Starting phenix.real_space_refine on Mon May 12 21:22:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itq_60875/05_2025/9itq_60875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itq_60875/05_2025/9itq_60875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itq_60875/05_2025/9itq_60875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itq_60875/05_2025/9itq_60875.map" model { file = "/net/cci-nas-00/data/ceres_data/9itq_60875/05_2025/9itq_60875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itq_60875/05_2025/9itq_60875.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 6236 2.51 5 N 1526 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9411 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "O" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "P" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Q" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Y" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "V" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 197 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "U" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "T" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1777 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 Chain: "Z" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1877 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 239} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 6.78, per 1000 atoms: 0.72 Number of scatterers: 9411 At special positions: 0 Unit cell: (89.28, 129.27, 80.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 1630 8.00 N 1526 7.00 C 6236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS T 135 " - pdb=" SG CYS T 173 " distance=2.91 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 1 sheets defined 85.5% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.888A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 4.190A pdb=" N GLY H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 72 removed outlier: 3.838A pdb=" N VAL H 46 " --> pdb=" O GLU H 42 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET H 49 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ALA H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 37 removed outlier: 4.586A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 3.512A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 72 Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix removed outlier: 4.426A pdb=" N GLY J 23 " --> pdb=" O GLY J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 72 removed outlier: 3.571A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 38 removed outlier: 3.653A pdb=" N VAL K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.760A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 3.587A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 71 removed outlier: 3.786A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE L 55 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.594A pdb=" N VAL M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix removed outlier: 4.042A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 3.607A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.556A pdb=" N ALA N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 38 Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.662A pdb=" N MET N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 4.057A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix removed outlier: 3.999A pdb=" N GLY O 23 " --> pdb=" O GLY O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 71 removed outlier: 3.589A pdb=" N ALA O 58 " --> pdb=" O ALA O 54 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 17 through 38 removed outlier: 4.117A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 3.734A pdb=" N GLY P 52 " --> pdb=" O TYR P 48 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.671A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.618A pdb=" N ASN Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 72 removed outlier: 3.691A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 48 removed outlier: 3.654A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 24 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix Processing helix chain 'V' and resid 8 through 45 removed outlier: 3.609A pdb=" N LEU V 28 " --> pdb=" O ILE V 24 " (cutoff:3.500A) Proline residue: V 32 - end of helix Processing helix chain 'X' and resid 11 through 41 Proline residue: X 32 - end of helix Processing helix chain 'U' and resid 10 through 42 removed outlier: 5.579A pdb=" N ARG U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) Proline residue: U 32 - end of helix Processing helix chain 'T' and resid 50 through 71 removed outlier: 3.649A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE T 56 " --> pdb=" O PHE T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 3.533A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.674A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.526A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 212 removed outlier: 3.913A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 220 removed outlier: 4.273A pdb=" N TYR T 217 " --> pdb=" O GLY T 214 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU T 218 " --> pdb=" O PRO T 215 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS T 220 " --> pdb=" O TYR T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 268 removed outlier: 3.981A pdb=" N PHE T 230 " --> pdb=" O GLY T 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE T 233 " --> pdb=" O SER T 229 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE T 234 " --> pdb=" O PHE T 230 " (cutoff:3.500A) Proline residue: T 243 - end of helix removed outlier: 3.632A pdb=" N ILE T 254 " --> pdb=" O LEU T 250 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.857A pdb=" N PHE T 285 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 70 removed outlier: 3.893A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 removed outlier: 3.593A pdb=" N ILE Z 87 " --> pdb=" O VAL Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 125 Proline residue: Z 108 - end of helix removed outlier: 4.211A pdb=" N VAL Z 117 " --> pdb=" O ILE Z 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY Z 120 " --> pdb=" O PHE Z 116 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.548A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Z 212 " --> pdb=" O TRP Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 220 removed outlier: 3.536A pdb=" N LYS Z 219 " --> pdb=" O PRO Z 215 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 225 removed outlier: 4.036A pdb=" N ASN Z 225 " --> pdb=" O PHE Z 222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 268 Proline residue: Z 243 - end of helix removed outlier: 3.511A pdb=" N ILE Z 254 " --> pdb=" O LEU Z 250 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 304 removed outlier: 4.577A pdb=" N PHE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 39 through 41 removed outlier: 7.273A pdb=" N ILE Z 48 " --> pdb=" O PHE Z 40 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 2.80 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.520 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.878 9568 Z= 0.492 Angle : 0.661 26.411 13062 Z= 0.385 Chirality : 0.044 0.220 1642 Planarity : 0.005 0.048 1666 Dihedral : 15.126 88.762 3009 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.50 % Allowed : 26.64 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1325 helix: 1.19 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.76 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 31 PHE 0.015 0.001 PHE N 68 TYR 0.009 0.001 TYR T 277 ARG 0.001 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.13857 ( 874) hydrogen bonds : angle 5.57961 ( 2607) SS BOND : bond 0.87785 ( 1) SS BOND : angle 19.67063 ( 2) covalent geometry : bond 0.00333 ( 9567) covalent geometry : angle 0.61449 (13060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 464 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9329 (ttm110) cc_final: 0.8958 (ttm110) REVERT: H 62 PHE cc_start: 0.9265 (m-80) cc_final: 0.8966 (m-80) REVERT: I 15 LEU cc_start: 0.9087 (tp) cc_final: 0.8493 (tp) REVERT: I 46 VAL cc_start: 0.9275 (t) cc_final: 0.8978 (p) REVERT: I 49 MET cc_start: 0.9619 (ttt) cc_final: 0.8931 (tmm) REVERT: I 53 ILE cc_start: 0.9600 (pt) cc_final: 0.9252 (pt) REVERT: I 59 LEU cc_start: 0.9600 (mp) cc_final: 0.9253 (mp) REVERT: I 62 PHE cc_start: 0.8877 (m-10) cc_final: 0.8522 (m-80) REVERT: I 68 PHE cc_start: 0.9015 (m-80) cc_final: 0.8806 (m-80) REVERT: J 40 GLU cc_start: 0.8709 (mm-30) cc_final: 0.7948 (mp0) REVERT: J 48 TYR cc_start: 0.9254 (m-80) cc_final: 0.8636 (m-80) REVERT: J 49 MET cc_start: 0.9579 (ppp) cc_final: 0.9357 (ppp) REVERT: K 33 GLN cc_start: 0.9292 (mm-40) cc_final: 0.8962 (mm110) REVERT: K 49 MET cc_start: 0.9582 (tmm) cc_final: 0.9083 (tmm) REVERT: K 53 ILE cc_start: 0.9611 (mm) cc_final: 0.9384 (mt) REVERT: K 62 PHE cc_start: 0.9436 (m-10) cc_final: 0.9235 (m-80) REVERT: L 48 TYR cc_start: 0.9323 (m-80) cc_final: 0.9097 (m-80) REVERT: M 32 VAL cc_start: 0.9877 (t) cc_final: 0.9600 (p) REVERT: M 33 GLN cc_start: 0.9098 (mm110) cc_final: 0.8645 (mm110) REVERT: M 46 VAL cc_start: 0.9567 (t) cc_final: 0.9156 (t) REVERT: M 49 MET cc_start: 0.9359 (ttp) cc_final: 0.8963 (tmm) REVERT: M 50 PHE cc_start: 0.9066 (m-80) cc_final: 0.8539 (m-80) REVERT: M 66 ILE cc_start: 0.9692 (mm) cc_final: 0.9375 (tt) REVERT: N 48 TYR cc_start: 0.9151 (m-80) cc_final: 0.8875 (m-80) REVERT: N 51 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8694 (pt) REVERT: N 55 PHE cc_start: 0.9376 (m-80) cc_final: 0.9075 (m-80) REVERT: N 57 GLU cc_start: 0.9583 (mm-30) cc_final: 0.9242 (tm-30) REVERT: O 29 SER cc_start: 0.9706 (t) cc_final: 0.9356 (p) REVERT: O 48 TYR cc_start: 0.8919 (m-80) cc_final: 0.8555 (m-80) REVERT: O 49 MET cc_start: 0.9497 (ttp) cc_final: 0.9267 (ptm) REVERT: O 62 PHE cc_start: 0.9012 (m-80) cc_final: 0.8712 (m-80) REVERT: O 66 ILE cc_start: 0.9385 (mm) cc_final: 0.8999 (mm) REVERT: P 29 SER cc_start: 0.9455 (t) cc_final: 0.9139 (t) REVERT: P 38 ASN cc_start: 0.9291 (t0) cc_final: 0.8844 (t0) REVERT: P 61 ILE cc_start: 0.9648 (mm) cc_final: 0.9443 (mm) REVERT: Q 28 VAL cc_start: 0.9713 (t) cc_final: 0.9501 (m) REVERT: Q 37 ARG cc_start: 0.8697 (mmp80) cc_final: 0.8104 (mmm160) REVERT: Q 43 ASN cc_start: 0.9252 (p0) cc_final: 0.8464 (t0) REVERT: Q 49 MET cc_start: 0.9553 (ttp) cc_final: 0.9137 (tmm) REVERT: T 102 TYR cc_start: 0.8850 (m-80) cc_final: 0.8637 (m-80) REVERT: T 122 TRP cc_start: 0.8812 (m-10) cc_final: 0.8513 (m-10) REVERT: T 200 ILE cc_start: 0.9436 (tt) cc_final: 0.9234 (pt) REVERT: T 206 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8456 (mm-30) REVERT: T 240 LEU cc_start: 0.9552 (mt) cc_final: 0.9263 (mt) REVERT: T 244 PHE cc_start: 0.9457 (m-80) cc_final: 0.9063 (m-80) REVERT: T 260 LEU cc_start: 0.9610 (tp) cc_final: 0.9367 (tp) REVERT: T 261 LEU cc_start: 0.9165 (mt) cc_final: 0.8816 (mt) REVERT: T 277 TYR cc_start: 0.8908 (m-80) cc_final: 0.8413 (m-80) REVERT: T 287 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9195 (tp40) REVERT: Z 75 MET cc_start: 0.9190 (tpt) cc_final: 0.8936 (mpp) REVERT: Z 93 ASN cc_start: 0.9078 (m-40) cc_final: 0.8838 (t0) REVERT: Z 95 PHE cc_start: 0.9424 (m-10) cc_final: 0.9031 (m-80) REVERT: Z 114 PHE cc_start: 0.9172 (t80) cc_final: 0.8838 (t80) REVERT: Z 190 ASP cc_start: 0.7796 (t0) cc_final: 0.7496 (p0) REVERT: Z 206 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8804 (mm-30) REVERT: Z 264 MET cc_start: 0.9396 (mmt) cc_final: 0.8860 (tpp) REVERT: Z 277 TYR cc_start: 0.8806 (m-80) cc_final: 0.8495 (m-80) REVERT: Z 282 PHE cc_start: 0.9357 (t80) cc_final: 0.9010 (t80) REVERT: Z 296 TYR cc_start: 0.9124 (t80) cc_final: 0.8682 (t80) REVERT: Z 298 PHE cc_start: 0.9283 (m-10) cc_final: 0.9046 (m-10) outliers start: 4 outliers final: 1 residues processed: 466 average time/residue: 0.1624 time to fit residues: 111.4641 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 : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain N residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN H 38 ASN J 33 GLN Z 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.070077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.057471 restraints weight = 44883.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058831 restraints weight = 30773.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059858 restraints weight = 23147.368| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9568 Z= 0.168 Angle : 0.696 10.978 13062 Z= 0.363 Chirality : 0.047 0.299 1642 Planarity : 0.005 0.068 1666 Dihedral : 4.140 31.002 1397 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.83 % Allowed : 29.37 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1325 helix: 1.29 (0.15), residues: 1061 sheet: None (None), residues: 0 loop : -1.98 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.024 0.001 PHE Z 202 TYR 0.021 0.002 TYR M 48 ARG 0.006 0.001 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 874) hydrogen bonds : angle 4.48087 ( 2607) SS BOND : bond 0.00170 ( 1) SS BOND : angle 1.68188 ( 2) covalent geometry : bond 0.00358 ( 9567) covalent geometry : angle 0.69579 (13060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 409 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9324 (ttm110) cc_final: 0.9044 (ttm110) REVERT: H 57 GLU cc_start: 0.9164 (tp30) cc_final: 0.8733 (tp30) REVERT: H 59 LEU cc_start: 0.9761 (mm) cc_final: 0.9551 (mp) REVERT: H 61 ILE cc_start: 0.9724 (mm) cc_final: 0.9397 (mm) REVERT: H 62 PHE cc_start: 0.9269 (m-80) cc_final: 0.8770 (m-80) REVERT: I 15 LEU cc_start: 0.9175 (tp) cc_final: 0.8549 (tp) REVERT: I 46 VAL cc_start: 0.9344 (t) cc_final: 0.9101 (p) REVERT: I 49 MET cc_start: 0.9619 (ttt) cc_final: 0.8950 (tmm) REVERT: I 59 LEU cc_start: 0.9626 (mp) cc_final: 0.9181 (mp) REVERT: I 68 PHE cc_start: 0.9054 (m-80) cc_final: 0.8591 (m-80) REVERT: J 40 GLU cc_start: 0.8674 (mm-30) cc_final: 0.7948 (mp0) REVERT: J 48 TYR cc_start: 0.9286 (m-80) cc_final: 0.8598 (m-80) REVERT: J 49 MET cc_start: 0.9616 (ppp) cc_final: 0.9077 (ppp) REVERT: J 57 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8765 (mt-10) REVERT: K 33 GLN cc_start: 0.9311 (mm-40) cc_final: 0.9073 (mm-40) REVERT: K 48 TYR cc_start: 0.9290 (m-80) cc_final: 0.8396 (m-80) REVERT: K 49 MET cc_start: 0.9569 (tmm) cc_final: 0.9270 (tmm) REVERT: M 32 VAL cc_start: 0.9874 (t) cc_final: 0.9638 (p) REVERT: M 33 GLN cc_start: 0.9125 (mm110) cc_final: 0.8742 (mm110) REVERT: M 46 VAL cc_start: 0.9523 (t) cc_final: 0.9195 (t) REVERT: M 49 MET cc_start: 0.9351 (ttp) cc_final: 0.9140 (ppp) REVERT: M 50 PHE cc_start: 0.9075 (m-80) cc_final: 0.8560 (m-80) REVERT: M 66 ILE cc_start: 0.9664 (mm) cc_final: 0.9385 (tt) REVERT: N 48 TYR cc_start: 0.9316 (m-80) cc_final: 0.8699 (m-80) REVERT: N 55 PHE cc_start: 0.9434 (m-80) cc_final: 0.9230 (m-80) REVERT: N 57 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9052 (tm-30) REVERT: N 68 PHE cc_start: 0.8957 (m-10) cc_final: 0.8745 (m-10) REVERT: O 29 SER cc_start: 0.9658 (t) cc_final: 0.9311 (p) REVERT: O 49 MET cc_start: 0.9461 (ttp) cc_final: 0.8804 (tmm) REVERT: O 62 PHE cc_start: 0.9033 (m-80) cc_final: 0.8686 (m-80) REVERT: O 66 ILE cc_start: 0.9479 (mm) cc_final: 0.9271 (mm) REVERT: P 43 ASN cc_start: 0.9366 (p0) cc_final: 0.9160 (p0) REVERT: P 57 GLU cc_start: 0.9556 (tp30) cc_final: 0.8973 (mm-30) REVERT: Q 28 VAL cc_start: 0.9859 (t) cc_final: 0.9654 (m) REVERT: Q 37 ARG cc_start: 0.8502 (mmp80) cc_final: 0.7976 (mmm160) REVERT: Q 38 ASN cc_start: 0.9019 (p0) cc_final: 0.8768 (p0) REVERT: Q 43 ASN cc_start: 0.8901 (p0) cc_final: 0.8693 (t0) REVERT: Q 57 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: T 89 GLU cc_start: 0.9305 (pt0) cc_final: 0.8998 (pp20) REVERT: T 122 TRP cc_start: 0.8895 (m-10) cc_final: 0.8466 (m-10) REVERT: T 200 ILE cc_start: 0.9444 (tt) cc_final: 0.9238 (pt) REVERT: T 206 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8406 (mm-30) REVERT: T 240 LEU cc_start: 0.9613 (mt) cc_final: 0.9399 (mt) REVERT: T 253 ASN cc_start: 0.9428 (m-40) cc_final: 0.8948 (m110) REVERT: T 264 MET cc_start: 0.9616 (mmm) cc_final: 0.9294 (mmm) REVERT: T 277 TYR cc_start: 0.9011 (m-80) cc_final: 0.8362 (m-80) REVERT: Z 85 GLU cc_start: 0.9261 (tt0) cc_final: 0.8534 (tm-30) REVERT: Z 89 GLU cc_start: 0.8812 (pt0) cc_final: 0.8056 (pt0) REVERT: Z 95 PHE cc_start: 0.9409 (m-10) cc_final: 0.8990 (m-80) REVERT: Z 114 PHE cc_start: 0.9362 (t80) cc_final: 0.9150 (t80) REVERT: Z 190 ASP cc_start: 0.7842 (t0) cc_final: 0.7553 (p0) REVERT: Z 202 PHE cc_start: 0.9207 (t80) cc_final: 0.8935 (t80) REVERT: Z 228 MET cc_start: 0.7103 (ttt) cc_final: 0.6872 (ttt) REVERT: Z 239 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9190 (mm-30) REVERT: Z 264 MET cc_start: 0.9443 (mmt) cc_final: 0.8928 (tpp) REVERT: Z 277 TYR cc_start: 0.8821 (m-80) cc_final: 0.8570 (m-80) REVERT: Z 282 PHE cc_start: 0.9405 (t80) cc_final: 0.9071 (t80) REVERT: Z 296 TYR cc_start: 0.9090 (t80) cc_final: 0.8676 (t80) outliers start: 39 outliers final: 23 residues processed: 427 average time/residue: 0.1558 time to fit residues: 99.5573 Evaluate side-chains 406 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 382 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** Z 287 GLN ** 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 = 0.3424 r_free = 0.3424 target = 0.070153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057859 restraints weight = 44249.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059150 restraints weight = 30620.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059971 restraints weight = 23521.004| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9568 Z= 0.160 Angle : 0.692 10.446 13062 Z= 0.356 Chirality : 0.048 0.378 1642 Planarity : 0.005 0.063 1666 Dihedral : 4.058 25.486 1393 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.82 % Allowed : 29.99 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1325 helix: 1.20 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 31 PHE 0.037 0.001 PHE I 62 TYR 0.033 0.002 TYR M 48 ARG 0.007 0.001 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 874) hydrogen bonds : angle 4.38575 ( 2607) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.62785 ( 2) covalent geometry : bond 0.00344 ( 9567) covalent geometry : angle 0.69233 (13060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 403 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9333 (ttm110) cc_final: 0.8908 (ttm110) REVERT: H 59 LEU cc_start: 0.9741 (mm) cc_final: 0.9503 (mp) REVERT: H 62 PHE cc_start: 0.9217 (m-80) cc_final: 0.8790 (m-80) REVERT: I 15 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8654 (tp) REVERT: I 49 MET cc_start: 0.9620 (ttt) cc_final: 0.9023 (tmm) REVERT: I 68 PHE cc_start: 0.9121 (m-80) cc_final: 0.8635 (m-80) REVERT: J 40 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7963 (mp0) REVERT: J 44 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7438 (ttt90) REVERT: J 48 TYR cc_start: 0.9284 (m-80) cc_final: 0.8619 (m-80) REVERT: J 49 MET cc_start: 0.9632 (ppp) cc_final: 0.9113 (ppp) REVERT: J 57 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8764 (mt-10) REVERT: K 33 GLN cc_start: 0.9300 (mm-40) cc_final: 0.9047 (mm-40) REVERT: L 43 ASN cc_start: 0.8815 (t0) cc_final: 0.8460 (m110) REVERT: L 48 TYR cc_start: 0.9402 (m-80) cc_final: 0.8682 (m-80) REVERT: M 32 VAL cc_start: 0.9874 (t) cc_final: 0.9629 (p) REVERT: M 46 VAL cc_start: 0.9482 (t) cc_final: 0.9131 (t) REVERT: M 50 PHE cc_start: 0.9068 (m-80) cc_final: 0.8602 (m-80) REVERT: N 41 ILE cc_start: 0.9623 (OUTLIER) cc_final: 0.9138 (tp) REVERT: N 48 TYR cc_start: 0.9335 (m-80) cc_final: 0.8726 (m-80) REVERT: N 55 PHE cc_start: 0.9461 (m-80) cc_final: 0.9115 (m-80) REVERT: O 29 SER cc_start: 0.9616 (t) cc_final: 0.9250 (p) REVERT: O 37 ARG cc_start: 0.9160 (mmt90) cc_final: 0.8667 (mtm180) REVERT: O 44 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7571 (mmm-85) REVERT: O 48 TYR cc_start: 0.8964 (m-80) cc_final: 0.8432 (m-80) REVERT: O 49 MET cc_start: 0.9459 (ttp) cc_final: 0.8786 (tmm) REVERT: O 57 GLU cc_start: 0.9225 (pt0) cc_final: 0.8987 (pp20) REVERT: O 62 PHE cc_start: 0.9082 (m-80) cc_final: 0.8727 (m-80) REVERT: O 66 ILE cc_start: 0.9523 (mm) cc_final: 0.9217 (mm) REVERT: O 70 ILE cc_start: 0.8687 (mm) cc_final: 0.8451 (mm) REVERT: P 37 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7937 (ttm170) REVERT: P 43 ASN cc_start: 0.9414 (p0) cc_final: 0.9196 (p0) REVERT: Q 28 VAL cc_start: 0.9793 (t) cc_final: 0.9580 (m) REVERT: Q 37 ARG cc_start: 0.8784 (mmp80) cc_final: 0.8202 (mmm160) REVERT: Q 38 ASN cc_start: 0.8989 (p0) cc_final: 0.8771 (p0) REVERT: Q 43 ASN cc_start: 0.8981 (p0) cc_final: 0.8775 (t0) REVERT: Q 49 MET cc_start: 0.9190 (tmm) cc_final: 0.8945 (tmm) REVERT: Q 57 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: T 89 GLU cc_start: 0.9262 (pt0) cc_final: 0.8970 (pp20) REVERT: T 122 TRP cc_start: 0.8901 (m-10) cc_final: 0.8587 (m-10) REVERT: T 206 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8404 (mm-30) REVERT: T 228 MET cc_start: 0.9034 (ppp) cc_final: 0.8762 (ppp) REVERT: T 240 LEU cc_start: 0.9612 (mt) cc_final: 0.9374 (mt) REVERT: T 253 ASN cc_start: 0.9342 (m-40) cc_final: 0.9007 (m-40) REVERT: T 264 MET cc_start: 0.9698 (mmm) cc_final: 0.9434 (mmm) REVERT: T 277 TYR cc_start: 0.8869 (m-80) cc_final: 0.8427 (m-80) REVERT: Z 85 GLU cc_start: 0.9274 (tt0) cc_final: 0.8424 (tm-30) REVERT: Z 89 GLU cc_start: 0.8910 (pt0) cc_final: 0.8019 (pt0) REVERT: Z 95 PHE cc_start: 0.9407 (m-10) cc_final: 0.8978 (m-80) REVERT: Z 206 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8988 (mm-30) REVERT: Z 228 MET cc_start: 0.7149 (ttt) cc_final: 0.6780 (ttt) REVERT: Z 239 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9248 (mm-30) REVERT: Z 264 MET cc_start: 0.9469 (mmt) cc_final: 0.8946 (tpp) REVERT: Z 277 TYR cc_start: 0.8877 (m-80) cc_final: 0.8532 (m-80) REVERT: Z 282 PHE cc_start: 0.9383 (t80) cc_final: 0.9091 (t80) REVERT: Z 296 TYR cc_start: 0.9118 (t80) cc_final: 0.8812 (t80) outliers start: 47 outliers final: 32 residues processed: 427 average time/residue: 0.1575 time to fit residues: 100.5122 Evaluate side-chains 409 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 373 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 80 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 105 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057948 restraints weight = 45060.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058978 restraints weight = 31624.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.059990 restraints weight = 25165.512| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9568 Z= 0.162 Angle : 0.723 10.156 13062 Z= 0.372 Chirality : 0.048 0.244 1642 Planarity : 0.005 0.055 1666 Dihedral : 4.106 25.034 1393 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.95 % Allowed : 32.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1325 helix: 1.09 (0.16), residues: 1065 sheet: None (None), residues: 0 loop : -2.11 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 208 HIS 0.000 0.000 HIS Z 31 PHE 0.034 0.001 PHE P 62 TYR 0.020 0.002 TYR K 48 ARG 0.005 0.000 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 874) hydrogen bonds : angle 4.40077 ( 2607) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.45387 ( 2) covalent geometry : bond 0.00353 ( 9567) covalent geometry : angle 0.72343 (13060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 392 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9310 (ttm110) cc_final: 0.8921 (ttm110) REVERT: H 48 TYR cc_start: 0.9118 (m-80) cc_final: 0.8908 (m-80) REVERT: H 59 LEU cc_start: 0.9764 (mm) cc_final: 0.9512 (mp) REVERT: H 62 PHE cc_start: 0.9204 (m-80) cc_final: 0.8735 (m-80) REVERT: I 49 MET cc_start: 0.9589 (ttt) cc_final: 0.8989 (tmm) REVERT: I 68 PHE cc_start: 0.9129 (m-80) cc_final: 0.8667 (m-80) REVERT: J 40 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8009 (mp0) REVERT: J 44 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7779 (mmm-85) REVERT: J 48 TYR cc_start: 0.9290 (m-80) cc_final: 0.8600 (m-80) REVERT: J 49 MET cc_start: 0.9629 (ppp) cc_final: 0.9107 (ppp) REVERT: J 57 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8792 (mt-10) REVERT: K 33 GLN cc_start: 0.9292 (mm-40) cc_final: 0.9074 (mm-40) REVERT: L 43 ASN cc_start: 0.8712 (t0) cc_final: 0.8286 (m110) REVERT: M 33 GLN cc_start: 0.9348 (mm110) cc_final: 0.9004 (mm110) REVERT: M 46 VAL cc_start: 0.9499 (t) cc_final: 0.9211 (t) REVERT: M 50 PHE cc_start: 0.9239 (m-80) cc_final: 0.8616 (m-80) REVERT: N 48 TYR cc_start: 0.9342 (m-80) cc_final: 0.8705 (m-80) REVERT: N 55 PHE cc_start: 0.9442 (m-80) cc_final: 0.9152 (m-80) REVERT: N 64 LEU cc_start: 0.9778 (tp) cc_final: 0.9453 (tp) REVERT: O 29 SER cc_start: 0.9584 (t) cc_final: 0.9247 (p) REVERT: O 37 ARG cc_start: 0.9081 (mmt90) cc_final: 0.8666 (mtm180) REVERT: O 44 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7556 (mmm-85) REVERT: O 48 TYR cc_start: 0.8942 (m-80) cc_final: 0.8314 (m-80) REVERT: O 49 MET cc_start: 0.9478 (ttp) cc_final: 0.8809 (tmm) REVERT: O 57 GLU cc_start: 0.9194 (pt0) cc_final: 0.8932 (pp20) REVERT: O 62 PHE cc_start: 0.9109 (m-80) cc_final: 0.8767 (m-80) REVERT: O 66 ILE cc_start: 0.9551 (mm) cc_final: 0.9244 (mm) REVERT: P 37 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7840 (ttm170) REVERT: P 42 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9022 (tt0) REVERT: P 43 ASN cc_start: 0.9429 (p0) cc_final: 0.9225 (p0) REVERT: P 48 TYR cc_start: 0.9210 (m-80) cc_final: 0.8991 (m-80) REVERT: P 57 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8778 (pt0) REVERT: Q 28 VAL cc_start: 0.9788 (t) cc_final: 0.9570 (m) REVERT: Q 37 ARG cc_start: 0.8813 (mmp80) cc_final: 0.8222 (mmm160) REVERT: Q 57 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: T 84 MET cc_start: 0.9077 (mmm) cc_final: 0.8433 (mpp) REVERT: T 122 TRP cc_start: 0.8958 (m-10) cc_final: 0.8611 (m-10) REVERT: T 206 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8408 (mm-30) REVERT: T 228 MET cc_start: 0.9052 (ppp) cc_final: 0.8510 (ppp) REVERT: T 253 ASN cc_start: 0.9572 (m-40) cc_final: 0.9221 (m110) REVERT: T 264 MET cc_start: 0.9680 (mmm) cc_final: 0.9370 (mmm) REVERT: T 277 TYR cc_start: 0.8836 (m-80) cc_final: 0.8408 (m-80) REVERT: Z 85 GLU cc_start: 0.9266 (tt0) cc_final: 0.8598 (tm-30) REVERT: Z 95 PHE cc_start: 0.9413 (m-10) cc_final: 0.8980 (m-80) REVERT: Z 228 MET cc_start: 0.7193 (ttt) cc_final: 0.6787 (ttt) REVERT: Z 264 MET cc_start: 0.9438 (mmt) cc_final: 0.8923 (tpp) REVERT: Z 277 TYR cc_start: 0.8869 (m-80) cc_final: 0.8543 (m-80) REVERT: Z 282 PHE cc_start: 0.9344 (t80) cc_final: 0.9000 (t80) REVERT: Z 286 ILE cc_start: 0.9627 (pt) cc_final: 0.9275 (pt) REVERT: Z 296 TYR cc_start: 0.9064 (t80) cc_final: 0.8858 (t80) outliers start: 48 outliers final: 31 residues processed: 417 average time/residue: 0.1541 time to fit residues: 96.0727 Evaluate side-chains 393 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 360 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 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 56 THR Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 233 ILE Chi-restraints excluded: chain T residue 261 LEU Chi-restraints excluded: chain T residue 271 LEU Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 88 LEU Chi-restraints excluded: chain Z residue 103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 37 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.070398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057832 restraints weight = 45075.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059103 restraints weight = 31938.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059852 restraints weight = 24843.652| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9568 Z= 0.166 Angle : 0.738 9.591 13062 Z= 0.379 Chirality : 0.051 0.423 1642 Planarity : 0.004 0.049 1666 Dihedral : 4.164 24.981 1393 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.32 % Allowed : 37.30 % Favored : 56.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1325 helix: 1.11 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.030 0.001 PHE Z 202 TYR 0.016 0.002 TYR L 48 ARG 0.004 0.000 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 874) hydrogen bonds : angle 4.42242 ( 2607) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.38581 ( 2) covalent geometry : bond 0.00371 ( 9567) covalent geometry : angle 0.73838 (13060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 384 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9325 (ttm110) cc_final: 0.8945 (ttm110) REVERT: H 48 TYR cc_start: 0.9140 (m-80) cc_final: 0.8925 (m-80) REVERT: H 62 PHE cc_start: 0.9188 (m-80) cc_final: 0.8847 (m-80) REVERT: I 15 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8332 (tp) REVERT: I 48 TYR cc_start: 0.9358 (m-80) cc_final: 0.9033 (m-80) REVERT: I 49 MET cc_start: 0.9587 (ttt) cc_final: 0.9007 (tmm) REVERT: I 68 PHE cc_start: 0.9165 (m-80) cc_final: 0.8669 (m-80) REVERT: J 40 GLU cc_start: 0.8708 (mm-30) cc_final: 0.7982 (mp0) REVERT: J 44 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7467 (ttt90) REVERT: J 48 TYR cc_start: 0.9279 (m-80) cc_final: 0.8670 (m-80) REVERT: J 49 MET cc_start: 0.9613 (ppp) cc_final: 0.9099 (ppp) REVERT: J 57 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8848 (mt-10) REVERT: K 15 LEU cc_start: 0.9143 (mm) cc_final: 0.8892 (mm) REVERT: K 33 GLN cc_start: 0.9321 (mm-40) cc_final: 0.9108 (mm-40) REVERT: K 48 TYR cc_start: 0.9264 (m-80) cc_final: 0.8191 (m-80) REVERT: K 57 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9251 (mm-30) REVERT: K 62 PHE cc_start: 0.9471 (m-80) cc_final: 0.8945 (m-80) REVERT: L 43 ASN cc_start: 0.8687 (t0) cc_final: 0.8236 (m-40) REVERT: M 33 GLN cc_start: 0.9367 (mm110) cc_final: 0.9148 (mm110) REVERT: M 46 VAL cc_start: 0.9407 (t) cc_final: 0.9163 (t) REVERT: M 49 MET cc_start: 0.9395 (ppp) cc_final: 0.9099 (ppp) REVERT: M 50 PHE cc_start: 0.9230 (m-80) cc_final: 0.8628 (m-80) REVERT: N 48 TYR cc_start: 0.9381 (m-80) cc_final: 0.8721 (m-80) REVERT: N 55 PHE cc_start: 0.9458 (m-80) cc_final: 0.9141 (m-80) REVERT: N 64 LEU cc_start: 0.9793 (tp) cc_final: 0.9590 (tt) REVERT: O 29 SER cc_start: 0.9560 (t) cc_final: 0.9222 (p) REVERT: O 37 ARG cc_start: 0.9076 (mmt90) cc_final: 0.8686 (mtm180) REVERT: O 44 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7482 (mmm-85) REVERT: O 48 TYR cc_start: 0.8958 (m-80) cc_final: 0.8331 (m-80) REVERT: O 49 MET cc_start: 0.9482 (ttp) cc_final: 0.8797 (tmm) REVERT: O 57 GLU cc_start: 0.9218 (pt0) cc_final: 0.8935 (pp20) REVERT: O 62 PHE cc_start: 0.9105 (m-80) cc_final: 0.8759 (m-80) REVERT: O 66 ILE cc_start: 0.9555 (mm) cc_final: 0.9250 (mm) REVERT: P 37 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7890 (ttm170) REVERT: P 42 GLU cc_start: 0.9275 (mt-10) cc_final: 0.9025 (tt0) REVERT: P 43 ASN cc_start: 0.9451 (p0) cc_final: 0.9215 (p0) REVERT: P 48 TYR cc_start: 0.9197 (m-80) cc_final: 0.8945 (m-80) REVERT: P 57 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8733 (pt0) REVERT: Q 28 VAL cc_start: 0.9792 (t) cc_final: 0.9585 (m) REVERT: Q 37 ARG cc_start: 0.8715 (mmp80) cc_final: 0.8147 (mmm160) REVERT: Q 57 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: T 84 MET cc_start: 0.9078 (mmm) cc_final: 0.8445 (mpp) REVERT: T 122 TRP cc_start: 0.8942 (m-10) cc_final: 0.8594 (m-10) REVERT: T 206 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8438 (mm-30) REVERT: T 228 MET cc_start: 0.9049 (ppp) cc_final: 0.8786 (ppp) REVERT: T 253 ASN cc_start: 0.9512 (m-40) cc_final: 0.9269 (m110) REVERT: T 255 PHE cc_start: 0.9658 (t80) cc_final: 0.9450 (t80) REVERT: T 264 MET cc_start: 0.9689 (mmm) cc_final: 0.9407 (mmm) REVERT: T 277 TYR cc_start: 0.8822 (m-80) cc_final: 0.8419 (m-80) REVERT: Z 85 GLU cc_start: 0.9273 (tt0) cc_final: 0.8596 (tm-30) REVERT: Z 95 PHE cc_start: 0.9411 (m-10) cc_final: 0.8979 (m-80) REVERT: Z 228 MET cc_start: 0.7186 (ttt) cc_final: 0.6812 (ttt) REVERT: Z 264 MET cc_start: 0.9455 (mmt) cc_final: 0.8964 (tpp) REVERT: Z 277 TYR cc_start: 0.8931 (m-80) cc_final: 0.8568 (m-80) REVERT: Z 282 PHE cc_start: 0.9352 (t80) cc_final: 0.8880 (t80) REVERT: Z 286 ILE cc_start: 0.9643 (pt) cc_final: 0.9207 (pt) REVERT: Z 296 TYR cc_start: 0.9017 (t80) cc_final: 0.8793 (t80) outliers start: 51 outliers final: 41 residues processed: 409 average time/residue: 0.1554 time to fit residues: 95.2003 Evaluate side-chains 408 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 364 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 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 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain 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 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.070581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057855 restraints weight = 44922.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.059000 restraints weight = 32110.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059907 restraints weight = 25271.737| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3524 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= 0.159 Angle : 0.750 12.130 13062 Z= 0.382 Chirality : 0.050 0.394 1642 Planarity : 0.004 0.048 1666 Dihedral : 4.197 24.947 1393 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.33 % Allowed : 39.78 % Favored : 54.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1325 helix: 1.04 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -1.65 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.000 0.000 HIS Z 31 PHE 0.034 0.001 PHE Z 202 TYR 0.019 0.002 TYR T 102 ARG 0.004 0.000 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 874) hydrogen bonds : angle 4.41184 ( 2607) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.34036 ( 2) covalent geometry : bond 0.00354 ( 9567) covalent geometry : angle 0.75037 (13060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 386 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9321 (ttm110) cc_final: 0.9081 (ttm110) REVERT: H 48 TYR cc_start: 0.9096 (m-80) cc_final: 0.8873 (m-80) REVERT: H 62 PHE cc_start: 0.9246 (m-80) cc_final: 0.8870 (m-80) REVERT: I 15 LEU cc_start: 0.9257 (mm) cc_final: 0.8264 (tp) REVERT: I 48 TYR cc_start: 0.9369 (m-80) cc_final: 0.9041 (m-80) REVERT: I 49 MET cc_start: 0.9576 (ttt) cc_final: 0.9026 (tmm) REVERT: I 57 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8884 (mp0) REVERT: I 68 PHE cc_start: 0.9172 (m-80) cc_final: 0.8687 (m-80) REVERT: J 40 GLU cc_start: 0.8716 (mm-30) cc_final: 0.7999 (mp0) REVERT: J 44 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7641 (mmm-85) REVERT: J 48 TYR cc_start: 0.9305 (m-80) cc_final: 0.8678 (m-80) REVERT: J 49 MET cc_start: 0.9621 (ppp) cc_final: 0.9097 (ppp) REVERT: K 48 TYR cc_start: 0.9265 (m-80) cc_final: 0.8193 (m-80) REVERT: K 57 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9116 (mm-30) REVERT: L 29 SER cc_start: 0.9426 (t) cc_final: 0.9193 (p) REVERT: L 43 ASN cc_start: 0.8661 (t0) cc_final: 0.8225 (m-40) REVERT: L 48 TYR cc_start: 0.9330 (m-80) cc_final: 0.9088 (m-80) REVERT: M 46 VAL cc_start: 0.9384 (t) cc_final: 0.9088 (t) REVERT: M 49 MET cc_start: 0.9380 (ppp) cc_final: 0.9016 (ppp) REVERT: M 50 PHE cc_start: 0.9236 (m-80) cc_final: 0.8636 (m-80) REVERT: N 48 TYR cc_start: 0.9423 (m-80) cc_final: 0.8796 (m-80) REVERT: N 55 PHE cc_start: 0.9466 (m-80) cc_final: 0.9139 (m-80) REVERT: O 29 SER cc_start: 0.9560 (t) cc_final: 0.9213 (p) REVERT: O 37 ARG cc_start: 0.9042 (mmt90) cc_final: 0.8715 (mtm180) REVERT: O 44 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7453 (mmm-85) REVERT: O 48 TYR cc_start: 0.8966 (m-80) cc_final: 0.8369 (m-80) REVERT: O 49 MET cc_start: 0.9481 (ttp) cc_final: 0.8770 (tmm) REVERT: O 57 GLU cc_start: 0.9219 (pt0) cc_final: 0.8935 (pp20) REVERT: O 62 PHE cc_start: 0.9122 (m-80) cc_final: 0.8774 (m-80) REVERT: O 66 ILE cc_start: 0.9528 (mm) cc_final: 0.9217 (mm) REVERT: P 37 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7813 (ttm170) REVERT: P 43 ASN cc_start: 0.9453 (p0) cc_final: 0.9198 (p0) REVERT: P 48 TYR cc_start: 0.9182 (m-80) cc_final: 0.8959 (m-80) REVERT: Q 28 VAL cc_start: 0.9814 (t) cc_final: 0.9589 (m) REVERT: Q 57 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: Q 61 ILE cc_start: 0.9082 (pt) cc_final: 0.8804 (pt) REVERT: T 206 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8460 (mm-30) REVERT: T 228 MET cc_start: 0.9041 (ppp) cc_final: 0.8778 (ppp) REVERT: T 240 LEU cc_start: 0.9484 (mm) cc_final: 0.9279 (mm) REVERT: T 253 ASN cc_start: 0.9574 (m-40) cc_final: 0.9313 (m110) REVERT: T 264 MET cc_start: 0.9693 (mmm) cc_final: 0.9417 (mmm) REVERT: T 277 TYR cc_start: 0.8818 (m-80) cc_final: 0.8443 (m-80) REVERT: Z 85 GLU cc_start: 0.9295 (tt0) cc_final: 0.8616 (tm-30) REVERT: Z 95 PHE cc_start: 0.9408 (m-10) cc_final: 0.8962 (m-80) REVERT: Z 228 MET cc_start: 0.7329 (ttt) cc_final: 0.6871 (ttt) REVERT: Z 264 MET cc_start: 0.9447 (mmt) cc_final: 0.8911 (tpp) REVERT: Z 282 PHE cc_start: 0.9359 (t80) cc_final: 0.9033 (t80) REVERT: Z 286 ILE cc_start: 0.9635 (pt) cc_final: 0.9273 (pt) REVERT: Z 296 TYR cc_start: 0.8990 (t80) cc_final: 0.8761 (t80) outliers start: 43 outliers final: 36 residues processed: 407 average time/residue: 0.1608 time to fit residues: 96.9843 Evaluate side-chains 406 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 367 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 22 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain 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 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 ASN Z 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.070761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058124 restraints weight = 46026.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059197 restraints weight = 32741.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060120 restraints weight = 25755.642| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9568 Z= 0.162 Angle : 0.769 9.952 13062 Z= 0.394 Chirality : 0.051 0.302 1642 Planarity : 0.004 0.047 1666 Dihedral : 4.245 25.023 1393 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.70 % Allowed : 42.13 % Favored : 52.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1325 helix: 1.11 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : -1.69 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP T 122 HIS 0.000 0.000 HIS Z 31 PHE 0.030 0.001 PHE Z 202 TYR 0.032 0.002 TYR M 48 ARG 0.006 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 874) hydrogen bonds : angle 4.39523 ( 2607) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.33224 ( 2) covalent geometry : bond 0.00363 ( 9567) covalent geometry : angle 0.76921 (13060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 384 time to evaluate : 1.147 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: 0.9105 (mt) cc_final: 0.8875 (mt) REVERT: H 37 ARG cc_start: 0.9276 (ttm110) cc_final: 0.9061 (ttm110) REVERT: H 48 TYR cc_start: 0.9095 (m-80) cc_final: 0.8889 (m-80) REVERT: H 62 PHE cc_start: 0.9206 (m-10) cc_final: 0.8958 (m-80) REVERT: I 15 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8380 (tp) REVERT: I 48 TYR cc_start: 0.9349 (m-80) cc_final: 0.9038 (m-80) REVERT: I 49 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.8983 (tmm) REVERT: I 57 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.8871 (mp0) REVERT: I 68 PHE cc_start: 0.9154 (m-80) cc_final: 0.8670 (m-80) REVERT: J 40 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8124 (mp0) REVERT: J 44 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7346 (ttt90) REVERT: J 48 TYR cc_start: 0.9283 (m-80) cc_final: 0.8754 (m-80) REVERT: J 49 MET cc_start: 0.9612 (ppp) cc_final: 0.9120 (ppp) REVERT: J 61 ILE cc_start: 0.9543 (mm) cc_final: 0.9309 (mp) REVERT: K 15 LEU cc_start: 0.9157 (mm) cc_final: 0.8929 (mm) REVERT: K 48 TYR cc_start: 0.9242 (m-80) cc_final: 0.8140 (m-80) REVERT: K 57 GLU cc_start: 0.9600 (mm-30) cc_final: 0.9100 (mm-30) REVERT: L 43 ASN cc_start: 0.8628 (t0) cc_final: 0.8222 (m110) REVERT: L 48 TYR cc_start: 0.9346 (m-80) cc_final: 0.9064 (m-80) REVERT: M 33 GLN cc_start: 0.9347 (mm110) cc_final: 0.8809 (mm110) REVERT: M 46 VAL cc_start: 0.9373 (t) cc_final: 0.9088 (t) REVERT: M 49 MET cc_start: 0.9358 (ppp) cc_final: 0.9038 (ppp) REVERT: M 50 PHE cc_start: 0.9208 (m-80) cc_final: 0.8652 (m-80) REVERT: N 15 LEU cc_start: 0.9619 (mm) cc_final: 0.9395 (mm) REVERT: N 18 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7823 (tt) REVERT: N 48 TYR cc_start: 0.9365 (m-80) cc_final: 0.8805 (m-80) REVERT: N 55 PHE cc_start: 0.9454 (m-80) cc_final: 0.9107 (m-80) REVERT: O 29 SER cc_start: 0.9532 (t) cc_final: 0.9162 (p) REVERT: O 37 ARG cc_start: 0.8954 (mmt90) cc_final: 0.8633 (mtm180) REVERT: O 44 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7343 (mmm-85) REVERT: O 48 TYR cc_start: 0.8933 (m-80) cc_final: 0.8301 (m-80) REVERT: O 49 MET cc_start: 0.9492 (ttp) cc_final: 0.8814 (tmm) REVERT: O 57 GLU cc_start: 0.9188 (pt0) cc_final: 0.8928 (pp20) REVERT: O 62 PHE cc_start: 0.9111 (m-80) cc_final: 0.8750 (m-80) REVERT: O 66 ILE cc_start: 0.9533 (mm) cc_final: 0.9220 (mm) REVERT: P 37 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7675 (ttm170) REVERT: P 43 ASN cc_start: 0.9432 (p0) cc_final: 0.9180 (p0) REVERT: P 48 TYR cc_start: 0.9162 (m-80) cc_final: 0.8905 (m-80) REVERT: P 57 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8611 (pt0) REVERT: Q 28 VAL cc_start: 0.9787 (t) cc_final: 0.9582 (m) REVERT: Q 37 ARG cc_start: 0.8691 (mmp80) cc_final: 0.8054 (mmm160) REVERT: Q 57 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: Q 61 ILE cc_start: 0.9076 (pt) cc_final: 0.8776 (pt) REVERT: T 206 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8446 (mm-30) REVERT: T 228 MET cc_start: 0.9042 (ppp) cc_final: 0.8778 (ppp) REVERT: T 253 ASN cc_start: 0.9563 (m-40) cc_final: 0.9290 (m110) REVERT: T 264 MET cc_start: 0.9683 (mmm) cc_final: 0.9406 (mmm) REVERT: Z 95 PHE cc_start: 0.9394 (m-10) cc_final: 0.8955 (m-80) REVERT: Z 228 MET cc_start: 0.7325 (ttt) cc_final: 0.6897 (ttt) REVERT: Z 242 LYS cc_start: 0.9398 (mttt) cc_final: 0.9180 (mtpp) REVERT: Z 264 MET cc_start: 0.9489 (mmt) cc_final: 0.8938 (tpp) REVERT: Z 272 LEU cc_start: 0.9334 (tp) cc_final: 0.8992 (tp) REVERT: Z 282 PHE cc_start: 0.9369 (t80) cc_final: 0.8866 (t80) REVERT: Z 286 ILE cc_start: 0.9641 (pt) cc_final: 0.9178 (pt) REVERT: Z 296 TYR cc_start: 0.8924 (t80) cc_final: 0.8716 (t80) outliers start: 46 outliers final: 34 residues processed: 404 average time/residue: 0.1550 time to fit residues: 93.3500 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 : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 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 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 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 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 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN K 33 GLN ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 ASN Z 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.071225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058152 restraints weight = 46093.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059432 restraints weight = 32845.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060306 restraints weight = 25539.163| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9568 Z= 0.167 Angle : 0.799 10.750 13062 Z= 0.410 Chirality : 0.053 0.513 1642 Planarity : 0.005 0.048 1666 Dihedral : 4.328 25.058 1393 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.33 % Allowed : 43.62 % Favored : 51.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1325 helix: 1.04 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -1.72 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP T 122 HIS 0.001 0.000 HIS Z 31 PHE 0.027 0.001 PHE Z 202 TYR 0.020 0.002 TYR N 48 ARG 0.007 0.000 ARG J 37 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 874) hydrogen bonds : angle 4.43752 ( 2607) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.28068 ( 2) covalent geometry : bond 0.00372 ( 9567) covalent geometry : angle 0.79902 (13060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 384 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9313 (ttm110) cc_final: 0.9084 (ttm110) REVERT: H 48 TYR cc_start: 0.9117 (m-80) cc_final: 0.8888 (m-80) REVERT: H 62 PHE cc_start: 0.9280 (m-10) cc_final: 0.9038 (m-80) REVERT: I 15 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8396 (tp) REVERT: I 48 TYR cc_start: 0.9361 (m-80) cc_final: 0.9077 (m-80) REVERT: I 49 MET cc_start: 0.9567 (OUTLIER) cc_final: 0.9051 (tmm) REVERT: I 51 ILE cc_start: 0.9324 (pt) cc_final: 0.9111 (pt) REVERT: I 57 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.8834 (mp0) REVERT: I 68 PHE cc_start: 0.9202 (m-80) cc_final: 0.8728 (m-80) REVERT: J 18 ILE cc_start: 0.8421 (tp) cc_final: 0.8171 (tp) REVERT: J 40 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8188 (mp0) REVERT: J 44 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6735 (ttt-90) REVERT: J 48 TYR cc_start: 0.9303 (m-80) cc_final: 0.8585 (m-80) REVERT: J 49 MET cc_start: 0.9626 (ppp) cc_final: 0.9137 (ppp) REVERT: K 15 LEU cc_start: 0.9133 (mm) cc_final: 0.8891 (mm) REVERT: K 48 TYR cc_start: 0.9254 (m-80) cc_final: 0.8164 (m-80) REVERT: K 57 GLU cc_start: 0.9631 (mm-30) cc_final: 0.9089 (mm-30) REVERT: L 43 ASN cc_start: 0.8667 (t0) cc_final: 0.8301 (m110) REVERT: M 46 VAL cc_start: 0.9382 (t) cc_final: 0.9178 (t) REVERT: M 49 MET cc_start: 0.9392 (ppp) cc_final: 0.9050 (ppp) REVERT: M 50 PHE cc_start: 0.9185 (m-80) cc_final: 0.8641 (m-80) REVERT: N 24 ILE cc_start: 0.9593 (mt) cc_final: 0.9359 (mm) REVERT: N 48 TYR cc_start: 0.9471 (m-80) cc_final: 0.8815 (m-80) REVERT: N 55 PHE cc_start: 0.9466 (m-80) cc_final: 0.9122 (m-80) REVERT: O 29 SER cc_start: 0.9537 (t) cc_final: 0.9165 (p) REVERT: O 37 ARG cc_start: 0.9001 (mmt90) cc_final: 0.8630 (mtm180) REVERT: O 44 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7395 (mmm-85) REVERT: O 48 TYR cc_start: 0.8965 (m-80) cc_final: 0.8309 (m-80) REVERT: O 57 GLU cc_start: 0.9171 (pt0) cc_final: 0.8778 (pp20) REVERT: O 62 PHE cc_start: 0.9118 (m-80) cc_final: 0.8757 (m-80) REVERT: O 66 ILE cc_start: 0.9525 (mm) cc_final: 0.9214 (mm) REVERT: P 37 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7707 (ttm170) REVERT: P 38 ASN cc_start: 0.8969 (t0) cc_final: 0.8755 (t0) REVERT: P 43 ASN cc_start: 0.9445 (p0) cc_final: 0.9210 (p0) REVERT: P 57 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8660 (pt0) REVERT: Q 28 VAL cc_start: 0.9748 (t) cc_final: 0.9538 (m) REVERT: Q 37 ARG cc_start: 0.8691 (mmp80) cc_final: 0.8034 (mmm160) REVERT: Q 57 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: Q 61 ILE cc_start: 0.9088 (pt) cc_final: 0.8799 (pt) REVERT: T 206 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8467 (mm-30) REVERT: T 228 MET cc_start: 0.9050 (ppp) cc_final: 0.8796 (ppp) REVERT: T 253 ASN cc_start: 0.9510 (m-40) cc_final: 0.9067 (m-40) REVERT: T 264 MET cc_start: 0.9688 (mmm) cc_final: 0.9442 (mmm) REVERT: Z 33 GLU cc_start: 0.8828 (pm20) cc_final: 0.8575 (mp0) REVERT: Z 74 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8713 (mp10) REVERT: Z 85 GLU cc_start: 0.9228 (tt0) cc_final: 0.8673 (tm-30) REVERT: Z 95 PHE cc_start: 0.9403 (m-10) cc_final: 0.8972 (m-80) REVERT: Z 228 MET cc_start: 0.7328 (ttt) cc_final: 0.6888 (ttt) REVERT: Z 249 ARG cc_start: 0.9364 (ttm110) cc_final: 0.8877 (ptp-110) REVERT: Z 264 MET cc_start: 0.9519 (mmt) cc_final: 0.9067 (mmm) REVERT: Z 272 LEU cc_start: 0.9232 (tp) cc_final: 0.8918 (tp) REVERT: Z 277 TYR cc_start: 0.9101 (m-80) cc_final: 0.8771 (m-80) REVERT: Z 282 PHE cc_start: 0.9356 (t80) cc_final: 0.8830 (t80) REVERT: Z 286 ILE cc_start: 0.9631 (pt) cc_final: 0.9149 (pt) REVERT: Z 296 TYR cc_start: 0.8945 (t80) cc_final: 0.8719 (t80) outliers start: 43 outliers final: 33 residues processed: 401 average time/residue: 0.1594 time to fit residues: 94.7150 Evaluate side-chains 403 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 365 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain 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 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 103 VAL Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 0.0770 chunk 47 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.070691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057995 restraints weight = 44380.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.058937 restraints weight = 31841.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.060017 restraints weight = 25534.275| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9568 Z= 0.169 Angle : 0.831 12.137 13062 Z= 0.422 Chirality : 0.054 0.358 1642 Planarity : 0.005 0.046 1666 Dihedral : 4.336 25.169 1393 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.96 % Allowed : 45.11 % Favored : 49.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1325 helix: 0.98 (0.16), residues: 1073 sheet: None (None), residues: 0 loop : -1.70 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 122 HIS 0.000 0.000 HIS Z 31 PHE 0.024 0.001 PHE Z 202 TYR 0.018 0.002 TYR P 48 ARG 0.009 0.001 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 874) hydrogen bonds : angle 4.45947 ( 2607) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.27238 ( 2) covalent geometry : bond 0.00387 ( 9567) covalent geometry : angle 0.83064 (13060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 378 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9285 (ttm110) cc_final: 0.9051 (ttm110) REVERT: H 48 TYR cc_start: 0.9109 (m-80) cc_final: 0.8880 (m-80) REVERT: I 15 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8386 (tp) REVERT: I 48 TYR cc_start: 0.9378 (m-80) cc_final: 0.9096 (m-80) REVERT: I 49 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.9052 (tmm) REVERT: I 51 ILE cc_start: 0.9360 (pt) cc_final: 0.9157 (pt) REVERT: I 57 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.8854 (mp0) REVERT: I 68 PHE cc_start: 0.9189 (m-80) cc_final: 0.8683 (m-80) REVERT: J 18 ILE cc_start: 0.8379 (tp) cc_final: 0.8118 (tp) REVERT: J 40 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8248 (mp0) REVERT: J 44 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6717 (ttt-90) REVERT: J 48 TYR cc_start: 0.9321 (m-80) cc_final: 0.8562 (m-80) REVERT: J 49 MET cc_start: 0.9611 (ppp) cc_final: 0.9122 (ppp) REVERT: K 15 LEU cc_start: 0.9147 (mm) cc_final: 0.8905 (mm) REVERT: K 48 TYR cc_start: 0.9285 (m-80) cc_final: 0.8186 (m-80) REVERT: K 57 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9087 (mm-30) REVERT: L 43 ASN cc_start: 0.8670 (t0) cc_final: 0.8312 (m110) REVERT: M 33 GLN cc_start: 0.9405 (mm110) cc_final: 0.8782 (mp10) REVERT: M 46 VAL cc_start: 0.9386 (t) cc_final: 0.9176 (t) REVERT: M 48 TYR cc_start: 0.9094 (m-80) cc_final: 0.8567 (m-80) REVERT: M 49 MET cc_start: 0.9404 (ppp) cc_final: 0.9082 (ppp) REVERT: M 50 PHE cc_start: 0.9157 (m-80) cc_final: 0.8610 (m-80) REVERT: N 15 LEU cc_start: 0.9622 (mm) cc_final: 0.9103 (mp) REVERT: N 18 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7822 (tt) REVERT: N 48 TYR cc_start: 0.9473 (m-80) cc_final: 0.8822 (m-80) REVERT: N 55 PHE cc_start: 0.9474 (m-80) cc_final: 0.9128 (m-80) REVERT: O 29 SER cc_start: 0.9558 (t) cc_final: 0.9168 (p) REVERT: O 37 ARG cc_start: 0.9001 (mmt90) cc_final: 0.8650 (mtm180) REVERT: O 44 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.7227 (mmm-85) REVERT: O 48 TYR cc_start: 0.8943 (m-80) cc_final: 0.8289 (m-80) REVERT: O 49 MET cc_start: 0.9445 (ttp) cc_final: 0.9004 (ppp) REVERT: O 57 GLU cc_start: 0.9183 (pt0) cc_final: 0.8779 (pp20) REVERT: O 62 PHE cc_start: 0.9119 (m-80) cc_final: 0.8752 (m-80) REVERT: O 66 ILE cc_start: 0.9514 (mm) cc_final: 0.9210 (mm) REVERT: P 37 ARG cc_start: 0.8087 (ttm170) cc_final: 0.7731 (ttm170) REVERT: P 42 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9049 (tt0) REVERT: P 43 ASN cc_start: 0.9479 (p0) cc_final: 0.9246 (p0) REVERT: P 48 TYR cc_start: 0.9230 (m-80) cc_final: 0.8923 (m-80) REVERT: P 57 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8687 (pt0) REVERT: Q 28 VAL cc_start: 0.9800 (t) cc_final: 0.9594 (m) REVERT: Q 37 ARG cc_start: 0.8697 (mmp80) cc_final: 0.8026 (mmm160) REVERT: Q 57 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: Q 61 ILE cc_start: 0.9077 (pt) cc_final: 0.8773 (pt) REVERT: T 114 PHE cc_start: 0.9582 (t80) cc_final: 0.9370 (t80) REVERT: T 206 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8462 (mm-30) REVERT: T 228 MET cc_start: 0.9068 (ppp) cc_final: 0.8829 (ppp) REVERT: T 264 MET cc_start: 0.9671 (mmm) cc_final: 0.9440 (mmm) REVERT: T 287 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8987 (tp40) REVERT: Z 74 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8351 (tp-100) REVERT: Z 85 GLU cc_start: 0.9183 (tt0) cc_final: 0.8573 (tm-30) REVERT: Z 95 PHE cc_start: 0.9420 (m-10) cc_final: 0.8982 (m-80) REVERT: Z 202 PHE cc_start: 0.9187 (t80) cc_final: 0.8955 (m-80) REVERT: Z 228 MET cc_start: 0.7343 (ttt) cc_final: 0.6961 (ttt) REVERT: Z 249 ARG cc_start: 0.9345 (ttm110) cc_final: 0.9141 (ptp-110) REVERT: Z 264 MET cc_start: 0.9519 (mmt) cc_final: 0.9312 (mmm) REVERT: Z 277 TYR cc_start: 0.9136 (m-80) cc_final: 0.8769 (m-80) REVERT: Z 282 PHE cc_start: 0.9359 (t80) cc_final: 0.8824 (t80) REVERT: Z 286 ILE cc_start: 0.9637 (pt) cc_final: 0.9137 (pt) REVERT: Z 296 TYR cc_start: 0.8965 (t80) cc_final: 0.8736 (t80) outliers start: 40 outliers final: 31 residues processed: 394 average time/residue: 0.1666 time to fit residues: 96.6938 Evaluate side-chains 408 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 371 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 50 PHE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 72 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain P residue 55 PHE Chi-restraints excluded: chain Q residue 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 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 84 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.071537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058520 restraints weight = 45672.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059697 restraints weight = 32742.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.060535 restraints weight = 25790.805| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4152 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= 0.176 Angle : 0.866 12.402 13062 Z= 0.440 Chirality : 0.055 0.331 1642 Planarity : 0.005 0.048 1666 Dihedral : 4.344 24.892 1393 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.83 % Allowed : 45.48 % Favored : 49.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1325 helix: 1.01 (0.16), residues: 1062 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 122 HIS 0.000 0.000 HIS Z 31 PHE 0.035 0.001 PHE H 62 TYR 0.015 0.001 TYR N 48 ARG 0.009 0.000 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 874) hydrogen bonds : angle 4.51649 ( 2607) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.25756 ( 2) covalent geometry : bond 0.00403 ( 9567) covalent geometry : angle 0.86579 (13060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 374 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.9267 (ttm110) cc_final: 0.9066 (ttm110) REVERT: H 48 TYR cc_start: 0.9071 (m-80) cc_final: 0.8843 (m-80) REVERT: H 62 PHE cc_start: 0.9337 (m-80) cc_final: 0.8951 (m-80) REVERT: I 15 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8392 (tp) REVERT: I 48 TYR cc_start: 0.9394 (m-80) cc_final: 0.9117 (m-80) REVERT: I 49 MET cc_start: 0.9556 (OUTLIER) cc_final: 0.9038 (tmm) REVERT: I 57 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8837 (mp0) REVERT: I 68 PHE cc_start: 0.9214 (m-80) cc_final: 0.8729 (m-80) REVERT: J 18 ILE cc_start: 0.8468 (tp) cc_final: 0.8234 (tp) REVERT: J 40 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8287 (mp0) REVERT: J 44 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6708 (ttt-90) REVERT: J 48 TYR cc_start: 0.9304 (m-80) cc_final: 0.8604 (m-80) REVERT: J 49 MET cc_start: 0.9604 (ppp) cc_final: 0.9121 (ppp) REVERT: K 48 TYR cc_start: 0.9258 (m-80) cc_final: 0.8196 (m-80) REVERT: K 49 MET cc_start: 0.9618 (ppp) cc_final: 0.9245 (ppp) REVERT: K 57 GLU cc_start: 0.9647 (mm-30) cc_final: 0.9112 (mm-30) REVERT: L 43 ASN cc_start: 0.8681 (t0) cc_final: 0.8335 (m110) REVERT: M 33 GLN cc_start: 0.9412 (mm110) cc_final: 0.8878 (mp10) REVERT: M 49 MET cc_start: 0.9381 (ppp) cc_final: 0.9048 (ppp) REVERT: M 50 PHE cc_start: 0.9184 (m-80) cc_final: 0.8639 (m-80) REVERT: N 15 LEU cc_start: 0.9652 (mm) cc_final: 0.9101 (mp) REVERT: N 18 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7818 (tt) REVERT: N 48 TYR cc_start: 0.9467 (m-80) cc_final: 0.8844 (m-80) REVERT: O 29 SER cc_start: 0.9529 (t) cc_final: 0.9152 (p) REVERT: O 37 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8659 (mtm180) REVERT: O 44 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7237 (mmm-85) REVERT: O 48 TYR cc_start: 0.8937 (m-80) cc_final: 0.8268 (m-80) REVERT: O 49 MET cc_start: 0.9431 (ttp) cc_final: 0.8998 (ppp) REVERT: O 62 PHE cc_start: 0.9137 (m-80) cc_final: 0.8766 (m-80) REVERT: O 66 ILE cc_start: 0.9530 (mm) cc_final: 0.9228 (mm) REVERT: P 37 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7764 (ttm170) REVERT: P 42 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8993 (tt0) REVERT: P 43 ASN cc_start: 0.9474 (p0) cc_final: 0.9246 (p0) REVERT: P 48 TYR cc_start: 0.9262 (m-80) cc_final: 0.9054 (m-80) REVERT: P 57 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8686 (pt0) REVERT: Q 37 ARG cc_start: 0.8678 (mmp80) cc_final: 0.7965 (mmm160) REVERT: Q 57 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: Q 61 ILE cc_start: 0.9055 (pt) cc_final: 0.8751 (pt) REVERT: T 114 PHE cc_start: 0.9569 (t80) cc_final: 0.9343 (t80) REVERT: T 206 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8486 (mm-30) REVERT: T 228 MET cc_start: 0.9056 (ppp) cc_final: 0.8819 (ppp) REVERT: T 264 MET cc_start: 0.9656 (mmm) cc_final: 0.9423 (mmm) REVERT: Z 33 GLU cc_start: 0.8834 (pm20) cc_final: 0.8600 (mp0) REVERT: Z 74 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8314 (tp-100) REVERT: Z 85 GLU cc_start: 0.9204 (tt0) cc_final: 0.8574 (tm-30) REVERT: Z 95 PHE cc_start: 0.9432 (m-10) cc_final: 0.8973 (m-80) REVERT: Z 228 MET cc_start: 0.7320 (ttt) cc_final: 0.6879 (ttt) REVERT: Z 242 LYS cc_start: 0.9404 (mttt) cc_final: 0.9184 (mtpp) REVERT: Z 249 ARG cc_start: 0.9347 (ttm110) cc_final: 0.9053 (ptp-110) REVERT: Z 264 MET cc_start: 0.9527 (mmt) cc_final: 0.9006 (tpp) REVERT: Z 277 TYR cc_start: 0.9127 (m-80) cc_final: 0.8693 (m-80) REVERT: Z 282 PHE cc_start: 0.9362 (t80) cc_final: 0.8830 (t80) REVERT: Z 286 ILE cc_start: 0.9644 (pt) cc_final: 0.9167 (pt) outliers start: 39 outliers final: 30 residues processed: 388 average time/residue: 0.1683 time to fit residues: 96.2899 Evaluate side-chains 404 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 368 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 28 VAL Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 44 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain 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 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 50 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain T residue 59 ASP 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 22 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 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 ** T 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.071921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058935 restraints weight = 44807.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059857 restraints weight = 32169.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.060715 restraints weight = 26065.993| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9568 Z= 0.174 Angle : 0.872 12.414 13062 Z= 0.444 Chirality : 0.055 0.308 1642 Planarity : 0.005 0.048 1666 Dihedral : 4.350 25.113 1393 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.58 % Allowed : 46.84 % Favored : 48.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1325 helix: 1.00 (0.16), residues: 1057 sheet: None (None), residues: 0 loop : -1.73 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 122 HIS 0.000 0.000 HIS Z 31 PHE 0.032 0.001 PHE H 62 TYR 0.014 0.001 TYR P 48 ARG 0.009 0.001 ARG Z 96 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 874) hydrogen bonds : angle 4.51555 ( 2607) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.23507 ( 2) covalent geometry : bond 0.00398 ( 9567) covalent geometry : angle 0.87179 (13060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3065.66 seconds wall clock time: 54 minutes 31.06 seconds (3271.06 seconds total)