Starting phenix.real_space_refine on Wed May 28 03:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j00_35879/05_2025/8j00_35879_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j00_35879/05_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_35879/05_2025/8j00_35879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j00_35879/05_2025/8j00_35879.map" model { file = "/net/cci-nas-00/data/ceres_data/8j00_35879/05_2025/8j00_35879_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j00_35879/05_2025/8j00_35879_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.09, per 1000 atoms: 0.47 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: 7.68 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.07 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: 10.07 Time building geometry restraints manager: 9.09 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: 0.03 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: 0.980 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: 0.480 Extract box with map and model: 1.100 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 58.680 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.010 ------------------------------------------------------------------------------- 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 : 10.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP D 288 HIS 0.003 0.001 HIS F 108 PHE 0.014 0.001 PHE D 297 TYR 0.012 0.001 TYR C 571 ARG 0.006 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.09525 ( 1151) hydrogen bonds : angle 5.69806 ( 3453) covalent geometry : bond 0.01128 (15560) covalent geometry : angle 0.91651 (20980) *********************** 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 : 2.278 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: 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: 0.7212 (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: 0.5872 (ptt) 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: -0.2766 (ttm) outliers start: 1 outliers final: 4 residues processed: 243 average time/residue: 2.0752 time to fit residues: 575.6022 Evaluate side-chains 203 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 155 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.181015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107409 restraints weight = 70030.505| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.26 r_work: 0.3300 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15560 Z= 0.157 Angle : 0.580 8.220 20980 Z= 0.291 Chirality : 0.034 0.171 2296 Planarity : 0.003 0.044 2636 Dihedral : 11.348 80.142 2244 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.28 % Allowed : 29.44 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.19), residues: 1844 helix: 2.35 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.23 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.003 0.001 HIS C 228 PHE 0.014 0.001 PHE F 142 TYR 0.007 0.001 TYR D 74 ARG 0.007 0.000 ARG F 91 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1151) hydrogen bonds : angle 4.59649 ( 3453) covalent geometry : bond 0.00330 (15560) covalent geometry : angle 0.58037 (20980) *********************** 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 263 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 2.343 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: 0.8110 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 130 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 579 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7857 (tp) REVERT: F 141 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7583 (tm-30) REVERT: F 145 MET cc_start: 0.6343 (ptt) cc_final: 0.6080 (ptt) REVERT: G 77 MET cc_start: 0.1184 (OUTLIER) cc_final: 0.0527 (tpp) REVERT: H 73 MET cc_start: -0.2243 (mmt) cc_final: -0.2713 (ttm) outliers start: 36 outliers final: 17 residues processed: 253 average time/residue: 1.9694 time to fit residues: 567.7518 Evaluate side-chains 232 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain D residue 81 LEU 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 138 ASN Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 158 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.182178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.109455 restraints weight = 69793.290| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.24 r_work: 0.3330 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15560 Z= 0.124 Angle : 0.515 7.851 20980 Z= 0.264 Chirality : 0.032 0.123 2296 Planarity : 0.003 0.025 2636 Dihedral : 6.361 35.555 2242 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.43 % Allowed : 26.08 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.19), residues: 1844 helix: 2.49 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.14 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 288 HIS 0.002 0.000 HIS H 108 PHE 0.012 0.001 PHE A 80 TYR 0.008 0.001 TYR C 127 ARG 0.005 0.000 ARG F 91 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 1151) hydrogen bonds : angle 4.34191 ( 3453) covalent geometry : bond 0.00260 (15560) covalent geometry : angle 0.51471 (20980) *********************** 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 281 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 227 time to evaluate : 2.531 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: B 565 MET cc_start: 0.7105 (tpt) cc_final: 0.6701 (mmm) REVERT: C 130 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 130 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 579 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7836 (tp) REVERT: E 73 MET cc_start: -0.2467 (mmt) cc_final: -0.3131 (ttm) REVERT: F 141 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7574 (tm-30) REVERT: F 145 MET cc_start: 0.6396 (ptt) cc_final: 0.6120 (ptt) REVERT: G 77 MET cc_start: 0.1166 (OUTLIER) cc_final: 0.0482 (tpp) REVERT: H 73 MET cc_start: -0.2316 (mmt) cc_final: -0.2798 (ttm) outliers start: 54 outliers final: 25 residues processed: 271 average time/residue: 2.1060 time to fit residues: 647.4859 Evaluate side-chains 239 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 2.264 ------------------------------------------------------------------------------- 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 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 74 TYR Chi-restraints excluded: chain C residue 81 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 D residue 74 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 169 CYS 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 F residue 138 ASN Chi-restraints excluded: chain G residue 77 MET Chi-restraints excluded: chain G residue 121 GLU 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 58 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.179479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107953 restraints weight = 70233.174| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.12 r_work: 0.3227 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15560 Z= 0.270 Angle : 0.569 7.853 20980 Z= 0.302 Chirality : 0.036 0.175 2296 Planarity : 0.003 0.036 2636 Dihedral : 6.285 32.362 2240 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.06 % Allowed : 26.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.19), residues: 1844 helix: 2.35 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.009 0.001 HIS F 108 PHE 0.013 0.001 PHE F 142 TYR 0.009 0.001 TYR D 127 ARG 0.007 0.000 ARG E 91 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 1151) hydrogen bonds : angle 4.48572 ( 3453) covalent geometry : bond 0.00590 (15560) covalent geometry : angle 0.56929 (20980) *********************** 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 281 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 2.463 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: C 130 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7767 (tm-30) REVERT: D 130 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7938 (tm-30) REVERT: D 579 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7830 (tp) REVERT: E 73 MET cc_start: -0.2484 (mmt) cc_final: -0.3124 (ttm) REVERT: F 141 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7585 (tm-30) REVERT: F 145 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.6092 (ptt) REVERT: G 77 MET cc_start: 0.1501 (OUTLIER) cc_final: 0.0987 (tpp) REVERT: G 142 PHE cc_start: 0.8778 (t80) cc_final: 0.8350 (t80) REVERT: G 145 MET cc_start: 0.6529 (OUTLIER) cc_final: 0.5526 (ppp) REVERT: G 146 MET cc_start: 0.7684 (mmm) cc_final: 0.7303 (mmm) REVERT: H 73 MET cc_start: -0.2370 (mmt) cc_final: -0.2818 (ttm) outliers start: 64 outliers final: 45 residues processed: 263 average time/residue: 1.8362 time to fit residues: 556.9345 Evaluate side-chains 260 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 110 SER 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 110 SER 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 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 81 LEU Chi-restraints excluded: chain C residue 110 SER 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 D residue 74 TYR Chi-restraints excluded: chain D residue 81 LEU 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 171 ILE 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 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 F residue 108 HIS 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 144 GLN 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 0 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 H 108 HIS H 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.181771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108415 restraints weight = 69770.535| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.24 r_work: 0.3318 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15560 Z= 0.129 Angle : 0.504 9.097 20980 Z= 0.264 Chirality : 0.032 0.145 2296 Planarity : 0.003 0.025 2636 Dihedral : 5.469 33.989 2238 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.24 % Allowed : 27.54 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.19), residues: 1844 helix: 2.54 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.18 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 288 HIS 0.010 0.001 HIS H 108 PHE 0.010 0.001 PHE D 297 TYR 0.007 0.001 TYR C 127 ARG 0.004 0.000 ARG F 91 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 1151) hydrogen bonds : angle 4.26209 ( 3453) covalent geometry : bond 0.00272 (15560) covalent geometry : angle 0.50441 (20980) *********************** 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 277 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 2.614 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: 0.8203 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 130 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 73 MET cc_start: -0.2419 (mmt) cc_final: -0.3037 (ttm) REVERT: F 141 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7550 (tm-30) REVERT: F 145 MET cc_start: 0.6453 (ptt) cc_final: 0.6106 (ptt) REVERT: G 77 MET cc_start: 0.1405 (OUTLIER) cc_final: 0.0840 (tpp) REVERT: G 142 PHE cc_start: 0.8806 (t80) cc_final: 0.8473 (t80) REVERT: G 145 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5503 (ppp) REVERT: H 73 MET cc_start: -0.2322 (mmt) cc_final: -0.2789 (ttm) outliers start: 51 outliers final: 34 residues processed: 259 average time/residue: 1.9083 time to fit residues: 568.0585 Evaluate side-chains 252 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 105 SER 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 300 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 105 SER 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 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU 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 180 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 169 CYS Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain E residue 121 GLU 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 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 109 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.180845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.107307 restraints weight = 69697.603| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.23 r_work: 0.3301 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15560 Z= 0.171 Angle : 0.531 9.161 20980 Z= 0.277 Chirality : 0.033 0.182 2296 Planarity : 0.003 0.037 2636 Dihedral : 5.374 38.104 2238 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.98 % Allowed : 28.05 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.19), residues: 1844 helix: 2.55 (0.12), residues: 1468 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 288 HIS 0.005 0.001 HIS H 108 PHE 0.015 0.001 PHE F 142 TYR 0.009 0.001 TYR A 118 ARG 0.006 0.000 ARG F 91 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 1151) hydrogen bonds : angle 4.27423 ( 3453) covalent geometry : bond 0.00370 (15560) covalent geometry : angle 0.53088 (20980) *********************** 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 267 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 2.476 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: B 553 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.8238 (tpp80) REVERT: C 130 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 130 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7835 (tm-30) REVERT: E 73 MET cc_start: -0.2458 (mmt) cc_final: -0.3062 (ttm) REVERT: F 141 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7524 (tm-30) REVERT: F 145 MET cc_start: 0.6466 (ptt) cc_final: 0.6119 (ptt) REVERT: G 142 PHE cc_start: 0.8774 (t80) cc_final: 0.8430 (t80) REVERT: G 145 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.5533 (ppp) REVERT: H 73 MET cc_start: -0.2547 (mmt) cc_final: -0.2951 (ttm) REVERT: H 113 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7099 (tm) outliers start: 47 outliers final: 34 residues processed: 257 average time/residue: 1.9968 time to fit residues: 584.4744 Evaluate side-chains 250 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 300 ILE 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 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 180 ILE 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 81 LEU 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 566 ASP Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 138 ASN 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 42 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.182068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.108822 restraints weight = 69531.070| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.26 r_work: 0.3326 rms_B_bonded: 2.52 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: 0.7393 moved from start: 0.2048 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= 0.121 Angle : 0.517 9.927 20980 Z= 0.266 Chirality : 0.032 0.176 2296 Planarity : 0.003 0.068 2636 Dihedral : 4.975 37.725 2236 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.86 % Allowed : 29.00 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.19), residues: 1844 helix: 2.68 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 288 HIS 0.004 0.001 HIS H 108 PHE 0.011 0.001 PHE E 13 TYR 0.011 0.001 TYR B 118 ARG 0.011 0.000 ARG E 91 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 1151) hydrogen bonds : angle 4.15146 ( 3453) covalent geometry : bond 0.00258 (15560) covalent geometry : angle 0.51665 (20980) *********************** 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 271 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 2.126 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: symmetry clash REVERT: C 130 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7663 (tm-30) REVERT: D 130 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7823 (tm-30) REVERT: E 73 MET cc_start: -0.2255 (mmt) cc_final: -0.2824 (ttm) REVERT: F 141 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7507 (tm-30) REVERT: F 145 MET cc_start: 0.6486 (ptt) cc_final: 0.6115 (ptt) REVERT: G 77 MET cc_start: 0.2277 (tpp) cc_final: 0.1450 (tpp) REVERT: G 142 PHE cc_start: 0.8759 (t80) cc_final: 0.8457 (t80) REVERT: G 145 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.5500 (ppp) REVERT: H 73 MET cc_start: -0.2586 (mmt) cc_final: -0.2951 (ttm) REVERT: H 125 MET cc_start: 0.7892 (mmm) cc_final: 0.7653 (mmp) outliers start: 45 outliers final: 28 residues processed: 263 average time/residue: 2.0337 time to fit residues: 607.4664 Evaluate side-chains 247 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 2.226 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 110 SER 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 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain D residue 74 TYR 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 550 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 138 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 11 optimal weight: 9.9990 chunk 170 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.179929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105664 restraints weight = 70077.835| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.25 r_work: 0.3295 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.005 0.043 15560 Z= 0.212 Angle : 0.562 10.063 20980 Z= 0.296 Chirality : 0.035 0.221 2296 Planarity : 0.004 0.075 2636 Dihedral : 5.541 46.191 2236 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.11 % Allowed : 29.63 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.19), residues: 1844 helix: 2.55 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.23 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 270 HIS 0.003 0.001 HIS F 108 PHE 0.016 0.001 PHE F 142 TYR 0.011 0.001 TYR A 118 ARG 0.012 0.000 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 1151) hydrogen bonds : angle 4.31597 ( 3453) covalent geometry : bond 0.00464 (15560) covalent geometry : angle 0.56150 (20980) *********************** 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 266 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 2.325 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: 0.8184 (tm-30) cc_final: 0.7689 (tm-30) REVERT: C 553 ARG cc_start: 0.8916 (tpp-160) cc_final: 0.8650 (tpp80) REVERT: D 130 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7856 (tm-30) REVERT: E 73 MET cc_start: -0.2413 (mmt) cc_final: -0.2945 (ttm) REVERT: F 141 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7523 (tm-30) REVERT: F 145 MET cc_start: 0.6463 (ptt) cc_final: 0.6192 (ptt) REVERT: G 142 PHE cc_start: 0.8805 (t80) cc_final: 0.8491 (t80) REVERT: G 145 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5518 (ppp) REVERT: H 73 MET cc_start: -0.2708 (mmt) cc_final: -0.3042 (ttm) REVERT: H 77 MET cc_start: 0.2908 (tpp) cc_final: 0.2309 (tpp) outliers start: 49 outliers final: 40 residues processed: 254 average time/residue: 1.8224 time to fit residues: 541.1737 Evaluate side-chains 248 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 169 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 296 THR 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 110 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain D residue 74 TYR 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 296 THR Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain D residue 326 GLN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 138 ASN 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 4 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.181493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107675 restraints weight = 69621.342| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.25 r_work: 0.3311 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15560 Z= 0.144 Angle : 0.548 10.810 20980 Z= 0.281 Chirality : 0.033 0.200 2296 Planarity : 0.003 0.064 2636 Dihedral : 5.181 45.033 2236 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.09 % Allowed : 30.77 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.19), residues: 1844 helix: 2.67 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.31 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 288 HIS 0.002 0.001 HIS E 108 PHE 0.018 0.001 PHE A 80 TYR 0.012 0.001 TYR B 118 ARG 0.011 0.000 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 1151) hydrogen bonds : angle 4.19488 ( 3453) covalent geometry : bond 0.00310 (15560) covalent geometry : angle 0.54837 (20980) *********************** 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 254 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 2.150 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7679 (tm-30) REVERT: C 553 ARG cc_start: 0.8870 (tpp-160) cc_final: 0.8639 (tpp80) REVERT: D 130 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 73 MET cc_start: -0.2397 (mmt) cc_final: -0.2902 (ttm) REVERT: F 110 MET cc_start: 0.7365 (mmm) cc_final: 0.7125 (mmm) REVERT: F 141 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7565 (tm-30) REVERT: F 145 MET cc_start: 0.6596 (ptt) cc_final: 0.6321 (ptt) REVERT: G 142 PHE cc_start: 0.8786 (t80) cc_final: 0.8392 (t80) REVERT: G 145 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.5585 (ppp) REVERT: H 73 MET cc_start: -0.2681 (mmt) cc_final: -0.3021 (ttm) outliers start: 33 outliers final: 33 residues processed: 249 average time/residue: 1.7913 time to fit residues: 515.2838 Evaluate side-chains 247 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 110 SER 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 81 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 74 TYR 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 121 GLU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 138 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 161 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 129 optimal weight: 50.0000 chunk 8 optimal weight: 0.9990 chunk 157 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.178398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.107222 restraints weight = 70149.501| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.10 r_work: 0.3214 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15560 Z= 0.290 Angle : 0.621 10.374 20980 Z= 0.329 Chirality : 0.038 0.266 2296 Planarity : 0.004 0.064 2636 Dihedral : 5.974 50.558 2236 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.19), residues: 1844 helix: 2.39 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 269 HIS 0.002 0.001 HIS H 108 PHE 0.019 0.001 PHE A 80 TYR 0.010 0.002 TYR C 141 ARG 0.011 0.001 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 1151) hydrogen bonds : angle 4.45320 ( 3453) covalent geometry : bond 0.00637 (15560) covalent geometry : angle 0.62059 (20980) ********************** 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 249 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 2.252 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: C 130 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 553 ARG cc_start: 0.8905 (tpp-160) cc_final: 0.8643 (tpp80) REVERT: D 130 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7950 (tm-30) REVERT: E 73 MET cc_start: -0.2322 (mmt) cc_final: -0.2831 (ttm) REVERT: E 125 MET cc_start: 0.7759 (mmm) cc_final: 0.7507 (mmp) REVERT: F 141 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7579 (tm-30) REVERT: F 145 MET cc_start: 0.6647 (ptt) cc_final: 0.6370 (ptt) REVERT: G 145 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5271 (tmm) REVERT: H 73 MET cc_start: -0.2800 (mmt) cc_final: -0.3169 (ttm) outliers start: 38 outliers final: 31 residues processed: 244 average time/residue: 1.7941 time to fit residues: 508.0092 Evaluate side-chains 235 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 169 CYS Chi-restraints excluded: chain C residue 180 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 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 F residue 121 GLU Chi-restraints excluded: chain F residue 138 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 118 optimal weight: 0.5980 chunk 143 optimal weight: 40.0000 chunk 111 optimal weight: 0.9990 chunk 129 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4497 r_free = 0.4497 target = 0.182279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108839 restraints weight = 69474.236| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.29 r_work: 0.3329 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2304 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= 0.119 Angle : 0.555 11.178 20980 Z= 0.283 Chirality : 0.033 0.191 2296 Planarity : 0.003 0.062 2636 Dihedral : 5.079 46.474 2236 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.59 % Allowed : 31.54 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.20), residues: 1844 helix: 2.69 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 288 HIS 0.003 0.001 HIS G 108 PHE 0.018 0.001 PHE A 80 TYR 0.008 0.001 TYR C 237 ARG 0.010 0.000 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 1151) hydrogen bonds : angle 4.15898 ( 3453) covalent geometry : bond 0.00256 (15560) covalent geometry : angle 0.55543 (20980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27830.86 seconds wall clock time: 474 minutes 42.08 seconds (28482.08 seconds total)