Starting phenix.real_space_refine on Mon Aug 25 19:35:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j00_35879/08_2025/8j00_35879_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j00_35879/08_2025/8j00_35879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j00_35879/08_2025/8j00_35879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j00_35879/08_2025/8j00_35879.map" model { file = "/net/cci-nas-00/data/ceres_data/8j00_35879/08_2025/8j00_35879_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j00_35879/08_2025/8j00_35879_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 9876 2.51 5 N 2560 2.21 5 O 2716 1.98 5 H 14944 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30184 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5371 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 6, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.24, per 1000 atoms: 0.17 Number of scatterers: 30184 At special positions: 0 Unit cell: (127.41, 127.41, 119.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 O 2716 8.00 N 2560 7.00 C 9876 6.00 H 14944 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 810.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 4 sheets defined 82.4% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 3.994A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.972A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 327 removed outlier: 4.239A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.887A pdb=" N ASN A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 Processing helix chain 'A' and resid 563 through 595 removed outlier: 3.985A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 115 removed outlier: 3.989A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.960A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 327 removed outlier: 4.239A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.910A pdb=" N ASN B 350 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 560 Processing helix chain 'B' and resid 563 through 595 removed outlier: 4.018A pdb=" N VAL B 567 " --> pdb=" O ASP B 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 115 removed outlier: 3.979A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 3.868A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 155 through 165 Processing helix chain 'C' and resid 166 through 184 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 327 removed outlier: 4.241A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix Processing helix chain 'C' and resid 333 through 350 removed outlier: 3.935A pdb=" N ASN C 350 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 560 Processing helix chain 'C' and resid 563 through 595 removed outlier: 4.014A pdb=" N VAL C 567 " --> pdb=" O ASP C 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 115 removed outlier: 3.982A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.857A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 155 through 165 Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 327 removed outlier: 4.239A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 333 through 350 removed outlier: 3.916A pdb=" N ASN D 350 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 560 Processing helix chain 'D' and resid 563 through 595 removed outlier: 3.980A pdb=" N VAL D 567 " --> pdb=" O ASP D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.747A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 94 removed outlier: 3.557A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 118 through 130 removed outlier: 3.515A pdb=" N ASP E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 148 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.712A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.507A pdb=" N VAL F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 148 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 65 through 74 Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 103 through 113 Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 140 through 148 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.529A pdb=" N LEU H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.528A pdb=" N ILE H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.500A pdb=" N VAL H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP H 130 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1151 hydrogen bonds defined for protein. 3453 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: 4.99 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14916 1.03 - 1.23: 76 1.23 - 1.43: 6640 1.43 - 1.62: 8708 1.62 - 1.82: 164 Bond restraints: 30504 Sorted by residual: bond pdb=" C07 P0T C 802 " pdb=" C09 P0T C 802 " ideal model delta sigma weight residual 1.336 1.601 -0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C07 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sigma weight residual 1.336 1.600 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C07 P0T B 802 " pdb=" C09 P0T B 802 " ideal model delta sigma weight residual 1.336 1.599 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C07 P0T A 802 " pdb=" C09 P0T A 802 " ideal model delta sigma weight residual 1.336 1.599 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C07 P0T B 801 " pdb=" C09 P0T B 801 " ideal model delta sigma weight residual 1.336 1.596 -0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 30499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 54795 6.03 - 12.06: 9 12.06 - 18.08: 0 18.08 - 24.11: 8 24.11 - 30.14: 8 Bond angle restraints: 54820 Sorted by residual: angle pdb=" C07 P0T D 801 " pdb=" C04 P0T D 801 " pdb=" C08 P0T D 801 " ideal model delta sigma weight residual 112.03 81.89 30.14 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C07 P0T C 801 " pdb=" C04 P0T C 801 " pdb=" C08 P0T C 801 " ideal model delta sigma weight residual 112.03 81.91 30.12 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C07 P0T A 801 " pdb=" C04 P0T A 801 " pdb=" C08 P0T A 801 " ideal model delta sigma weight residual 112.03 81.93 30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C07 P0T B 801 " pdb=" C04 P0T B 801 " pdb=" C08 P0T B 801 " ideal model delta sigma weight residual 112.03 81.96 30.07 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C07 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C08 P0T B 802 " ideal model delta sigma weight residual 112.03 83.66 28.37 3.00e+00 1.11e-01 8.94e+01 ... (remaining 54815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 12876 23.07 - 46.15: 1091 46.15 - 69.22: 290 69.22 - 92.30: 27 92.30 - 115.37: 24 Dihedral angle restraints: 14308 sinusoidal: 7692 harmonic: 6616 Sorted by residual: dihedral pdb=" CA ARG B 560 " pdb=" C ARG B 560 " pdb=" N PRO B 561 " pdb=" CA PRO B 561 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C03 P0T D 801 " pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " pdb=" C09 P0T D 801 " ideal model delta sinusoidal sigma weight residual 49.00 -66.37 115.37 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C03 P0T C 801 " pdb=" C05 P0T C 801 " pdb=" C06 P0T C 801 " pdb=" C09 P0T C 801 " ideal model delta sinusoidal sigma weight residual 49.00 -66.37 115.37 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 14305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1530 0.026 - 0.053: 526 0.053 - 0.079: 164 0.079 - 0.105: 63 0.105 - 0.131: 13 Chirality restraints: 2296 Sorted by residual: chirality pdb=" CB THR A 298 " pdb=" CA THR A 298 " pdb=" OG1 THR A 298 " pdb=" CG2 THR A 298 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CB THR C 298 " pdb=" CA THR C 298 " pdb=" OG1 THR C 298 " pdb=" CG2 THR C 298 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE G 64 " pdb=" N ILE G 64 " pdb=" C ILE G 64 " pdb=" CB ILE G 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 2293 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 130 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" CD GLU D 130 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU D 130 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU D 130 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 130 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" CD GLU A 130 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU A 130 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 130 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 97 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C ALA D 97 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA D 97 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR D 98 " -0.008 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1564 2.16 - 2.77: 58553 2.77 - 3.38: 89802 3.38 - 3.99: 106504 3.99 - 4.60: 168474 Nonbonded interactions: 424897 Sorted by model distance: nonbonded pdb=" HG1 THR H 118 " pdb=" OE1 GLU H 121 " model vdw 1.552 2.450 nonbonded pdb=" HG1 THR F 118 " pdb=" OE1 GLU F 121 " model vdw 1.555 2.450 nonbonded pdb=" O LEU D 272 " pdb=" HG1 THR D 276 " model vdw 1.556 2.450 nonbonded pdb=" O LEU A 272 " pdb=" HG1 THR A 276 " model vdw 1.557 2.450 nonbonded pdb=" HG1 THR E 118 " pdb=" OE1 GLU E 121 " model vdw 1.560 2.450 ... (remaining 424892 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic 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: 0.800 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: 0.130 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 22.630 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.011 0.265 15560 Z= 0.563 Angle : 0.917 30.140 20980 Z= 0.390 Chirality : 0.032 0.131 2296 Planarity : 0.003 0.031 2636 Dihedral : 19.379 115.375 5760 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.06 % Allowed : 29.00 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.20), residues: 1844 helix: 1.99 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 553 TYR 0.012 0.001 TYR C 571 PHE 0.014 0.001 PHE D 297 TRP 0.007 0.001 TRP D 288 HIS 0.003 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.01128 (15560) covalent geometry : angle 0.91651 (20980) hydrogen bonds : bond 0.09525 ( 1151) hydrogen bonds : angle 5.69806 ( 3453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 ASN cc_start: 0.8796 (m-40) cc_final: 0.8332 (t0) REVERT: C 130 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7213 (tm-30) REVERT: D 123 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7932 (tm-30) REVERT: D 130 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 106 LEU cc_start: 0.8830 (tp) cc_final: 0.8609 (tp) REVERT: E 145 MET cc_start: 0.6369 (tmm) cc_final: 0.5902 (ptt) REVERT: F 116 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8270 (mmmm) REVERT: F 141 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7593 (tm-30) REVERT: G 77 MET cc_start: 0.1188 (tpp) cc_final: 0.0662 (tpp) REVERT: H 73 MET cc_start: -0.2510 (mmt) cc_final: -0.2765 (ttm) outliers start: 1 outliers final: 4 residues processed: 243 average time/residue: 0.9019 time to fit residues: 247.4759 Evaluate side-chains 204 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 200 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.177754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106337 restraints weight = 70593.612| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.18 r_work: 0.3193 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15560 Z= 0.333 Angle : 0.644 8.216 20980 Z= 0.338 Chirality : 0.039 0.175 2296 Planarity : 0.004 0.043 2636 Dihedral : 12.841 110.682 2244 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.06 % Allowed : 29.44 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.19), residues: 1844 helix: 1.96 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 91 TYR 0.012 0.002 TYR B 74 PHE 0.016 0.002 PHE B 80 TRP 0.009 0.002 TRP D 269 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00727 (15560) covalent geometry : angle 0.64356 (20980) hydrogen bonds : bond 0.04502 ( 1151) hydrogen bonds : angle 4.86014 ( 3453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 553 ARG cc_start: 0.8709 (tpp80) cc_final: 0.8440 (tpp80) REVERT: C 130 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 81 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7704 (mp) REVERT: D 130 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 579 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7905 (tp) REVERT: E 77 MET cc_start: 0.2922 (tpp) cc_final: 0.2638 (tpp) REVERT: F 77 MET cc_start: 0.1978 (tpp) cc_final: 0.1641 (tpp) REVERT: F 141 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7671 (tm-30) REVERT: F 145 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.6040 (ptt) REVERT: G 77 MET cc_start: 0.1670 (OUTLIER) cc_final: 0.1114 (tpp) REVERT: H 73 MET cc_start: -0.2316 (mmt) cc_final: -0.2812 (ttm) REVERT: H 77 MET cc_start: 0.2539 (tpp) cc_final: 0.2212 (tpp) REVERT: H 145 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5216 (ppp) REVERT: H 146 MET cc_start: 0.7662 (mmm) cc_final: 0.7380 (mmm) outliers start: 64 outliers final: 40 residues processed: 265 average time/residue: 0.8396 time to fit residues: 253.7647 Evaluate side-chains 241 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 142 PHE Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 114 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 HIS G 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.181489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.108086 restraints weight = 70146.024| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.26 r_work: 0.3315 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15560 Z= 0.123 Angle : 0.529 8.398 20980 Z= 0.270 Chirality : 0.032 0.123 2296 Planarity : 0.003 0.040 2636 Dihedral : 8.625 77.671 2240 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.43 % Allowed : 28.74 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.19), residues: 1844 helix: 2.33 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 91 TYR 0.007 0.001 TYR C 74 PHE 0.012 0.001 PHE A 80 TRP 0.006 0.001 TRP B 288 HIS 0.006 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00255 (15560) covalent geometry : angle 0.52891 (20980) hydrogen bonds : bond 0.03836 ( 1151) hydrogen bonds : angle 4.43752 ( 3453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 130 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7873 (tm-30) REVERT: D 579 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7849 (tp) REVERT: E 73 MET cc_start: -0.2550 (mmt) cc_final: -0.3223 (ttm) REVERT: F 141 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 145 MET cc_start: 0.6436 (ptt) cc_final: 0.6144 (ptt) REVERT: G 77 MET cc_start: 0.1386 (OUTLIER) cc_final: 0.0872 (tpp) REVERT: G 145 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.5429 (ppp) REVERT: G 146 MET cc_start: 0.7782 (mmm) cc_final: 0.7501 (mmm) REVERT: H 73 MET cc_start: -0.2426 (mmt) cc_final: -0.2893 (ttm) outliers start: 54 outliers final: 30 residues processed: 259 average time/residue: 0.8611 time to fit residues: 253.5864 Evaluate side-chains 243 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 104 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 HIS G 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.181812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108631 restraints weight = 69538.841| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.27 r_work: 0.3324 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15560 Z= 0.122 Angle : 0.511 6.917 20980 Z= 0.265 Chirality : 0.032 0.131 2296 Planarity : 0.003 0.039 2636 Dihedral : 5.649 29.029 2240 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.17 % Allowed : 27.22 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.19), residues: 1844 helix: 2.48 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.14 (0.38), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 560 TYR 0.008 0.001 TYR C 127 PHE 0.015 0.001 PHE F 142 TRP 0.007 0.001 TRP A 288 HIS 0.003 0.000 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00258 (15560) covalent geometry : angle 0.51100 (20980) hydrogen bonds : bond 0.03598 ( 1151) hydrogen bonds : angle 4.28029 ( 3453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 279 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7723 (tm-30) REVERT: D 130 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7872 (tm-30) REVERT: D 579 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7818 (tp) REVERT: E 73 MET cc_start: -0.2391 (mmt) cc_final: -0.3050 (ttm) REVERT: G 77 MET cc_start: 0.1465 (OUTLIER) cc_final: 0.0874 (tpp) REVERT: G 145 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.5467 (ppp) REVERT: G 146 MET cc_start: 0.7591 (mmm) cc_final: 0.7265 (mmm) REVERT: H 73 MET cc_start: -0.2342 (mmt) cc_final: -0.2825 (ttm) outliers start: 50 outliers final: 30 residues processed: 268 average time/residue: 0.9049 time to fit residues: 275.0213 Evaluate side-chains 246 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN H 108 HIS H 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.180543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.107091 restraints weight = 69999.423| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.24 r_work: 0.3298 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15560 Z= 0.171 Angle : 0.517 7.860 20980 Z= 0.272 Chirality : 0.032 0.153 2296 Planarity : 0.003 0.043 2636 Dihedral : 5.535 36.524 2240 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.30 % Allowed : 27.98 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.19), residues: 1844 helix: 2.52 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.15 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 91 TYR 0.009 0.001 TYR C 127 PHE 0.011 0.001 PHE B 80 TRP 0.006 0.001 TRP A 288 HIS 0.009 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00368 (15560) covalent geometry : angle 0.51733 (20980) hydrogen bonds : bond 0.03644 ( 1151) hydrogen bonds : angle 4.30205 ( 3453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7721 (tm-30) REVERT: D 130 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7865 (tm-30) REVERT: D 579 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7790 (tp) REVERT: E 73 MET cc_start: -0.2345 (mmt) cc_final: -0.2974 (ttm) REVERT: G 145 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5544 (ppp) REVERT: G 146 MET cc_start: 0.7580 (mmm) cc_final: 0.7301 (mmm) REVERT: H 73 MET cc_start: -0.2354 (mmt) cc_final: -0.2809 (ttm) outliers start: 52 outliers final: 36 residues processed: 260 average time/residue: 0.8178 time to fit residues: 243.8634 Evaluate side-chains 249 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 149 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.179163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.108104 restraints weight = 69899.587| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.08 r_work: 0.3228 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15560 Z= 0.248 Angle : 0.566 9.217 20980 Z= 0.300 Chirality : 0.035 0.190 2296 Planarity : 0.003 0.027 2636 Dihedral : 5.881 44.018 2238 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.62 % Allowed : 27.73 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.19), residues: 1844 helix: 2.40 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.20 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 91 TYR 0.009 0.001 TYR D 237 PHE 0.015 0.001 PHE F 142 TRP 0.006 0.001 TRP D 269 HIS 0.013 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00539 (15560) covalent geometry : angle 0.56594 (20980) hydrogen bonds : bond 0.03852 ( 1151) hydrogen bonds : angle 4.40704 ( 3453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 130 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7912 (tm-30) REVERT: D 579 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7766 (tp) REVERT: E 73 MET cc_start: -0.2551 (mmt) cc_final: -0.3127 (ttm) REVERT: G 145 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.5519 (ppp) REVERT: G 146 MET cc_start: 0.7631 (mmm) cc_final: 0.7386 (mmm) REVERT: H 73 MET cc_start: -0.2641 (mmt) cc_final: -0.3040 (ttm) REVERT: H 77 MET cc_start: 0.2717 (tpp) cc_final: 0.2290 (tpp) REVERT: H 110 MET cc_start: 0.7312 (mmm) cc_final: 0.7095 (mmm) REVERT: H 113 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6787 (tp) REVERT: H 125 MET cc_start: 0.7888 (mmm) cc_final: 0.7665 (mmp) outliers start: 57 outliers final: 36 residues processed: 253 average time/residue: 0.8727 time to fit residues: 252.0533 Evaluate side-chains 245 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 119 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 chunk 16 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 156 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 129 optimal weight: 50.0000 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN H 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.180824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107288 restraints weight = 69829.354| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.26 r_work: 0.3301 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15560 Z= 0.155 Angle : 0.523 9.423 20980 Z= 0.273 Chirality : 0.032 0.163 2296 Planarity : 0.003 0.026 2636 Dihedral : 5.438 44.677 2236 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.54 % Allowed : 29.51 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.19), residues: 1844 helix: 2.52 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 560 TYR 0.010 0.001 TYR A 118 PHE 0.017 0.001 PHE C 80 TRP 0.006 0.001 TRP A 288 HIS 0.006 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00333 (15560) covalent geometry : angle 0.52322 (20980) hydrogen bonds : bond 0.03586 ( 1151) hydrogen bonds : angle 4.26013 ( 3453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7670 (tm-30) REVERT: D 130 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7834 (tm-30) REVERT: E 73 MET cc_start: -0.2407 (mmt) cc_final: -0.2949 (ttm) REVERT: G 77 MET cc_start: 0.2402 (tpp) cc_final: 0.1660 (tpp) REVERT: G 145 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.5491 (ppp) REVERT: G 146 MET cc_start: 0.7498 (mmm) cc_final: 0.7125 (mmm) REVERT: H 73 MET cc_start: -0.2725 (mmt) cc_final: -0.3098 (ttm) REVERT: H 113 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6891 (tp) outliers start: 40 outliers final: 34 residues processed: 258 average time/residue: 0.9265 time to fit residues: 270.8170 Evaluate side-chains 243 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 136 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 134 optimal weight: 40.0000 chunk 80 optimal weight: 0.5980 chunk 172 optimal weight: 40.0000 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.180932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.108315 restraints weight = 69346.484| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.24 r_work: 0.3319 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15560 Z= 0.136 Angle : 0.539 11.499 20980 Z= 0.277 Chirality : 0.032 0.180 2296 Planarity : 0.003 0.059 2636 Dihedral : 5.143 44.547 2236 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.41 % Allowed : 30.52 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.19), residues: 1844 helix: 2.58 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.17 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 91 TYR 0.012 0.001 TYR A 141 PHE 0.019 0.001 PHE F 142 TRP 0.007 0.001 TRP A 288 HIS 0.002 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00291 (15560) covalent geometry : angle 0.53893 (20980) hydrogen bonds : bond 0.03495 ( 1151) hydrogen bonds : angle 4.21246 ( 3453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 130 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7813 (tm-30) REVERT: E 73 MET cc_start: -0.2435 (mmt) cc_final: -0.2958 (ttm) REVERT: E 125 MET cc_start: 0.7734 (mmm) cc_final: 0.7434 (mmp) REVERT: F 110 MET cc_start: 0.7403 (mmm) cc_final: 0.7203 (mmm) REVERT: F 125 MET cc_start: 0.7716 (mmm) cc_final: 0.7511 (mmp) REVERT: G 77 MET cc_start: 0.2245 (tpp) cc_final: 0.1517 (tpp) REVERT: G 110 MET cc_start: 0.7264 (mmm) cc_final: 0.6876 (mmm) REVERT: G 145 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.5407 (ppp) REVERT: G 146 MET cc_start: 0.7389 (mmm) cc_final: 0.7000 (mmm) REVERT: H 73 MET cc_start: -0.2760 (mmt) cc_final: -0.3090 (ttm) REVERT: H 110 MET cc_start: 0.7328 (mmm) cc_final: 0.6995 (mmm) outliers start: 38 outliers final: 30 residues processed: 251 average time/residue: 0.9707 time to fit residues: 275.8238 Evaluate side-chains 237 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 170 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.180024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105535 restraints weight = 69839.776| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.27 r_work: 0.3294 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15560 Z= 0.200 Angle : 0.562 9.920 20980 Z= 0.295 Chirality : 0.034 0.221 2296 Planarity : 0.003 0.062 2636 Dihedral : 5.452 48.300 2236 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.41 % Allowed : 30.77 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.19), residues: 1844 helix: 2.50 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.18 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 91 TYR 0.012 0.001 TYR C 141 PHE 0.016 0.001 PHE C 80 TRP 0.005 0.001 TRP B 270 HIS 0.002 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00436 (15560) covalent geometry : angle 0.56242 (20980) hydrogen bonds : bond 0.03673 ( 1151) hydrogen bonds : angle 4.31712 ( 3453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7702 (tm-30) REVERT: C 553 ARG cc_start: 0.8913 (tpp-160) cc_final: 0.8703 (tpp80) REVERT: D 130 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7875 (tm-30) REVERT: E 73 MET cc_start: -0.2449 (mmt) cc_final: -0.2974 (ttm) REVERT: F 125 MET cc_start: 0.7757 (mmm) cc_final: 0.7525 (mmp) REVERT: G 145 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5419 (ppp) REVERT: G 146 MET cc_start: 0.7392 (mmm) cc_final: 0.7091 (mmm) REVERT: H 73 MET cc_start: -0.2890 (mmt) cc_final: -0.3222 (ttm) REVERT: H 113 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6954 (tp) outliers start: 38 outliers final: 35 residues processed: 244 average time/residue: 0.8811 time to fit residues: 243.9956 Evaluate side-chains 242 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 326 GLN Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 0.3980 chunk 143 optimal weight: 40.0000 chunk 123 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.181443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107979 restraints weight = 69177.326| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.28 r_work: 0.3308 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15560 Z= 0.124 Angle : 0.558 12.357 20980 Z= 0.283 Chirality : 0.032 0.196 2296 Planarity : 0.003 0.060 2636 Dihedral : 5.060 46.065 2236 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.90 % Allowed : 31.35 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.20), residues: 1844 helix: 2.64 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 91 TYR 0.012 0.001 TYR D 118 PHE 0.015 0.001 PHE C 80 TRP 0.008 0.001 TRP A 288 HIS 0.003 0.001 HIS G 108 Details of bonding type rmsd covalent geometry : bond 0.00265 (15560) covalent geometry : angle 0.55772 (20980) hydrogen bonds : bond 0.03452 ( 1151) hydrogen bonds : angle 4.17371 ( 3453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7616 (tm-30) REVERT: C 553 ARG cc_start: 0.8879 (tpp-160) cc_final: 0.8674 (tpp80) REVERT: D 130 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7746 (tm-30) REVERT: E 73 MET cc_start: -0.2455 (mmt) cc_final: -0.2998 (ttm) REVERT: E 110 MET cc_start: 0.7252 (mmm) cc_final: 0.6969 (mmm) REVERT: E 125 MET cc_start: 0.7749 (mmm) cc_final: 0.7518 (mmp) REVERT: F 110 MET cc_start: 0.7327 (mmm) cc_final: 0.7081 (mmm) REVERT: F 125 MET cc_start: 0.7746 (mmm) cc_final: 0.7498 (mmp) REVERT: G 145 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5224 (tmm) REVERT: G 146 MET cc_start: 0.7321 (mmm) cc_final: 0.6846 (mmm) REVERT: H 73 MET cc_start: -0.2727 (mmt) cc_final: -0.3065 (ttm) REVERT: H 113 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6965 (tp) outliers start: 30 outliers final: 32 residues processed: 244 average time/residue: 0.8836 time to fit residues: 244.7987 Evaluate side-chains 238 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 154 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 170 optimal weight: 40.0000 chunk 124 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.180444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.106730 restraints weight = 69747.995| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.31 r_work: 0.3258 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15560 Z= 0.165 Angle : 0.566 10.838 20980 Z= 0.292 Chirality : 0.033 0.231 2296 Planarity : 0.003 0.078 2636 Dihedral : 5.197 48.040 2236 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.90 % Allowed : 31.79 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.19), residues: 1844 helix: 2.61 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 91 TYR 0.013 0.001 TYR A 118 PHE 0.020 0.001 PHE A 80 TRP 0.006 0.001 TRP A 288 HIS 0.003 0.001 HIS E 108 Details of bonding type rmsd covalent geometry : bond 0.00358 (15560) covalent geometry : angle 0.56620 (20980) hydrogen bonds : bond 0.03529 ( 1151) hydrogen bonds : angle 4.23607 ( 3453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13033.43 seconds wall clock time: 220 minutes 15.53 seconds (13215.53 seconds total)