REVERT: O 44 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7173 (mmm-85) REVERT: O 48 TYR cc_start: 0.8905 (m-80) cc_final: 0.8262 (m-80) REVERT: O 49 MET cc_start: 0.9437 (ttp) cc_final: 0.9004 (ppp) REVERT: O 57 GLU cc_start: 0.9169 (pt0) cc_final: 0.8793 (pp20) REVERT: O 62 PHE cc_start: 0.9143 (m-80) cc_final: 0.8765 (m-80) REVERT: O 66 ILE cc_start: 0.9544 (mm) cc_final: 0.9241 (mm) REVERT: P 37 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7731 (ttm170) REVERT: P 42 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8977 (tt0) REVERT: P 43 ASN cc_start: 0.9458 (p0) cc_final: 0.9226 (p0) REVERT: P 57 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8739 (pt0) REVERT: Q 37 ARG cc_start: 0.8652 (mmp80) cc_final: 0.7971 (mmm160) REVERT: Q 57 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: Q 61 ILE cc_start: 0.9084 (pt) cc_final: 0.8799 (pt) REVERT: T 122 TRP cc_start: 0.8944 (m-10) cc_final: 0.8717 (m-10) REVERT: T 206 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8483 (mm-30) REVERT: T 228 MET cc_start: 0.9037 (ppp) cc_final: 0.8812 (ppp) REVERT: T 253 ASN cc_start: 0.9553 (m-40) cc_final: 0.9233 (m110) REVERT: T 264 MET cc_start: 0.9681 (mmm) cc_final: 0.9440 (mmm) REVERT: T 277 TYR cc_start: 0.8827 (m-80) cc_final: 0.8461 (m-80) REVERT: Z 74 GLN cc_start: 0.9074 (tp40) cc_final: 0.8712 (mp10) REVERT: Z 85 GLU cc_start: 0.9164 (tt0) cc_final: 0.8530 (tm-30) REVERT: Z 95 PHE cc_start: 0.9437 (m-10) cc_final: 0.8989 (m-80) REVERT: Z 228 MET cc_start: 0.7324 (ttt) cc_final: 0.6876 (ttt) REVERT: Z 242 LYS cc_start: 0.9440 (mttt) cc_final: 0.9184 (mtpp) REVERT: Z 264 MET cc_start: 0.9439 (mmt) cc_final: 0.8934 (tpp) REVERT: Z 277 TYR cc_start: 0.8959 (m-80) cc_final: 0.8554 (m-80) REVERT: Z 282 PHE cc_start: 0.9350 (t80) cc_final: 0.9021 (t80) REVERT: Z 286 ILE cc_start: 0.9607 (pt) cc_final: 0.9256 (pt) outliers start: 48 outliers final: 39 residues processed: 401 average time/residue: 0.1634 time to fit residues: 97.2169 Evaluate side-chains 415 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 372 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 84 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Z 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.071516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058481 restraints weight = 45790.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059740 restraints weight = 32331.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.060711 restraints weight = 25149.866| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9568 Z= 0.174 Angle : 0.873 13.067 13062 Z= 0.440 Chirality : 0.054 0.317 1642 Planarity : 0.005 0.048 1666 Dihedral : 4.336 24.997 1393 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.70 % Allowed : 44.36 % Favored : 49.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1325 helix: 1.07 (0.16), residues: 1048 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.032 0.001 PHE Z 202 TYR 0.015 0.001 TYR N 48 ARG 0.010 0.001 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 874) hydrogen bonds : angle 4.52893 ( 2607) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.24553 ( 2) covalent geometry : bond 0.00402 ( 9567) covalent geometry : angle 0.87309 (13060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 382 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 TYR cc_start: 0.9155 (m-80) cc_final: 0.8767 (m-80) REVERT: H 62 PHE cc_start: 0.9332 (m-80) cc_final: 0.8902 (m-80) REVERT: I 15 LEU cc_start: 0.9318 (mm) cc_final: 0.8398 (tp) REVERT: I 48 TYR cc_start: 0.9378 (m-80) cc_final: 0.9055 (m-80) REVERT: I 49 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9062 (tmm) REVERT: I 57 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8815 (mp0) REVERT: I 68 PHE cc_start: 0.9138 (m-80) cc_final: 0.8637 (m-80) REVERT: J 18 ILE cc_start: 0.8489 (tp) cc_final: 0.8150 (tp) REVERT: J 40 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8244 (mp0) REVERT: J 44 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6628 (ttt-90) REVERT: J 48 TYR cc_start: 0.9286 (m-80) cc_final: 0.8568 (m-80) REVERT: J 49 MET cc_start: 0.9595 (ppp) cc_final: 0.9113 (ppp) REVERT: K 15 LEU cc_start: 0.9202 (mm) cc_final: 0.8930 (mm) REVERT: K 48 TYR cc_start: 0.9266 (m-80) cc_final: 0.8186 (m-80) REVERT: K 49 MET cc_start: 0.9523 (ppp) cc_final: 0.9087 (ppp) REVERT: K 57 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9106 (mm-30) REVERT: L 43 ASN cc_start: 0.8644 (t0) cc_final: 0.8292 (m110) REVERT: M 33 GLN cc_start: 0.9446 (mm110) cc_final: 0.8908 (mm110) REVERT: M 48 TYR cc_start: 0.9423 (m-80) cc_final: 0.9017 (m-80) REVERT: M 49 MET cc_start: 0.9360 (ppp) cc_final: 0.8965 (ppp) REVERT: M 50 PHE cc_start: 0.9188 (m-80) cc_final: 0.8499 (m-80) REVERT: N 18 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7824 (tt) REVERT: N 24 ILE cc_start: 0.9590 (mt) cc_final: 0.9349 (mm) REVERT: N 48 TYR cc_start: 0.9410 (m-80) cc_final: 0.8754 (m-80) REVERT: N 55 PHE cc_start: 0.9467 (m-80) cc_final: 0.9218 (m-80) REVERT: O 29 SER cc_start: 0.9530 (t) cc_final: 0.9181 (p) REVERT: O 37 ARG cc_start: 0.8945 (mmt90) cc_final: 0.8551 (mtm180) REVERT: O 44 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7169 (mmm-85) REVERT: O 48 TYR cc_start: 0.8922 (m-80) cc_final: 0.8271 (m-80) REVERT: O 49 MET cc_start: 0.9431 (ttp) cc_final: 0.9002 (ppp) REVERT: O 62 PHE cc_start: 0.9149 (m-80) cc_final: 0.8768 (m-80) REVERT: O 66 ILE cc_start: 0.9544 (mm) cc_final: 0.9240 (mm) REVERT: P 37 ARG cc_start: 0.8085 (ttm170) cc_final: 0.7647 (ttm170) REVERT: P 42 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8981 (tt0) REVERT: P 43 ASN cc_start: 0.9463 (p0) cc_final: 0.9238 (p0) REVERT: P 57 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8710 (pt0) REVERT: Q 37 ARG cc_start: 0.8646 (mmp80) cc_final: 0.8080 (mmm160) REVERT: Q 57 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: Q 61 ILE cc_start: 0.9063 (pt) cc_final: 0.8755 (pt) REVERT: Q 62 PHE cc_start: 0.9117 (m-80) cc_final: 0.8908 (m-80) REVERT: T 114 PHE cc_start: 0.9564 (t80) cc_final: 0.9325 (t80) REVERT: T 122 TRP cc_start: 0.8956 (m-10) cc_final: 0.8727 (m-10) REVERT: T 206 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8471 (mm-30) REVERT: T 228 MET cc_start: 0.9036 (ppp) cc_final: 0.8802 (ppp) REVERT: T 264 MET cc_start: 0.9683 (mmm) cc_final: 0.9445 (mmm) REVERT: T 277 TYR cc_start: 0.8826 (m-80) cc_final: 0.8453 (m-80) REVERT: Z 74 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8447 (tp40) REVERT: Z 85 GLU cc_start: 0.9182 (tt0) cc_final: 0.8550 (tm-30) REVERT: Z 95 PHE cc_start: 0.9432 (m-10) cc_final: 0.8981 (m-80) REVERT: Z 202 PHE cc_start: 0.9178 (t80) cc_final: 0.8879 (m-80) REVERT: Z 228 MET cc_start: 0.7374 (ttt) cc_final: 0.6974 (ttt) REVERT: Z 242 LYS cc_start: 0.9435 (mttt) cc_final: 0.9179 (mtpp) REVERT: Z 249 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (ptp90) REVERT: Z 264 MET cc_start: 0.9445 (mmt) cc_final: 0.8931 (tpp) REVERT: Z 277 TYR cc_start: 0.8911 (m-80) cc_final: 0.8547 (m-80) REVERT: Z 282 PHE cc_start: 0.9349 (t80) cc_final: 0.8879 (t80) REVERT: Z 286 ILE cc_start: 0.9625 (pt) cc_final: 0.9200 (pt) outliers start: 46 outliers final: 36 residues processed: 398 average time/residue: 0.1649 time to fit residues: 97.1319 Evaluate side-chains 420 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 378 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 251 PHE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 249 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 22 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.069450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056872 restraints weight = 46860.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057827 restraints weight = 32622.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058886 restraints weight = 26042.148| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 9568 Z= 0.223 Angle : 0.876 11.384 13062 Z= 0.452 Chirality : 0.054 0.313 1642 Planarity : 0.005 0.049 1666 Dihedral : 4.378 23.924 1393 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.95 % Allowed : 44.61 % Favored : 49.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1325 helix: 0.96 (0.16), residues: 1066 sheet: None (None), residues: 0 loop : -1.84 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.028 0.002 PHE Z 202 TYR 0.017 0.002 TYR M 48 ARG 0.012 0.001 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 874) hydrogen bonds : angle 4.68946 ( 2607) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.38750 ( 2) covalent geometry : bond 0.00507 ( 9567) covalent geometry : angle 0.87560 (13060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.18 seconds wall clock time: 56 minutes 23.62 seconds (3383.62 seconds total)