Starting phenix.real_space_refine on Wed Feb 4 06:56:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itq_60875/02_2026/9itq_60875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itq_60875/02_2026/9itq_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 { model { file = "/net/cci-nas-00/data/ceres_data/9itq_60875/02_2026/9itq_60875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itq_60875/02_2026/9itq_60875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itq_60875/02_2026/9itq_60875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itq_60875/02_2026/9itq_60875.map" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 3} 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: {'ASN:plan1': 4, 'PHE:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 2} 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: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} 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: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 1} 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: {'ARG:plan': 3, 'PHE:plan': 7, 'TYR:plan': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2} 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: {'ARG:plan': 1, 'PHE:plan': 4, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 2.12, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 318.3 milliseconds 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: 0.22 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: 1.49 Time building geometry restraints manager: 1.03 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: 5.660 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.270 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG N 44 TYR 0.009 0.001 TYR T 277 PHE 0.015 0.001 PHE N 68 TRP 0.005 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9567) covalent geometry : angle 0.61449 (13060) SS BOND : bond 0.87785 ( 1) SS BOND : angle 19.67063 ( 2) hydrogen bonds : bond 0.13857 ( 874) hydrogen bonds : angle 5.57961 ( 2607) *********************** 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 : 0.329 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: 0.9293 (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: 0.9065 (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: 0.8874 (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: 0.9013 (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: 0.8698 (mmp80) cc_final: 0.8104 (mmm160) REVERT: Q 43 ASN cc_start: 0.9252 (p0) cc_final: 0.8463 (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: 0.0578 time to fit residues: 40.8637 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 : 0.313 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.057030 restraints weight = 45798.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.058162 restraints weight = 31275.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059165 restraints weight = 24168.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.059985 restraints weight = 19637.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060448 restraints weight = 16586.849| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9568 Z= 0.182 Angle : 0.702 11.195 13062 Z= 0.367 Chirality : 0.047 0.306 1642 Planarity : 0.005 0.068 1666 Dihedral : 4.139 30.945 1397 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.96 % Allowed : 29.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.23), residues: 1325 helix: 1.28 (0.15), residues: 1061 sheet: None (None), residues: 0 loop : -1.96 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 96 TYR 0.021 0.002 TYR M 48 PHE 0.023 0.001 PHE Z 202 TRP 0.007 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9567) covalent geometry : angle 0.70178 (13060) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.16767 ( 2) hydrogen bonds : bond 0.05230 ( 874) hydrogen bonds : angle 4.50625 ( 2607) *********************** 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 446 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 406 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9332 (ttm110) cc_final: 0.9045 (ttm110) REVERT: H 57 GLU cc_start: 0.9083 (tp30) cc_final: 0.8662 (tp30) REVERT: H 59 LEU cc_start: 0.9761 (mm) cc_final: 0.9540 (mp) REVERT: H 61 ILE cc_start: 0.9719 (mm) cc_final: 0.9390 (mm) REVERT: H 62 PHE cc_start: 0.9265 (m-80) cc_final: 0.8763 (m-80) REVERT: I 46 VAL cc_start: 0.9331 (t) cc_final: 0.9085 (p) REVERT: I 49 MET cc_start: 0.9623 (ttt) cc_final: 0.8964 (tmm) REVERT: I 59 LEU cc_start: 0.9626 (mp) cc_final: 0.9187 (mp) REVERT: I 68 PHE cc_start: 0.9072 (m-80) cc_final: 0.8603 (m-80) REVERT: J 40 GLU cc_start: 0.8666 (mm-30) cc_final: 0.7920 (mp0) REVERT: J 48 TYR cc_start: 0.9289 (m-80) cc_final: 0.8595 (m-80) REVERT: J 49 MET cc_start: 0.9626 (ppp) cc_final: 0.9097 (ppp) REVERT: J 57 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8763 (mt-10) REVERT: K 33 GLN cc_start: 0.9310 (mm-40) cc_final: 0.9072 (mm-40) REVERT: K 48 TYR cc_start: 0.9307 (m-80) cc_final: 0.8375 (m-80) REVERT: K 49 MET cc_start: 0.9566 (tmm) cc_final: 0.9065 (tmm) REVERT: K 62 PHE cc_start: 0.9483 (m-10) cc_final: 0.9215 (m-80) REVERT: M 32 VAL cc_start: 0.9879 (t) cc_final: 0.9642 (p) REVERT: M 46 VAL cc_start: 0.9515 (t) cc_final: 0.9182 (t) REVERT: M 49 MET cc_start: 0.9353 (ttp) cc_final: 0.9126 (ppp) REVERT: M 50 PHE cc_start: 0.9127 (m-80) cc_final: 0.8603 (m-80) REVERT: M 66 ILE cc_start: 0.9673 (mm) cc_final: 0.9392 (tt) REVERT: N 48 TYR cc_start: 0.9347 (m-80) cc_final: 0.8709 (m-80) REVERT: N 55 PHE cc_start: 0.9424 (m-80) cc_final: 0.9204 (m-80) REVERT: N 57 GLU cc_start: 0.9469 (mm-30) cc_final: 0.8994 (tm-30) REVERT: O 29 SER cc_start: 0.9663 (t) cc_final: 0.9313 (p) REVERT: O 49 MET cc_start: 0.9472 (ttp) cc_final: 0.8814 (tmm) REVERT: O 62 PHE cc_start: 0.9065 (m-80) cc_final: 0.8712 (m-80) REVERT: O 66 ILE cc_start: 0.9490 (mm) cc_final: 0.9250 (mm) REVERT: P 43 ASN cc_start: 0.9365 (p0) cc_final: 0.9147 (p0) REVERT: P 49 MET cc_start: 0.9400 (tpt) cc_final: 0.9193 (tpt) REVERT: P 57 GLU cc_start: 0.9542 (tp30) cc_final: 0.8964 (mm-30) REVERT: Q 37 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8000 (mmm160) REVERT: Q 38 ASN cc_start: 0.9071 (p0) cc_final: 0.8806 (p0) REVERT: Q 43 ASN cc_start: 0.8923 (p0) cc_final: 0.8722 (t0) REVERT: Q 57 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: T 89 GLU cc_start: 0.9307 (pt0) cc_final: 0.8997 (pp20) REVERT: T 122 TRP cc_start: 0.8914 (m-10) cc_final: 0.8690 (m-10) REVERT: T 200 ILE cc_start: 0.9442 (tt) cc_final: 0.9241 (pt) REVERT: T 206 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8403 (mm-30) REVERT: T 240 LEU cc_start: 0.9617 (mt) cc_final: 0.9395 (mt) REVERT: T 253 ASN cc_start: 0.9431 (m-40) cc_final: 0.8946 (m110) REVERT: T 264 MET cc_start: 0.9591 (mmm) cc_final: 0.9234 (mmm) REVERT: T 277 TYR cc_start: 0.8981 (m-80) cc_final: 0.8354 (m-80) REVERT: Z 85 GLU cc_start: 0.9260 (tt0) cc_final: 0.8527 (tm-30) REVERT: Z 89 GLU cc_start: 0.8800 (pt0) cc_final: 0.8058 (pt0) REVERT: Z 95 PHE cc_start: 0.9410 (m-10) cc_final: 0.8998 (m-80) REVERT: Z 190 ASP cc_start: 0.7828 (t0) cc_final: 0.7538 (p0) REVERT: Z 202 PHE cc_start: 0.9212 (t80) cc_final: 0.8932 (t80) REVERT: Z 264 MET cc_start: 0.9417 (mmt) cc_final: 0.8909 (tpp) REVERT: Z 277 TYR cc_start: 0.8841 (m-80) cc_final: 0.8590 (m-80) REVERT: Z 282 PHE cc_start: 0.9408 (t80) cc_final: 0.9082 (t80) REVERT: Z 296 TYR cc_start: 0.9101 (t80) cc_final: 0.8725 (t80) outliers start: 40 outliers final: 24 residues processed: 426 average time/residue: 0.0569 time to fit residues: 37.1792 Evaluate side-chains 404 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 379 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL 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 22 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 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.069771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.057338 restraints weight = 44234.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058658 restraints weight = 30188.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059668 restraints weight = 22927.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.060373 restraints weight = 18535.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060868 restraints weight = 15777.781| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2731 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= 0.163 Angle : 0.703 9.982 13062 Z= 0.362 Chirality : 0.048 0.340 1642 Planarity : 0.005 0.063 1666 Dihedral : 4.110 24.309 1393 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.20 % Allowed : 30.86 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1325 helix: 1.18 (0.16), residues: 1054 sheet: None (None), residues: 0 loop : -1.99 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 96 TYR 0.017 0.002 TYR M 48 PHE 0.036 0.001 PHE I 62 TRP 0.007 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9567) covalent geometry : angle 0.70256 (13060) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.59377 ( 2) hydrogen bonds : bond 0.04995 ( 874) hydrogen bonds : angle 4.40893 ( 2607) *********************** 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 444 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 402 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9090 (mt) cc_final: 0.8873 (mt) REVERT: H 37 ARG cc_start: 0.9326 (ttm110) cc_final: 0.8900 (ttm110) REVERT: H 59 LEU cc_start: 0.9754 (mm) cc_final: 0.9501 (mp) REVERT: H 62 PHE cc_start: 0.9187 (m-80) cc_final: 0.8741 (m-80) REVERT: I 15 LEU cc_start: 0.9325 (mm) cc_final: 0.8421 (tp) REVERT: I 46 VAL cc_start: 0.9348 (t) cc_final: 0.9107 (p) REVERT: I 49 MET cc_start: 0.9616 (ttt) cc_final: 0.8993 (tmm) REVERT: I 59 LEU cc_start: 0.9646 (mp) cc_final: 0.9443 (mp) REVERT: I 68 PHE cc_start: 0.9081 (m-80) cc_final: 0.8705 (m-80) REVERT: J 18 ILE cc_start: 0.8364 (tp) cc_final: 0.8005 (tp) REVERT: J 40 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7917 (mp0) REVERT: J 44 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7430 (ttt90) REVERT: J 48 TYR cc_start: 0.9276 (m-80) cc_final: 0.8615 (m-80) REVERT: J 49 MET cc_start: 0.9631 (ppp) cc_final: 0.9107 (ppp) REVERT: J 57 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8841 (mt-10) REVERT: K 33 GLN cc_start: 0.9280 (mm-40) cc_final: 0.9035 (mm-40) REVERT: K 48 TYR cc_start: 0.9224 (m-80) cc_final: 0.8221 (m-80) REVERT: L 43 ASN cc_start: 0.8766 (t0) cc_final: 0.8409 (m110) REVERT: M 33 GLN cc_start: 0.9382 (mm110) cc_final: 0.9004 (mm110) REVERT: M 46 VAL cc_start: 0.9472 (t) cc_final: 0.9208 (t) REVERT: M 50 PHE cc_start: 0.9101 (m-80) cc_final: 0.8614 (m-80) REVERT: M 66 ILE cc_start: 0.9647 (mm) cc_final: 0.9441 (tt) REVERT: N 48 TYR cc_start: 0.9332 (m-80) cc_final: 0.8729 (m-80) REVERT: N 55 PHE cc_start: 0.9421 (m-80) cc_final: 0.9099 (m-80) REVERT: N 64 LEU cc_start: 0.9745 (tp) cc_final: 0.9532 (tp) REVERT: O 29 SER cc_start: 0.9625 (t) cc_final: 0.9260 (p) REVERT: O 37 ARG cc_start: 0.9157 (mmt90) cc_final: 0.8640 (mtm180) REVERT: O 44 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.7245 (mmm-85) REVERT: O 48 TYR cc_start: 0.8961 (m-80) cc_final: 0.8414 (m-80) REVERT: O 49 MET cc_start: 0.9466 (ttp) cc_final: 0.8787 (tmm) REVERT: O 57 GLU cc_start: 0.9183 (pt0) cc_final: 0.8954 (pp20) REVERT: O 62 PHE cc_start: 0.9055 (m-80) cc_final: 0.8727 (m-80) REVERT: O 66 ILE cc_start: 0.9541 (mm) cc_final: 0.9258 (mm) REVERT: O 70 ILE cc_start: 0.8707 (mm) cc_final: 0.8472 (mm) REVERT: P 29 SER cc_start: 0.9347 (t) cc_final: 0.9084 (p) REVERT: P 43 ASN cc_start: 0.9406 (p0) cc_final: 0.9162 (p0) REVERT: Q 37 ARG cc_start: 0.8748 (mmp80) cc_final: 0.8197 (mmm160) REVERT: Q 43 ASN cc_start: 0.8959 (p0) cc_final: 0.8713 (t0) REVERT: Q 49 MET cc_start: 0.9168 (tmm) cc_final: 0.8938 (tmm) REVERT: Q 57 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: T 89 GLU cc_start: 0.9248 (pt0) cc_final: 0.8964 (pp20) REVERT: T 122 TRP cc_start: 0.8910 (m-10) cc_final: 0.8586 (m-10) REVERT: T 206 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8403 (mm-30) REVERT: T 228 MET cc_start: 0.9008 (ppp) cc_final: 0.8734 (ppp) REVERT: T 240 LEU cc_start: 0.9612 (mt) cc_final: 0.9369 (mt) REVERT: T 253 ASN cc_start: 0.9365 (m-40) cc_final: 0.9021 (m-40) REVERT: T 260 LEU cc_start: 0.9619 (tp) cc_final: 0.9346 (tt) REVERT: T 264 MET cc_start: 0.9640 (mmm) cc_final: 0.9291 (mmm) REVERT: T 277 TYR cc_start: 0.8858 (m-80) cc_final: 0.8427 (m-80) REVERT: Z 85 GLU cc_start: 0.9250 (tt0) cc_final: 0.8373 (tm-30) REVERT: Z 89 GLU cc_start: 0.8872 (pt0) cc_final: 0.7955 (pt0) REVERT: Z 95 PHE cc_start: 0.9395 (m-10) cc_final: 0.8967 (m-80) REVERT: Z 206 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8924 (mm-30) REVERT: Z 228 MET cc_start: 0.6803 (ttt) cc_final: 0.6583 (ttt) REVERT: Z 264 MET cc_start: 0.9418 (mmt) cc_final: 0.8905 (tpp) REVERT: Z 277 TYR cc_start: 0.8880 (m-80) cc_final: 0.8555 (m-80) REVERT: Z 282 PHE cc_start: 0.9365 (t80) cc_final: 0.9036 (t80) REVERT: Z 286 ILE cc_start: 0.9612 (pt) cc_final: 0.9324 (pt) REVERT: Z 296 TYR cc_start: 0.9088 (t80) cc_final: 0.8798 (t80) REVERT: Z 298 PHE cc_start: 0.9322 (m-10) cc_final: 0.9095 (m-80) outliers start: 42 outliers final: 27 residues processed: 425 average time/residue: 0.0593 time to fit residues: 38.5981 Evaluate side-chains 410 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 381 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 O residue 22 VAL Chi-restraints excluded: chain O residue 45 VAL 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 81 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 119 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Z 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057592 restraints weight = 45017.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.058830 restraints weight = 31176.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059704 restraints weight = 23868.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060349 restraints weight = 19537.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.060832 restraints weight = 16743.764| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2998 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= 0.161 Angle : 0.710 11.582 13062 Z= 0.366 Chirality : 0.047 0.245 1642 Planarity : 0.004 0.056 1666 Dihedral : 4.136 24.939 1393 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.33 % Allowed : 33.46 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1325 helix: 1.18 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.98 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 96 TYR 0.030 0.002 TYR M 48 PHE 0.033 0.001 PHE P 62 TRP 0.007 0.001 TRP T 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9567) covalent geometry : angle 0.71028 (13060) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.45208 ( 2) hydrogen bonds : bond 0.04789 ( 874) hydrogen bonds : angle 4.38154 ( 2607) *********************** 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 437 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 394 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9133 (mt) cc_final: 0.8905 (mt) REVERT: H 37 ARG cc_start: 0.9305 (ttm110) cc_final: 0.8904 (ttm110) REVERT: H 59 LEU cc_start: 0.9760 (mm) cc_final: 0.9507 (mp) REVERT: H 62 PHE cc_start: 0.9179 (m-80) cc_final: 0.8718 (m-80) REVERT: I 46 VAL cc_start: 0.9305 (t) cc_final: 0.9049 (p) REVERT: I 49 MET cc_start: 0.9601 (ttt) cc_final: 0.8971 (tmm) REVERT: I 68 PHE cc_start: 0.9186 (m-80) cc_final: 0.8687 (m-80) REVERT: J 40 GLU cc_start: 0.8711 (mm-30) cc_final: 0.7973 (mp0) REVERT: J 44 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7824 (mmm-85) REVERT: J 48 TYR cc_start: 0.9305 (m-80) cc_final: 0.8614 (m-80) REVERT: J 49 MET cc_start: 0.9648 (ppp) cc_final: 0.9129 (ppp) REVERT: J 57 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8781 (mt-10) REVERT: K 33 GLN cc_start: 0.9299 (mm-40) cc_final: 0.9071 (mm-40) REVERT: K 57 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9171 (mm-30) REVERT: K 62 PHE cc_start: 0.9475 (m-10) cc_final: 0.9170 (m-80) REVERT: L 43 ASN cc_start: 0.8651 (t0) cc_final: 0.8203 (m-40) REVERT: L 48 TYR cc_start: 0.9339 (m-80) cc_final: 0.9053 (m-80) REVERT: M 5 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8788 (p0) REVERT: M 33 GLN cc_start: 0.9410 (mm110) cc_final: 0.9172 (mm110) REVERT: M 46 VAL cc_start: 0.9409 (t) cc_final: 0.9011 (t) REVERT: M 50 PHE cc_start: 0.9250 (m-80) cc_final: 0.8619 (m-80) REVERT: N 18 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7826 (tt) REVERT: N 48 TYR cc_start: 0.9377 (m-80) cc_final: 0.8721 (m-80) REVERT: N 55 PHE cc_start: 0.9418 (m-80) cc_final: 0.9133 (m-80) REVERT: O 29 SER cc_start: 0.9606 (t) cc_final: 0.9239 (p) REVERT: O 37 ARG cc_start: 0.9181 (mmt90) cc_final: 0.8708 (mtm180) REVERT: O 44 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.7536 (mmm-85) REVERT: O 48 TYR cc_start: 0.8995 (m-80) cc_final: 0.8351 (m-80) REVERT: O 49 MET cc_start: 0.9487 (ttp) cc_final: 0.8796 (tmm) REVERT: O 57 GLU cc_start: 0.9181 (pt0) cc_final: 0.8921 (pp20) REVERT: O 62 PHE cc_start: 0.9101 (m-80) cc_final: 0.8762 (m-80) REVERT: O 66 ILE cc_start: 0.9541 (mm) cc_final: 0.9217 (mm) REVERT: P 29 SER cc_start: 0.9349 (t) cc_final: 0.9078 (p) REVERT: P 37 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7865 (ttm170) REVERT: P 42 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9074 (tt0) REVERT: P 43 ASN cc_start: 0.9434 (p0) cc_final: 0.9202 (p0) REVERT: P 57 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8800 (pt0) REVERT: Q 37 ARG cc_start: 0.8721 (mmp80) cc_final: 0.8209 (mmm160) REVERT: Q 43 ASN cc_start: 0.8983 (p0) cc_final: 0.8766 (t0) REVERT: Q 57 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: T 84 MET cc_start: 0.9072 (mmm) cc_final: 0.8436 (mpp) REVERT: T 89 GLU cc_start: 0.9119 (pt0) cc_final: 0.8911 (pp20) REVERT: T 122 TRP cc_start: 0.8953 (m-10) cc_final: 0.8593 (m-10) REVERT: T 206 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8413 (mm-30) REVERT: T 228 MET cc_start: 0.9028 (ppp) cc_final: 0.8490 (ppp) REVERT: T 240 LEU cc_start: 0.9605 (mt) cc_final: 0.9397 (mm) REVERT: T 253 ASN cc_start: 0.9563 (m-40) cc_final: 0.9215 (m-40) REVERT: T 264 MET cc_start: 0.9666 (mmm) cc_final: 0.9443 (mmm) REVERT: T 277 TYR cc_start: 0.8826 (m-80) cc_final: 0.8405 (m-80) REVERT: Z 85 GLU cc_start: 0.9256 (tt0) cc_final: 0.8543 (tm-30) REVERT: Z 95 PHE cc_start: 0.9392 (m-10) cc_final: 0.8971 (m-80) REVERT: Z 264 MET cc_start: 0.9420 (mmt) cc_final: 0.8930 (tpp) REVERT: Z 277 TYR cc_start: 0.8874 (m-80) cc_final: 0.8542 (m-80) REVERT: Z 282 PHE cc_start: 0.9344 (t80) cc_final: 0.9028 (t80) REVERT: Z 286 ILE cc_start: 0.9639 (pt) cc_final: 0.9328 (pt) REVERT: Z 296 TYR cc_start: 0.9093 (t80) cc_final: 0.8825 (t80) outliers start: 43 outliers final: 32 residues processed: 415 average time/residue: 0.0570 time to fit residues: 36.3394 Evaluate side-chains 406 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 370 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL 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 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 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 5 ASN 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 45 VAL Chi-restraints excluded: chain P residue 55 PHE 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 Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 191 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.069936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057643 restraints weight = 44500.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.058897 restraints weight = 30728.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059853 restraints weight = 23537.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.060552 restraints weight = 19187.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.061031 restraints weight = 16391.622| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9568 Z= 0.159 Angle : 0.727 13.541 13062 Z= 0.373 Chirality : 0.049 0.393 1642 Planarity : 0.004 0.051 1666 Dihedral : 4.186 25.270 1393 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 6.20 % Allowed : 36.31 % Favored : 57.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1325 helix: 1.17 (0.16), residues: 1061 sheet: None (None), residues: 0 loop : -2.00 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 96 TYR 0.019 0.002 TYR L 48 PHE 0.034 0.001 PHE Z 202 TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9567) covalent geometry : angle 0.72689 (13060) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.39725 ( 2) hydrogen bonds : bond 0.04726 ( 874) hydrogen bonds : angle 4.40333 ( 2607) *********************** 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 442 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 392 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9163 (mt) cc_final: 0.8955 (mt) REVERT: H 37 ARG cc_start: 0.9266 (ttm110) cc_final: 0.8908 (ttm110) REVERT: H 59 LEU cc_start: 0.9761 (mm) cc_final: 0.9559 (mp) REVERT: H 62 PHE cc_start: 0.9113 (m-80) cc_final: 0.8765 (m-80) REVERT: I 15 LEU cc_start: 0.9287 (mm) cc_final: 0.8410 (tp) REVERT: I 46 VAL cc_start: 0.9301 (t) cc_final: 0.9080 (t) REVERT: I 48 TYR cc_start: 0.9345 (m-80) cc_final: 0.9063 (m-80) REVERT: I 49 MET cc_start: 0.9578 (ttt) cc_final: 0.8978 (tmm) REVERT: I 57 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8789 (mp0) REVERT: I 68 PHE cc_start: 0.9111 (m-80) cc_final: 0.8623 (m-80) REVERT: J 40 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7950 (mp0) REVERT: J 44 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7496 (ttt90) REVERT: J 48 TYR cc_start: 0.9248 (m-80) cc_final: 0.8685 (m-80) REVERT: J 49 MET cc_start: 0.9603 (ppp) cc_final: 0.9089 (ppp) REVERT: J 57 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8767 (mt-10) REVERT: K 33 GLN cc_start: 0.9298 (mm-40) cc_final: 0.9086 (mm-40) REVERT: K 48 TYR cc_start: 0.9217 (m-80) cc_final: 0.8162 (m-80) REVERT: K 49 MET cc_start: 0.9530 (ppp) cc_final: 0.9268 (ppp) REVERT: K 57 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9035 (mm-30) REVERT: K 62 PHE cc_start: 0.9434 (m-10) cc_final: 0.9098 (m-80) REVERT: L 43 ASN cc_start: 0.8570 (t0) cc_final: 0.8119 (m110) REVERT: M 5 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8705 (p0) REVERT: M 33 GLN cc_start: 0.9401 (mm110) cc_final: 0.9156 (mm110) REVERT: M 46 VAL cc_start: 0.9381 (t) cc_final: 0.9109 (t) REVERT: M 49 MET cc_start: 0.9379 (ppp) cc_final: 0.9068 (ppp) REVERT: M 50 PHE cc_start: 0.9228 (m-80) cc_final: 0.8619 (m-80) REVERT: N 41 ILE cc_start: 0.9448 (tp) cc_final: 0.9074 (tp) REVERT: N 48 TYR cc_start: 0.9315 (m-80) cc_final: 0.8679 (m-80) REVERT: N 55 PHE cc_start: 0.9413 (m-80) cc_final: 0.9123 (m-80) REVERT: O 29 SER cc_start: 0.9547 (t) cc_final: 0.9217 (p) REVERT: O 37 ARG cc_start: 0.9047 (mmt90) cc_final: 0.8633 (mtm180) REVERT: O 44 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7334 (mmm-85) REVERT: O 48 TYR cc_start: 0.8886 (m-80) cc_final: 0.8299 (m-80) REVERT: O 49 MET cc_start: 0.9466 (ttp) cc_final: 0.8784 (tmm) REVERT: O 57 GLU cc_start: 0.9137 (pt0) cc_final: 0.8882 (pp20) REVERT: O 62 PHE cc_start: 0.9011 (m-80) cc_final: 0.8699 (m-80) REVERT: O 66 ILE cc_start: 0.9550 (mm) cc_final: 0.9242 (mm) REVERT: P 24 ILE cc_start: 0.9583 (mm) cc_final: 0.9374 (mm) REVERT: P 37 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7841 (ttm170) REVERT: P 42 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8984 (tt0) REVERT: P 43 ASN cc_start: 0.9396 (p0) cc_final: 0.9132 (p0) REVERT: P 57 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8721 (pt0) REVERT: Q 37 ARG cc_start: 0.8684 (mmp80) cc_final: 0.8322 (mmm160) REVERT: Q 57 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: T 84 MET cc_start: 0.9004 (mmm) cc_final: 0.8388 (mpp) REVERT: T 122 TRP cc_start: 0.8950 (m-10) cc_final: 0.8605 (m-10) REVERT: T 206 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8377 (mm-30) REVERT: T 228 MET cc_start: 0.9003 (ppp) cc_final: 0.8745 (ppp) REVERT: T 240 LEU cc_start: 0.9636 (mt) cc_final: 0.9393 (mt) REVERT: T 253 ASN cc_start: 0.9482 (m-40) cc_final: 0.9240 (m-40) REVERT: T 264 MET cc_start: 0.9654 (mmm) cc_final: 0.9379 (mmm) REVERT: T 277 TYR cc_start: 0.8825 (m-80) cc_final: 0.8432 (m-80) REVERT: Z 85 GLU cc_start: 0.9196 (tt0) cc_final: 0.8498 (tm-30) REVERT: Z 95 PHE cc_start: 0.9373 (m-10) cc_final: 0.8958 (m-80) REVERT: Z 264 MET cc_start: 0.9388 (mmt) cc_final: 0.8937 (tpp) REVERT: Z 277 TYR cc_start: 0.8850 (m-80) cc_final: 0.8521 (m-80) REVERT: Z 282 PHE cc_start: 0.9326 (t80) cc_final: 0.9017 (t80) REVERT: Z 286 ILE cc_start: 0.9645 (pt) cc_final: 0.9305 (pt) REVERT: Z 296 TYR cc_start: 0.9001 (t80) cc_final: 0.8701 (t80) outliers start: 50 outliers final: 36 residues processed: 415 average time/residue: 0.0602 time to fit residues: 38.4473 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 : 0.286 ------------------------------------------------------------------------------- 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 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 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 5 ASN 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 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 Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.069404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056972 restraints weight = 45970.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058088 restraints weight = 32281.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.059091 restraints weight = 25282.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059730 restraints weight = 20780.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060191 restraints weight = 17819.799| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9568 Z= 0.181 Angle : 0.739 11.666 13062 Z= 0.385 Chirality : 0.050 0.321 1642 Planarity : 0.005 0.050 1666 Dihedral : 4.224 24.441 1393 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.57 % Allowed : 38.91 % Favored : 54.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.23), residues: 1325 helix: 1.18 (0.16), residues: 1057 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 37 TYR 0.023 0.002 TYR L 48 PHE 0.039 0.001 PHE Z 202 TRP 0.008 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9567) covalent geometry : angle 0.73892 (13060) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.36904 ( 2) hydrogen bonds : bond 0.04735 ( 874) hydrogen bonds : angle 4.47783 ( 2607) *********************** 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 431 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 378 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9159 (mt) cc_final: 0.8927 (mt) REVERT: H 37 ARG cc_start: 0.9305 (ttm110) cc_final: 0.9088 (ttm110) REVERT: H 62 PHE cc_start: 0.9205 (m-80) cc_final: 0.8874 (m-80) REVERT: I 57 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8779 (mp0) REVERT: I 68 PHE cc_start: 0.9191 (m-80) cc_final: 0.8783 (m-80) REVERT: J 40 GLU cc_start: 0.8717 (mm-30) cc_final: 0.7995 (mp0) REVERT: J 44 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7574 (mmm-85) REVERT: J 48 TYR cc_start: 0.9305 (m-80) cc_final: 0.8521 (m-80) REVERT: J 49 MET cc_start: 0.9610 (ppp) cc_final: 0.9091 (ppp) REVERT: J 57 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8882 (mt-10) REVERT: K 48 TYR cc_start: 0.9250 (m-80) cc_final: 0.8137 (m-80) REVERT: K 49 MET cc_start: 0.9553 (ppp) cc_final: 0.9346 (ppp) REVERT: K 57 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9090 (mm-30) REVERT: L 29 SER cc_start: 0.9438 (t) cc_final: 0.9188 (p) REVERT: L 43 ASN cc_start: 0.8627 (t0) cc_final: 0.8194 (m-40) REVERT: M 33 GLN cc_start: 0.9425 (mm110) cc_final: 0.9184 (mm110) REVERT: M 46 VAL cc_start: 0.9389 (t) cc_final: 0.9120 (t) REVERT: M 49 MET cc_start: 0.9398 (ppp) cc_final: 0.9023 (ppp) REVERT: M 50 PHE cc_start: 0.9262 (m-80) cc_final: 0.8662 (m-80) REVERT: N 24 ILE cc_start: 0.9610 (mt) cc_final: 0.9354 (mm) REVERT: N 48 TYR cc_start: 0.9452 (m-80) cc_final: 0.8705 (m-80) REVERT: N 55 PHE cc_start: 0.9451 (m-80) cc_final: 0.9137 (m-80) REVERT: O 29 SER cc_start: 0.9586 (t) cc_final: 0.9245 (p) REVERT: O 37 ARG cc_start: 0.9144 (mmt90) cc_final: 0.8693 (mtm180) REVERT: O 44 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.7479 (mmm-85) REVERT: O 48 TYR cc_start: 0.8978 (m-80) cc_final: 0.8384 (m-80) REVERT: O 49 MET cc_start: 0.9493 (ttp) cc_final: 0.8778 (tmm) REVERT: O 57 GLU cc_start: 0.9183 (pt0) cc_final: 0.8932 (pp20) REVERT: O 62 PHE cc_start: 0.9153 (m-80) cc_final: 0.8806 (m-80) REVERT: O 66 ILE cc_start: 0.9547 (mm) cc_final: 0.9242 (mm) REVERT: P 37 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7923 (ttm170) REVERT: P 42 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9001 (tt0) REVERT: P 43 ASN cc_start: 0.9446 (p0) cc_final: 0.9197 (p0) REVERT: P 57 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8716 (pt0) REVERT: Q 37 ARG cc_start: 0.8711 (mmp80) cc_final: 0.8227 (mmm160) REVERT: Q 57 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: T 84 MET cc_start: 0.9062 (mmm) cc_final: 0.8447 (mpp) REVERT: T 122 TRP cc_start: 0.8981 (m-10) cc_final: 0.8652 (m-10) REVERT: T 206 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8419 (mm-30) REVERT: T 228 MET cc_start: 0.9025 (ppp) cc_final: 0.8754 (ppp) REVERT: T 240 LEU cc_start: 0.9637 (mt) cc_final: 0.9431 (mm) REVERT: T 253 ASN cc_start: 0.9509 (m-40) cc_final: 0.9251 (m-40) REVERT: T 264 MET cc_start: 0.9683 (mmm) cc_final: 0.9412 (mmm) REVERT: T 277 TYR cc_start: 0.8848 (m-80) cc_final: 0.8447 (m-80) REVERT: Z 85 GLU cc_start: 0.9250 (tt0) cc_final: 0.8524 (tm-30) REVERT: Z 95 PHE cc_start: 0.9419 (m-10) cc_final: 0.8978 (m-80) REVERT: Z 264 MET cc_start: 0.9400 (mmt) cc_final: 0.8904 (tpp) REVERT: Z 277 TYR cc_start: 0.8923 (m-80) cc_final: 0.8562 (m-80) REVERT: Z 282 PHE cc_start: 0.9386 (t80) cc_final: 0.9059 (t80) REVERT: Z 286 ILE cc_start: 0.9654 (pt) cc_final: 0.9267 (pt) REVERT: Z 296 TYR cc_start: 0.9069 (t80) cc_final: 0.8717 (t80) outliers start: 53 outliers final: 44 residues processed: 402 average time/residue: 0.0610 time to fit residues: 37.6594 Evaluate side-chains 412 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 365 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 22 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 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 35 ILE 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 7 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 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 59 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 88 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 124 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.070524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.057798 restraints weight = 45149.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058945 restraints weight = 31740.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059853 restraints weight = 24832.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060597 restraints weight = 20558.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061103 restraints weight = 17745.897| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3683 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= 0.161 Angle : 0.777 14.505 13062 Z= 0.395 Chirality : 0.050 0.283 1642 Planarity : 0.005 0.049 1666 Dihedral : 4.279 25.342 1393 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.82 % Allowed : 41.39 % Favored : 52.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.23), residues: 1325 helix: 1.13 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 96 TYR 0.030 0.002 TYR M 48 PHE 0.030 0.001 PHE Z 202 TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9567) covalent geometry : angle 0.77714 (13060) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.30191 ( 2) hydrogen bonds : bond 0.04689 ( 874) hydrogen bonds : angle 4.41537 ( 2607) *********************** 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 435 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 388 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9095 (mt) cc_final: 0.8872 (mt) REVERT: H 37 ARG cc_start: 0.9273 (ttm110) cc_final: 0.9064 (ttm110) REVERT: H 62 PHE cc_start: 0.9185 (m-80) cc_final: 0.8884 (m-80) REVERT: I 57 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8840 (mp0) REVERT: I 68 PHE cc_start: 0.9150 (m-80) cc_final: 0.8727 (m-80) REVERT: J 40 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8004 (mp0) REVERT: J 44 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7365 (ttt90) REVERT: J 48 TYR cc_start: 0.9257 (m-80) cc_final: 0.8756 (m-80) REVERT: J 49 MET cc_start: 0.9604 (ppp) cc_final: 0.9102 (ppp) REVERT: K 15 LEU cc_start: 0.9200 (mm) cc_final: 0.8966 (mm) REVERT: K 48 TYR cc_start: 0.9232 (m-80) cc_final: 0.8131 (m-80) REVERT: K 49 MET cc_start: 0.9555 (ppp) cc_final: 0.9332 (ppp) REVERT: K 57 GLU cc_start: 0.9622 (mm-30) cc_final: 0.9061 (mm-30) REVERT: L 29 SER cc_start: 0.9523 (t) cc_final: 0.9189 (p) REVERT: L 43 ASN cc_start: 0.8594 (t0) cc_final: 0.8204 (m110) REVERT: M 33 GLN cc_start: 0.9452 (mm110) cc_final: 0.9081 (mm110) REVERT: M 46 VAL cc_start: 0.9335 (t) cc_final: 0.9116 (t) REVERT: M 49 MET cc_start: 0.9382 (ppp) cc_final: 0.9047 (ppp) REVERT: M 50 PHE cc_start: 0.9213 (m-80) cc_final: 0.8649 (m-80) REVERT: N 18 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7831 (tt) REVERT: N 24 ILE cc_start: 0.9599 (mt) cc_final: 0.9341 (mm) REVERT: N 48 TYR cc_start: 0.9392 (m-80) cc_final: 0.8748 (m-80) REVERT: N 55 PHE cc_start: 0.9450 (m-80) cc_final: 0.9120 (m-80) REVERT: O 29 SER cc_start: 0.9542 (t) cc_final: 0.9188 (p) REVERT: O 37 ARG cc_start: 0.9012 (mmt90) cc_final: 0.8618 (mtm180) REVERT: O 44 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7319 (mmm-85) REVERT: O 48 TYR cc_start: 0.8945 (m-80) cc_final: 0.8315 (m-80) REVERT: O 49 MET cc_start: 0.9506 (ttp) cc_final: 0.8830 (tmm) REVERT: O 53 ILE cc_start: 0.9308 (mt) cc_final: 0.8685 (mp) REVERT: O 57 GLU cc_start: 0.9170 (pt0) cc_final: 0.8920 (pp20) REVERT: O 62 PHE cc_start: 0.9084 (m-80) cc_final: 0.8748 (m-80) REVERT: O 66 ILE cc_start: 0.9541 (mm) cc_final: 0.9232 (mm) REVERT: P 37 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7779 (ttm170) REVERT: P 42 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8980 (tt0) REVERT: P 43 ASN cc_start: 0.9446 (p0) cc_final: 0.9218 (p0) REVERT: P 57 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8692 (pt0) REVERT: Q 37 ARG cc_start: 0.8684 (mmp80) cc_final: 0.8112 (mmm160) REVERT: Q 57 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: T 84 MET cc_start: 0.9024 (mmm) cc_final: 0.8403 (mpp) REVERT: T 122 TRP cc_start: 0.8949 (m-10) cc_final: 0.8749 (m-10) REVERT: T 206 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8404 (mm-30) REVERT: T 228 MET cc_start: 0.9001 (ppp) cc_final: 0.8739 (ppp) REVERT: T 240 LEU cc_start: 0.9603 (mt) cc_final: 0.9396 (mm) REVERT: T 253 ASN cc_start: 0.9493 (m-40) cc_final: 0.9247 (m-40) REVERT: T 264 MET cc_start: 0.9675 (mmm) cc_final: 0.9403 (mmm) REVERT: T 277 TYR cc_start: 0.8833 (m-80) cc_final: 0.8428 (m-80) REVERT: Z 95 PHE cc_start: 0.9385 (m-10) cc_final: 0.8928 (m-80) REVERT: Z 264 MET cc_start: 0.9407 (mmt) cc_final: 0.8916 (tpp) REVERT: Z 277 TYR cc_start: 0.8916 (m-80) cc_final: 0.8553 (m-80) REVERT: Z 282 PHE cc_start: 0.9348 (t80) cc_final: 0.8982 (t80) REVERT: Z 286 ILE cc_start: 0.9661 (pt) cc_final: 0.9326 (pt) REVERT: Z 296 TYR cc_start: 0.8996 (t80) cc_final: 0.8655 (t80) outliers start: 47 outliers final: 36 residues processed: 409 average time/residue: 0.0686 time to fit residues: 42.4895 Evaluate side-chains 410 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 370 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 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 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 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 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 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 Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 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 ** 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 = 0.3428 r_free = 0.3428 target = 0.070176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.057572 restraints weight = 45783.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.058639 restraints weight = 32312.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059660 restraints weight = 25481.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.060309 restraints weight = 21027.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.060711 restraints weight = 17997.903| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9568 Z= 0.172 Angle : 0.801 12.177 13062 Z= 0.410 Chirality : 0.054 0.557 1642 Planarity : 0.005 0.050 1666 Dihedral : 4.358 24.799 1393 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.32 % Allowed : 42.26 % Favored : 51.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1325 helix: 1.08 (0.16), residues: 1059 sheet: None (None), residues: 0 loop : -1.77 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 249 TYR 0.020 0.001 TYR N 48 PHE 0.034 0.001 PHE Z 202 TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9567) covalent geometry : angle 0.80125 (13060) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.29519 ( 2) hydrogen bonds : bond 0.04774 ( 874) hydrogen bonds : angle 4.47570 ( 2607) *********************** 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 432 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 381 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9093 (mt) cc_final: 0.8876 (mt) REVERT: H 37 ARG cc_start: 0.9290 (ttm110) cc_final: 0.9055 (ttm110) REVERT: H 62 PHE cc_start: 0.9242 (m-10) cc_final: 0.9041 (m-80) REVERT: I 57 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8873 (mp0) REVERT: I 68 PHE cc_start: 0.9165 (m-80) cc_final: 0.8702 (m-80) REVERT: J 40 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8166 (mp0) REVERT: J 44 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6790 (ttt-90) REVERT: J 48 TYR cc_start: 0.9295 (m-80) cc_final: 0.8617 (m-80) REVERT: J 49 MET cc_start: 0.9613 (ppp) cc_final: 0.9117 (ppp) REVERT: J 61 ILE cc_start: 0.9561 (mm) cc_final: 0.9343 (mp) REVERT: K 15 LEU cc_start: 0.9135 (mm) cc_final: 0.8908 (mm) REVERT: K 48 TYR cc_start: 0.9272 (m-80) cc_final: 0.8159 (m-80) REVERT: K 49 MET cc_start: 0.9563 (ppp) cc_final: 0.9335 (ppp) REVERT: K 57 GLU cc_start: 0.9642 (mm-30) cc_final: 0.9072 (mm-30) REVERT: K 66 ILE cc_start: 0.9471 (mm) cc_final: 0.9239 (tp) REVERT: L 29 SER cc_start: 0.9555 (t) cc_final: 0.9206 (p) REVERT: L 43 ASN cc_start: 0.8605 (t0) cc_final: 0.8200 (m110) REVERT: M 33 GLN cc_start: 0.9466 (mm110) cc_final: 0.8895 (mm110) REVERT: M 46 VAL cc_start: 0.9364 (t) cc_final: 0.9131 (t) REVERT: M 49 MET cc_start: 0.9398 (ppp) cc_final: 0.9034 (ppp) REVERT: M 50 PHE cc_start: 0.9218 (m-80) cc_final: 0.8638 (m-80) REVERT: N 18 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7862 (tt) REVERT: N 24 ILE cc_start: 0.9615 (mt) cc_final: 0.9399 (mm) REVERT: N 48 TYR cc_start: 0.9507 (m-80) cc_final: 0.8825 (m-80) REVERT: N 55 PHE cc_start: 0.9461 (m-80) cc_final: 0.9116 (m-80) REVERT: O 29 SER cc_start: 0.9566 (t) cc_final: 0.9193 (p) REVERT: O 37 ARG cc_start: 0.9024 (mmt90) cc_final: 0.8651 (mtm180) REVERT: O 44 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.7503 (mmm-85) REVERT: O 48 TYR cc_start: 0.8976 (m-80) cc_final: 0.8307 (m-80) REVERT: O 49 MET cc_start: 0.9476 (ttp) cc_final: 0.8759 (tmm) REVERT: O 53 ILE cc_start: 0.9291 (mt) cc_final: 0.8660 (mp) REVERT: O 57 GLU cc_start: 0.9175 (pt0) cc_final: 0.8856 (pp20) REVERT: O 62 PHE cc_start: 0.9147 (m-80) cc_final: 0.8784 (m-80) REVERT: O 66 ILE cc_start: 0.9550 (mm) cc_final: 0.9249 (mm) REVERT: P 37 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7836 (ttm170) REVERT: P 43 ASN cc_start: 0.9451 (p0) cc_final: 0.9217 (p0) REVERT: P 57 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8714 (pt0) REVERT: Q 37 ARG cc_start: 0.8712 (mmp80) cc_final: 0.7992 (mmm160) REVERT: Q 57 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: Q 61 ILE cc_start: 0.9094 (pt) cc_final: 0.8780 (pt) REVERT: T 84 MET cc_start: 0.9051 (mmm) cc_final: 0.8429 (mpp) REVERT: T 122 TRP cc_start: 0.8983 (m-10) cc_final: 0.8773 (m-10) REVERT: T 206 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8424 (mm-30) REVERT: T 228 MET cc_start: 0.9013 (ppp) cc_final: 0.8756 (ppp) REVERT: T 240 LEU cc_start: 0.9584 (mt) cc_final: 0.9378 (mm) REVERT: T 253 ASN cc_start: 0.9519 (m-40) cc_final: 0.9256 (m110) REVERT: T 264 MET cc_start: 0.9680 (mmm) cc_final: 0.9430 (mmm) REVERT: T 277 TYR cc_start: 0.8845 (m-80) cc_final: 0.8442 (m-80) REVERT: Z 74 GLN cc_start: 0.9075 (tp40) cc_final: 0.8725 (mp10) REVERT: Z 85 GLU cc_start: 0.9207 (tt0) cc_final: 0.8574 (tm-30) REVERT: Z 95 PHE cc_start: 0.9421 (m-10) cc_final: 0.8959 (m-80) REVERT: Z 249 ARG cc_start: 0.9381 (ttm110) cc_final: 0.9090 (ptp-110) REVERT: Z 264 MET cc_start: 0.9423 (mmt) cc_final: 0.8911 (tpp) REVERT: Z 277 TYR cc_start: 0.8971 (m-80) cc_final: 0.8565 (m-80) REVERT: Z 282 PHE cc_start: 0.9345 (t80) cc_final: 0.8989 (t80) REVERT: Z 286 ILE cc_start: 0.9675 (pt) cc_final: 0.9329 (pt) REVERT: Z 296 TYR cc_start: 0.8999 (t80) cc_final: 0.8633 (t80) outliers start: 51 outliers final: 39 residues processed: 403 average time/residue: 0.0670 time to fit residues: 40.8945 Evaluate side-chains 414 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 371 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 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 59 LEU 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 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 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 88 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 191 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3448 r_free = 0.3448 target = 0.071056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058136 restraints weight = 45576.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.059380 restraints weight = 32127.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060354 restraints weight = 24879.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061039 restraints weight = 20272.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.061425 restraints weight = 17407.371| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9568 Z= 0.171 Angle : 0.838 13.100 13062 Z= 0.422 Chirality : 0.054 0.355 1642 Planarity : 0.005 0.047 1666 Dihedral : 4.377 25.170 1393 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.45 % Allowed : 43.25 % Favored : 51.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.23), residues: 1325 helix: 1.06 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : -1.92 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 249 TYR 0.016 0.001 TYR N 48 PHE 0.027 0.001 PHE Z 202 TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9567) covalent geometry : angle 0.83763 (13060) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.22806 ( 2) hydrogen bonds : bond 0.04754 ( 874) hydrogen bonds : angle 4.47496 ( 2607) *********************** 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 425 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9121 (mt) cc_final: 0.8912 (mt) REVERT: H 37 ARG cc_start: 0.9231 (ttm110) cc_final: 0.9021 (ttm110) REVERT: H 62 PHE cc_start: 0.9249 (m-10) cc_final: 0.9030 (m-80) REVERT: I 57 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: I 68 PHE cc_start: 0.9114 (m-80) cc_final: 0.8662 (m-80) REVERT: J 40 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8192 (mp0) REVERT: J 44 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7368 (ttm-80) REVERT: J 48 TYR cc_start: 0.9270 (m-80) cc_final: 0.8576 (m-80) REVERT: J 49 MET cc_start: 0.9599 (ppp) cc_final: 0.9107 (ppp) REVERT: K 15 LEU cc_start: 0.9154 (mm) cc_final: 0.8919 (mm) REVERT: K 48 TYR cc_start: 0.9242 (m-80) cc_final: 0.8137 (m-80) REVERT: K 49 MET cc_start: 0.9554 (ppp) cc_final: 0.9338 (ppp) REVERT: K 57 GLU cc_start: 0.9640 (mm-30) cc_final: 0.9072 (mm-30) REVERT: K 66 ILE cc_start: 0.9477 (mm) cc_final: 0.9249 (tp) REVERT: L 29 SER cc_start: 0.9538 (t) cc_final: 0.9194 (p) REVERT: L 43 ASN cc_start: 0.8560 (t0) cc_final: 0.8173 (m110) REVERT: M 33 GLN cc_start: 0.9444 (mm110) cc_final: 0.8935 (mm110) REVERT: M 46 VAL cc_start: 0.9360 (t) cc_final: 0.9152 (t) REVERT: M 48 TYR cc_start: 0.9111 (m-80) cc_final: 0.8591 (m-80) REVERT: M 49 MET cc_start: 0.9372 (ppp) cc_final: 0.9059 (ppp) REVERT: M 50 PHE cc_start: 0.9179 (m-80) cc_final: 0.8620 (m-80) REVERT: N 18 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7838 (tt) REVERT: N 24 ILE cc_start: 0.9613 (mt) cc_final: 0.9386 (mm) REVERT: N 48 TYR cc_start: 0.9428 (m-80) cc_final: 0.8787 (m-80) REVERT: N 55 PHE cc_start: 0.9441 (m-80) cc_final: 0.9101 (m-80) REVERT: O 29 SER cc_start: 0.9535 (t) cc_final: 0.9179 (p) REVERT: O 37 ARG cc_start: 0.8904 (mmt90) cc_final: 0.8594 (mtm180) REVERT: O 44 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7348 (mmm-85) REVERT: O 48 TYR cc_start: 0.8897 (m-80) cc_final: 0.8257 (m-80) REVERT: O 49 MET cc_start: 0.9471 (ttp) cc_final: 0.8833 (tmm) REVERT: O 57 GLU cc_start: 0.9141 (pt0) cc_final: 0.8712 (pp20) REVERT: O 62 PHE cc_start: 0.9100 (m-80) cc_final: 0.8744 (m-80) REVERT: O 66 ILE cc_start: 0.9547 (mm) cc_final: 0.9245 (mm) REVERT: P 37 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7745 (ttm170) REVERT: P 43 ASN cc_start: 0.9418 (p0) cc_final: 0.9181 (p0) REVERT: P 57 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8734 (pt0) REVERT: Q 37 ARG cc_start: 0.8634 (mmp80) cc_final: 0.7890 (mmm160) REVERT: Q 57 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: Q 62 PHE cc_start: 0.9111 (m-80) cc_final: 0.8888 (m-80) REVERT: T 84 MET cc_start: 0.9024 (mmm) cc_final: 0.8422 (mpp) REVERT: T 89 GLU cc_start: 0.9146 (pt0) cc_final: 0.8607 (pt0) REVERT: T 122 TRP cc_start: 0.8967 (m-10) cc_final: 0.8758 (m-10) REVERT: T 206 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8418 (mm-30) REVERT: T 228 MET cc_start: 0.9051 (ppp) cc_final: 0.8803 (ppp) REVERT: T 240 LEU cc_start: 0.9580 (mt) cc_final: 0.9374 (mm) REVERT: T 264 MET cc_start: 0.9655 (mmm) cc_final: 0.9414 (mmm) REVERT: T 277 TYR cc_start: 0.8822 (m-80) cc_final: 0.8460 (m-80) REVERT: Z 74 GLN cc_start: 0.9073 (tp40) cc_final: 0.8406 (tp40) REVERT: Z 85 GLU cc_start: 0.9177 (tt0) cc_final: 0.8534 (tm-30) REVERT: Z 95 PHE cc_start: 0.9409 (m-10) cc_final: 0.8924 (m-80) REVERT: Z 249 ARG cc_start: 0.9380 (ttm110) cc_final: 0.9057 (ptp-110) REVERT: Z 264 MET cc_start: 0.9407 (mmt) cc_final: 0.8907 (tpp) REVERT: Z 277 TYR cc_start: 0.8901 (m-80) cc_final: 0.8536 (m-80) REVERT: Z 282 PHE cc_start: 0.9304 (t80) cc_final: 0.8795 (t80) REVERT: Z 286 ILE cc_start: 0.9680 (pt) cc_final: 0.9179 (pt) REVERT: Z 296 TYR cc_start: 0.8914 (t80) cc_final: 0.8561 (t80) outliers start: 44 outliers final: 33 residues processed: 399 average time/residue: 0.0654 time to fit residues: 39.6615 Evaluate side-chains 412 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 375 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 45 VAL 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 45 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.0050 chunk 15 optimal weight: 0.0770 chunk 131 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 GLN Z 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.072125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.059059 restraints weight = 45046.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060250 restraints weight = 32539.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.061193 restraints weight = 25558.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.061815 restraints weight = 21178.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.062308 restraints weight = 18299.335| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9568 Z= 0.174 Angle : 0.873 13.784 13062 Z= 0.439 Chirality : 0.056 0.354 1642 Planarity : 0.005 0.050 1666 Dihedral : 4.392 25.318 1393 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.58 % Allowed : 44.61 % Favored : 50.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1325 helix: 1.09 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 96 TYR 0.016 0.001 TYR N 48 PHE 0.037 0.001 PHE T 255 TRP 0.006 0.001 TRP T 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9567) covalent geometry : angle 0.87355 (13060) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.25319 ( 2) hydrogen bonds : bond 0.04775 ( 874) hydrogen bonds : angle 4.48472 ( 2607) ********************** 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 421 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 384 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9119 (mt) cc_final: 0.8909 (mt) REVERT: H 37 ARG cc_start: 0.9231 (ttm110) cc_final: 0.9008 (ttm110) REVERT: H 62 PHE cc_start: 0.9216 (m-10) cc_final: 0.8931 (m-80) REVERT: I 49 MET cc_start: 0.9315 (tpt) cc_final: 0.8872 (tpt) REVERT: I 55 PHE cc_start: 0.9312 (m-80) cc_final: 0.9061 (m-80) REVERT: I 57 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.8830 (mp0) REVERT: I 68 PHE cc_start: 0.9154 (m-80) cc_final: 0.8630 (m-80) REVERT: J 4 LEU cc_start: 0.9155 (tp) cc_final: 0.8894 (tp) REVERT: J 40 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8274 (mp0) REVERT: J 44 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7351 (ttm-80) REVERT: J 48 TYR cc_start: 0.9281 (m-80) cc_final: 0.8599 (m-80) REVERT: J 49 MET cc_start: 0.9598 (ppp) cc_final: 0.9138 (ppp) REVERT: K 15 LEU cc_start: 0.9098 (mm) cc_final: 0.8842 (mm) REVERT: K 48 TYR cc_start: 0.9267 (m-80) cc_final: 0.8193 (m-80) REVERT: K 49 MET cc_start: 0.9575 (ppp) cc_final: 0.9343 (ppp) REVERT: K 57 GLU cc_start: 0.9643 (mm-30) cc_final: 0.9074 (mm-30) REVERT: L 29 SER cc_start: 0.9533 (t) cc_final: 0.9189 (p) REVERT: L 43 ASN cc_start: 0.8608 (t0) cc_final: 0.8224 (m110) REVERT: M 33 GLN cc_start: 0.9452 (mm110) cc_final: 0.8966 (mm110) REVERT: M 49 MET cc_start: 0.9387 (ppp) cc_final: 0.9050 (ppp) REVERT: M 50 PHE cc_start: 0.9148 (m-80) cc_final: 0.8600 (m-80) REVERT: N 15 LEU cc_start: 0.9630 (mm) cc_final: 0.9309 (mp) REVERT: N 18 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7899 (tt) REVERT: N 48 TYR cc_start: 0.9446 (m-80) cc_final: 0.8808 (m-80) REVERT: N 55 PHE cc_start: 0.9459 (m-80) cc_final: 0.9114 (m-80) REVERT: O 29 SER cc_start: 0.9568 (t) cc_final: 0.9208 (p) REVERT: O 37 ARG cc_start: 0.8940 (mmt90) cc_final: 0.8643 (mtm180) REVERT: O 44 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7329 (mmm-85) REVERT: O 48 TYR cc_start: 0.8924 (m-80) cc_final: 0.8258 (m-80) REVERT: O 57 GLU cc_start: 0.9136 (pt0) cc_final: 0.8673 (pp20) REVERT: O 62 PHE cc_start: 0.9078 (m-80) cc_final: 0.8726 (m-80) REVERT: O 66 ILE cc_start: 0.9539 (mm) cc_final: 0.9231 (mm) REVERT: P 37 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7775 (ttm170) REVERT: P 43 ASN cc_start: 0.9435 (p0) cc_final: 0.9204 (p0) REVERT: P 57 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8633 (pt0) REVERT: Q 37 ARG cc_start: 0.8631 (mmp80) cc_final: 0.7921 (mmm160) REVERT: Q 57 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: Q 61 ILE cc_start: 0.9069 (pt) cc_final: 0.8717 (pt) REVERT: Q 62 PHE cc_start: 0.9106 (m-80) cc_final: 0.8878 (m-80) REVERT: T 84 MET cc_start: 0.9065 (mmm) cc_final: 0.8444 (mpp) REVERT: T 89 GLU cc_start: 0.9180 (pt0) cc_final: 0.8669 (pt0) REVERT: T 114 PHE cc_start: 0.9588 (t80) cc_final: 0.9370 (t80) REVERT: T 122 TRP cc_start: 0.8955 (m-10) cc_final: 0.8744 (m-10) REVERT: T 206 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8444 (mm-30) REVERT: T 228 MET cc_start: 0.9081 (ppp) cc_final: 0.8836 (ppp) REVERT: T 264 MET cc_start: 0.9646 (mmm) cc_final: 0.9324 (mmm) REVERT: T 277 TYR cc_start: 0.8810 (m-80) cc_final: 0.8449 (m-80) REVERT: Z 74 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8436 (tp40) REVERT: Z 85 GLU cc_start: 0.9256 (tt0) cc_final: 0.8641 (tm-30) REVERT: Z 95 PHE cc_start: 0.9443 (m-10) cc_final: 0.8955 (m-80) REVERT: Z 191 LEU cc_start: 0.9361 (mm) cc_final: 0.8965 (pt) REVERT: Z 249 ARG cc_start: 0.9460 (ttm110) cc_final: 0.9103 (ptp90) REVERT: Z 264 MET cc_start: 0.9421 (mmt) cc_final: 0.8910 (tpp) REVERT: Z 277 TYR cc_start: 0.8910 (m-80) cc_final: 0.8549 (m-80) REVERT: Z 282 PHE cc_start: 0.9342 (t80) cc_final: 0.9030 (t80) REVERT: Z 296 TYR cc_start: 0.8997 (t80) cc_final: 0.8656 (t80) outliers start: 37 outliers final: 28 residues processed: 400 average time/residue: 0.0677 time to fit residues: 40.9633 Evaluate side-chains 405 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 373 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 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 L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR 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 45 VAL Chi-restraints excluded: chain Q residue 6 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** T 253 ASN ** 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 = 0.3437 r_free = 0.3437 target = 0.070771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058011 restraints weight = 45441.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059123 restraints weight = 32213.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060122 restraints weight = 25361.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.060685 restraints weight = 20808.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061220 restraints weight = 18200.144| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9568 Z= 0.194 Angle : 0.870 12.423 13062 Z= 0.445 Chirality : 0.054 0.294 1642 Planarity : 0.005 0.049 1666 Dihedral : 4.393 24.555 1393 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.46 % Allowed : 45.97 % Favored : 49.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1325 helix: 1.07 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -1.81 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 96 TYR 0.011 0.001 TYR N 48 PHE 0.035 0.002 PHE T 255 TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 9567) covalent geometry : angle 0.87011 (13060) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.28835 ( 2) hydrogen bonds : bond 0.04797 ( 874) hydrogen bonds : angle 4.57099 ( 2607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1468.08 seconds wall clock time: 25 minutes 57.90 seconds (1557.90 seconds total)