Starting phenix.real_space_refine on Mon Jul 6 02:07:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j01_35880/07_2026/8j01_35880_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j01_35880/07_2026/8j01_35880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j01_35880/07_2026/8j01_35880_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j01_35880/07_2026/8j01_35880_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j01_35880/07_2026/8j01_35880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j01_35880/07_2026/8j01_35880.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 10548 2.51 5 N 2684 2.21 5 O 2900 1.98 5 H 15620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31852 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 Chain: "C" 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: "D" Number of atoms: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 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: 5741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5741 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 27 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: "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: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'P0T': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.39, per 1000 atoms: 0.17 Number of scatterers: 31852 At special positions: 0 Unit cell: (119.97, 120.9, 125.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 12 15.00 O 2900 8.00 N 2684 7.00 C 10548 6.00 H 15620 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 868.2 milliseconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 0 sheets defined 84.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 115 removed outlier: 3.563A pdb=" N ILE A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.844A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.577A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) 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 254 Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.685A pdb=" N PHE A 261 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 262' Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 348 removed outlier: 4.362A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Proline residue: A 308 - end of helix Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.465A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 559 Processing helix chain 'A' and resid 563 through 600 removed outlier: 3.562A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Proline residue: A 597 - end of helix Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 90 through 115 removed outlier: 3.562A pdb=" N ILE B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.838A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 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 254 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.633A pdb=" N PHE B 261 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 348 removed outlier: 4.322A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Proline residue: B 308 - end of helix Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.392A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 559 Processing helix chain 'B' and resid 563 through 600 removed outlier: 3.581A pdb=" N VAL B 567 " --> pdb=" O ASP B 563 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.821A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 90 through 115 Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.863A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 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 254 Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.601A pdb=" N PHE D 261 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 262' Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 349 removed outlier: 4.213A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) Proline residue: D 308 - end of helix Proline residue: D 335 - end of helix Processing helix chain 'D' and resid 356 through 367 removed outlier: 4.347A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR D 363 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 559 Processing helix chain 'D' and resid 563 through 600 removed outlier: 3.533A pdb=" N VAL D 567 " --> pdb=" O ASP D 563 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Proline residue: D 597 - end of helix 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 Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.682A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 90 through 115 removed outlier: 3.511A pdb=" N ILE G 94 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 3.863A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 165 removed outlier: 3.604A pdb=" N ARG G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 184 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 254 Processing helix chain 'G' and resid 258 through 262 removed outlier: 3.664A pdb=" N PHE G 261 " --> pdb=" O ASN G 258 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP G 262 " --> pdb=" O ASP G 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 258 through 262' Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 349 removed outlier: 4.227A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) Proline residue: G 308 - end of helix Proline residue: G 335 - end of helix Processing helix chain 'G' and resid 356 through 367 removed outlier: 4.307A pdb=" N TYR G 362 " --> pdb=" O SER G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 559 Processing helix chain 'G' and resid 563 through 600 removed outlier: 3.548A pdb=" N VAL G 567 " --> pdb=" O ASP G 563 " (cutoff:3.500A) Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 102 through 111 removed outlier: 3.840A pdb=" N THR H 111 " --> pdb=" O ARG H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 148 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 Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.644A pdb=" N ASP E 81 " --> pdb=" O MET E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.688A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 148 1241 hydrogen bonds defined for protein. 3723 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: 7.47 Time building geometry restraints manager: 3.66 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: 15592 1.03 - 1.23: 84 1.23 - 1.43: 6976 1.43 - 1.62: 9360 1.62 - 1.82: 180 Bond restraints: 32192 Sorted by residual: bond pdb=" C07 P0T B 803 " pdb=" C09 P0T B 803 " 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 G 802 " pdb=" C09 P0T G 802 " ideal model delta sigma weight residual 1.336 1.598 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C07 P0T D 802 " pdb=" C09 P0T D 802 " ideal model delta sigma weight residual 1.336 1.598 -0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C07 P0T A 802 " pdb=" C09 P0T A 802 " ideal model delta sigma weight residual 1.336 1.597 -0.261 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C07 P0T G 801 " pdb=" C09 P0T G 801 " ideal model delta sigma weight residual 1.336 1.595 -0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 32187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.02: 57700 6.02 - 12.04: 68 12.04 - 18.06: 8 18.06 - 24.08: 12 24.08 - 30.10: 8 Bond angle restraints: 57796 Sorted by residual: 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 D 801 " pdb=" C04 P0T D 801 " pdb=" C08 P0T D 801 " ideal model delta sigma weight residual 112.03 81.98 30.05 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 82.02 30.01 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C07 P0T G 801 " pdb=" C04 P0T G 801 " pdb=" C08 P0T G 801 " ideal model delta sigma weight residual 112.03 82.36 29.67 3.00e+00 1.11e-01 9.78e+01 angle pdb=" C07 P0T A 802 " pdb=" C04 P0T A 802 " pdb=" C08 P0T A 802 " ideal model delta sigma weight residual 112.03 83.68 28.35 3.00e+00 1.11e-01 8.93e+01 ... (remaining 57791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 13569 22.56 - 45.12: 1075 45.12 - 67.68: 337 67.68 - 90.24: 39 90.24 - 112.80: 24 Dihedral angle restraints: 15044 sinusoidal: 8104 harmonic: 6940 Sorted by residual: dihedral pdb=" C06 P0T B 803 " pdb=" C03 P0T B 803 " pdb=" C05 P0T B 803 " pdb=" C10 P0T B 803 " ideal model delta sinusoidal sigma weight residual 186.18 73.38 112.80 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" C06 P0T G 802 " pdb=" C03 P0T G 802 " pdb=" C05 P0T G 802 " pdb=" C10 P0T G 802 " ideal model delta sinusoidal sigma weight residual 186.18 73.39 112.79 1 3.00e+01 1.11e-03 1.48e+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 -63.30 112.30 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 15041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1651 0.025 - 0.050: 526 0.050 - 0.074: 200 0.074 - 0.099: 72 0.099 - 0.124: 23 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CA PRO H 67 " pdb=" N PRO H 67 " pdb=" C PRO H 67 " pdb=" CB PRO H 67 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CB THR F 35 " pdb=" CA THR F 35 " pdb=" OG1 THR F 35 " pdb=" CG2 THR F 35 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 2469 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO H 67 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 87 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO G 88 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 88 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 88 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 87 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 88 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " -0.016 5.00e-02 4.00e+02 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1213 2.14 - 2.76: 59532 2.76 - 3.37: 95066 3.37 - 3.99: 112117 3.99 - 4.60: 179104 Nonbonded interactions: 447032 Sorted by model distance: nonbonded pdb="HH21 ARG D 332 " pdb=" O ARG D 560 " model vdw 1.526 2.450 nonbonded pdb="HH21 ARG A 332 " pdb=" O ARG A 560 " model vdw 1.547 2.450 nonbonded pdb="HH21 ARG G 332 " pdb=" O ARG G 560 " model vdw 1.562 2.450 nonbonded pdb=" O PRO H 67 " pdb=" HG1 THR H 71 " model vdw 1.564 2.450 nonbonded pdb="HE22 GLN A 341 " pdb=" O LEU E 113 " model vdw 1.575 2.450 ... (remaining 447027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 600 or resid 802)) selection = (chain 'B' and (resid 70 through 600 or resid 802)) selection = (chain 'D' and (resid 70 through 600 or resid 802)) selection = (chain 'G' and (resid 70 through 600 or resid 802)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.040 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 0.264 16576 Z= 0.570 Angle : 1.100 30.102 22324 Z= 0.432 Chirality : 0.032 0.124 2472 Planarity : 0.003 0.032 2780 Dihedral : 19.300 112.798 6080 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.60 % Allowed : 21.30 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.19), residues: 1956 helix: 1.90 (0.13), residues: 1580 sheet: None (None), residues: 0 loop : 0.24 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 332 TYR 0.010 0.001 TYR C 139 PHE 0.009 0.001 PHE B 168 TRP 0.012 0.001 TRP B 344 HIS 0.002 0.001 HIS D 260 Details of bonding type rmsd/Z covalent geometry : bond 0.01141 / 0.57 (16572) covalent geometry : angle 1.10043 / 0.43 (22324) hydrogen bonds : bond 0.11111 / 7.34 ( 1241) hydrogen bonds : angle 4.99171 / 3.75 ( 3723) Misc. bond : bond 0.00026 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 231 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.555 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: B 146 TRP cc_start: 0.5635 (t60) cc_final: 0.5358 (t60) REVERT: B 155 ARG cc_start: 0.5217 (mmt180) cc_final: 0.4591 (mmm160) REVERT: B 158 ARG cc_start: 0.4941 (mtt180) cc_final: 0.4492 (tpt170) REVERT: C 40 LEU cc_start: 0.8601 (mm) cc_final: 0.8275 (tp) REVERT: D 158 ARG cc_start: 0.4911 (mtt180) cc_final: 0.4291 (tpt170) REVERT: F 52 MET cc_start: 0.7564 (ttm) cc_final: 0.7048 (ttm) outliers start: 10 outliers final: 8 residues processed: 221 average time/residue: 0.2848 time to fit residues: 92.0430 Evaluate side-chains 187 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 571 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN D 570 GLN G 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.161311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108256 restraints weight = 78853.352| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.29 r_work: 0.3364 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16576 Z= 0.135 Angle : 0.581 9.438 22324 Z= 0.293 Chirality : 0.033 0.167 2472 Planarity : 0.003 0.033 2780 Dihedral : 10.707 70.973 2372 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.21 % Allowed : 19.39 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.19), residues: 1956 helix: 1.93 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : 0.20 (0.39), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 87 TYR 0.010 0.001 TYR C 139 PHE 0.015 0.001 PHE C 66 TRP 0.011 0.001 TRP D 344 HIS 0.002 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (16572) covalent geometry : angle 0.58084 / 0.29 (22324) hydrogen bonds : bond 0.04736 / 3.14 ( 1241) hydrogen bonds : angle 4.50016 / 3.36 ( 3723) Misc. bond : bond 0.00021 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.831 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: B 155 ARG cc_start: 0.5066 (mmt180) cc_final: 0.4305 (mmm160) REVERT: B 158 ARG cc_start: 0.4975 (mtt180) cc_final: 0.4473 (tpt170) REVERT: C 40 LEU cc_start: 0.8691 (mm) cc_final: 0.8381 (tp) REVERT: C 110 MET cc_start: 0.8844 (mmm) cc_final: 0.8490 (mmp) REVERT: D 158 ARG cc_start: 0.4802 (mtt180) cc_final: 0.4159 (tpt170) REVERT: H 51 ASP cc_start: 0.8125 (t0) cc_final: 0.7611 (m-30) outliers start: 37 outliers final: 25 residues processed: 216 average time/residue: 0.2823 time to fit residues: 90.6150 Evaluate side-chains 208 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 GLN C 112 ASN G 570 GLN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.156998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103049 restraints weight = 78598.574| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.93 r_work: 0.3241 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16576 Z= 0.240 Angle : 0.580 8.239 22324 Z= 0.317 Chirality : 0.035 0.136 2472 Planarity : 0.004 0.033 2780 Dihedral : 8.617 84.817 2368 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.80 % Allowed : 20.88 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.19), residues: 1956 helix: 1.73 (0.12), residues: 1612 sheet: None (None), residues: 0 loop : 0.01 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 353 TYR 0.012 0.002 TYR B 562 PHE 0.014 0.002 PHE D 304 TRP 0.012 0.002 TRP B 344 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.24 (16572) covalent geometry : angle 0.58011 / 0.32 (22324) hydrogen bonds : bond 0.05438 / 3.60 ( 1241) hydrogen bonds : angle 4.62139 / 3.45 ( 3723) Misc. bond : bond 0.00020 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 224 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.889 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: A 93 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6310 (t80) REVERT: A 158 ARG cc_start: 0.5089 (mtt180) cc_final: 0.4521 (tpt170) REVERT: B 155 ARG cc_start: 0.4947 (mmt180) cc_final: 0.4244 (mmm160) REVERT: B 158 ARG cc_start: 0.5015 (mtt180) cc_final: 0.4497 (tpt170) REVERT: C 40 LEU cc_start: 0.8713 (mm) cc_final: 0.8419 (tp) REVERT: D 158 ARG cc_start: 0.4898 (mtt180) cc_final: 0.4198 (tpt170) REVERT: G 158 ARG cc_start: 0.4865 (mtt180) cc_final: 0.4156 (tpt170) REVERT: H 51 ASP cc_start: 0.8433 (t0) cc_final: 0.7979 (m-30) outliers start: 47 outliers final: 35 residues processed: 204 average time/residue: 0.3122 time to fit residues: 92.9161 Evaluate side-chains 207 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE 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 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 117 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.156143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100838 restraints weight = 79206.563| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.30 r_work: 0.3246 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16576 Z= 0.290 Angle : 0.607 9.010 22324 Z= 0.333 Chirality : 0.037 0.142 2472 Planarity : 0.004 0.046 2780 Dihedral : 8.433 86.815 2364 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.18 % Allowed : 20.47 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 1956 helix: 1.44 (0.12), residues: 1612 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 353 TYR 0.013 0.002 TYR A 562 PHE 0.014 0.002 PHE B 137 TRP 0.011 0.002 TRP B 344 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 (16572) covalent geometry : angle 0.60663 / 0.33 (22324) hydrogen bonds : bond 0.05609 / 3.74 ( 1241) hydrogen bonds : angle 4.73284 / 3.53 ( 3723) Misc. bond : bond 0.00020 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 173 time to evaluate : 0.934 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: A 158 ARG cc_start: 0.5219 (mtt180) cc_final: 0.4608 (tpt170) REVERT: B 131 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7378 (tp) REVERT: B 155 ARG cc_start: 0.4980 (mmt180) cc_final: 0.4221 (mmm160) REVERT: B 158 ARG cc_start: 0.5206 (mtt180) cc_final: 0.4658 (tpt170) REVERT: C 40 LEU cc_start: 0.8733 (mm) cc_final: 0.8402 (tp) REVERT: D 158 ARG cc_start: 0.4884 (mtt180) cc_final: 0.4209 (tpt170) REVERT: D 231 GLU cc_start: 0.8758 (mp0) cc_final: 0.8318 (mp0) REVERT: G 158 ARG cc_start: 0.4848 (mtt180) cc_final: 0.4168 (tpt170) REVERT: H 51 ASP cc_start: 0.8507 (t0) cc_final: 0.8085 (m-30) REVERT: H 110 MET cc_start: 0.8993 (mmm) cc_final: 0.8690 (mmp) outliers start: 70 outliers final: 51 residues processed: 219 average time/residue: 0.2860 time to fit residues: 93.4948 Evaluate side-chains 218 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 587 SER Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 121 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.156166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102017 restraints weight = 78613.575| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.91 r_work: 0.3235 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16576 Z= 0.226 Angle : 0.554 8.783 22324 Z= 0.306 Chirality : 0.034 0.131 2472 Planarity : 0.003 0.034 2780 Dihedral : 7.998 85.506 2364 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 21.90 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 1956 helix: 1.49 (0.12), residues: 1612 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 560 TYR 0.011 0.001 TYR B 562 PHE 0.012 0.001 PHE C 66 TRP 0.011 0.002 TRP B 344 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (16572) covalent geometry : angle 0.55437 / 0.31 (22324) hydrogen bonds : bond 0.05305 / 3.53 ( 1241) hydrogen bonds : angle 4.64258 / 3.46 ( 3723) Misc. bond : bond 0.00011 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 234 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5252 (mtt180) cc_final: 0.4672 (tpt170) REVERT: B 131 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7357 (tp) REVERT: B 155 ARG cc_start: 0.4958 (mmt180) cc_final: 0.4095 (mmm160) REVERT: B 158 ARG cc_start: 0.5185 (mtt180) cc_final: 0.4624 (tpt170) REVERT: B 231 GLU cc_start: 0.8778 (mp0) cc_final: 0.8351 (mp0) REVERT: C 40 LEU cc_start: 0.8750 (mm) cc_final: 0.8398 (tp) REVERT: D 158 ARG cc_start: 0.4861 (mtt180) cc_final: 0.4179 (tpt170) REVERT: D 578 MET cc_start: 0.8783 (ttm) cc_final: 0.8548 (ttm) REVERT: G 158 ARG cc_start: 0.4811 (mtt180) cc_final: 0.4137 (tpt170) REVERT: H 51 ASP cc_start: 0.8681 (t0) cc_final: 0.8198 (m-30) REVERT: H 110 MET cc_start: 0.8962 (mmm) cc_final: 0.8705 (mmp) REVERT: H 144 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8630 (tm-30) outliers start: 58 outliers final: 46 residues processed: 213 average time/residue: 0.2972 time to fit residues: 94.4059 Evaluate side-chains 217 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 156 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.157583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103715 restraints weight = 78024.440| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.87 r_work: 0.3263 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16576 Z= 0.172 Angle : 0.514 9.073 22324 Z= 0.283 Chirality : 0.033 0.125 2472 Planarity : 0.003 0.039 2780 Dihedral : 7.392 82.114 2364 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.94 % Allowed : 21.30 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.19), residues: 1956 helix: 1.67 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 541 TYR 0.008 0.001 TYR B 562 PHE 0.013 0.001 PHE C 66 TRP 0.012 0.002 TRP B 344 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (16572) covalent geometry : angle 0.51430 / 0.28 (22324) hydrogen bonds : bond 0.04938 / 3.29 ( 1241) hydrogen bonds : angle 4.49076 / 3.34 ( 3723) Misc. bond : bond 0.00007 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 245 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5149 (mtt180) cc_final: 0.4546 (tpt170) REVERT: B 155 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4169 (mmm160) REVERT: B 158 ARG cc_start: 0.5163 (mtt180) cc_final: 0.4622 (tpt170) REVERT: B 231 GLU cc_start: 0.8755 (mp0) cc_final: 0.8381 (mp0) REVERT: C 40 LEU cc_start: 0.8712 (mm) cc_final: 0.8375 (tp) REVERT: C 144 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8709 (tm-30) REVERT: D 158 ARG cc_start: 0.4854 (mtt180) cc_final: 0.4177 (tpt170) REVERT: D 231 GLU cc_start: 0.8743 (mp0) cc_final: 0.8373 (mp0) REVERT: D 578 MET cc_start: 0.8765 (ttm) cc_final: 0.8532 (ttm) REVERT: G 131 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7347 (tp) REVERT: G 158 ARG cc_start: 0.4801 (mtt180) cc_final: 0.4132 (tpt170) REVERT: H 40 LEU cc_start: 0.8499 (mm) cc_final: 0.8147 (tp) REVERT: H 51 ASP cc_start: 0.8700 (t0) cc_final: 0.8196 (m-30) outliers start: 66 outliers final: 48 residues processed: 223 average time/residue: 0.3008 time to fit residues: 99.3861 Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 587 SER Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 82 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 GLN F 112 ASN G 96 HIS E 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.154915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099302 restraints weight = 78781.638| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.28 r_work: 0.3237 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16576 Z= 0.290 Angle : 0.613 8.977 22324 Z= 0.335 Chirality : 0.037 0.142 2472 Planarity : 0.004 0.132 2780 Dihedral : 8.364 88.658 2362 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.12 % Allowed : 21.66 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 1956 helix: 1.42 (0.12), residues: 1612 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 353 TYR 0.011 0.002 TYR B 562 PHE 0.013 0.002 PHE B 137 TRP 0.011 0.002 TRP B 344 HIS 0.003 0.001 HIS G 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.29 (16572) covalent geometry : angle 0.61302 / 0.33 (22324) hydrogen bonds : bond 0.05555 / 3.70 ( 1241) hydrogen bonds : angle 4.71843 / 3.51 ( 3723) Misc. bond : bond 0.00085 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 242 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 173 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5281 (mtt180) cc_final: 0.4752 (tpt170) REVERT: B 78 GLN cc_start: 0.4053 (OUTLIER) cc_final: 0.3489 (tt0) REVERT: B 155 ARG cc_start: 0.5031 (OUTLIER) cc_final: 0.4167 (mmm160) REVERT: B 158 ARG cc_start: 0.5225 (mtt180) cc_final: 0.4667 (tpt170) REVERT: B 231 GLU cc_start: 0.8768 (mp0) cc_final: 0.8345 (mp0) REVERT: C 40 LEU cc_start: 0.8723 (mm) cc_final: 0.8373 (tp) REVERT: C 144 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8726 (tm-30) REVERT: D 158 ARG cc_start: 0.4831 (mtt180) cc_final: 0.4167 (tpt170) REVERT: D 231 GLU cc_start: 0.8750 (mp0) cc_final: 0.8303 (mp0) REVERT: D 578 MET cc_start: 0.8772 (ttm) cc_final: 0.8528 (ttm) REVERT: F 121 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: G 78 GLN cc_start: 0.4523 (OUTLIER) cc_final: 0.4006 (tt0) REVERT: G 131 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7413 (tp) REVERT: G 158 ARG cc_start: 0.4873 (mtt180) cc_final: 0.4179 (tpt170) REVERT: H 51 ASP cc_start: 0.8760 (t0) cc_final: 0.8216 (m-30) outliers start: 69 outliers final: 61 residues processed: 218 average time/residue: 0.2969 time to fit residues: 95.5786 Evaluate side-chains 234 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 78 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 587 SER Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.157721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103938 restraints weight = 78183.896| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.89 r_work: 0.3261 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16576 Z= 0.159 Angle : 0.522 9.761 22324 Z= 0.285 Chirality : 0.033 0.132 2472 Planarity : 0.004 0.129 2780 Dihedral : 7.361 82.352 2362 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.88 % Allowed : 21.96 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 1956 helix: 1.66 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 87 TYR 0.010 0.001 TYR B 562 PHE 0.013 0.001 PHE C 66 TRP 0.014 0.002 TRP B 146 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16572) covalent geometry : angle 0.52203 / 0.29 (22324) hydrogen bonds : bond 0.04946 / 3.30 ( 1241) hydrogen bonds : angle 4.49094 / 3.34 ( 3723) Misc. bond : bond 0.00224 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 178 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5155 (mtt180) cc_final: 0.4551 (tpt170) REVERT: B 155 ARG cc_start: 0.5050 (OUTLIER) cc_final: 0.4157 (mmm160) REVERT: B 158 ARG cc_start: 0.5179 (mtt180) cc_final: 0.4633 (tpt170) REVERT: B 231 GLU cc_start: 0.8748 (mp0) cc_final: 0.8348 (mp0) REVERT: C 40 LEU cc_start: 0.8724 (mm) cc_final: 0.8391 (tp) REVERT: C 144 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8708 (tm-30) REVERT: D 158 ARG cc_start: 0.4787 (mtt180) cc_final: 0.4130 (tpt170) REVERT: D 231 GLU cc_start: 0.8720 (mp0) cc_final: 0.8314 (mp0) REVERT: D 578 MET cc_start: 0.8768 (ttm) cc_final: 0.8562 (ttm) REVERT: F 121 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: G 131 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7361 (tp) REVERT: G 158 ARG cc_start: 0.4827 (mtt180) cc_final: 0.4143 (tpt170) REVERT: H 40 LEU cc_start: 0.8487 (mm) cc_final: 0.8155 (tp) REVERT: H 51 ASP cc_start: 0.8738 (t0) cc_final: 0.8205 (m-30) REVERT: E 110 MET cc_start: 0.8849 (mmm) cc_final: 0.8569 (mmp) outliers start: 65 outliers final: 54 residues processed: 224 average time/residue: 0.2859 time to fit residues: 94.4858 Evaluate side-chains 228 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 171 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 587 SER Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.158696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104377 restraints weight = 78211.126| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.64 r_work: 0.3293 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16576 Z= 0.143 Angle : 0.502 9.443 22324 Z= 0.275 Chirality : 0.032 0.129 2472 Planarity : 0.003 0.066 2780 Dihedral : 6.752 79.976 2358 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.46 % Allowed : 22.14 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1956 helix: 1.81 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 87 TYR 0.012 0.001 TYR B 74 PHE 0.014 0.001 PHE C 66 TRP 0.025 0.002 TRP B 146 HIS 0.002 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (16572) covalent geometry : angle 0.50201 / 0.27 (22324) hydrogen bonds : bond 0.04673 / 3.11 ( 1241) hydrogen bonds : angle 4.37067 / 3.26 ( 3723) Misc. bond : bond 0.00117 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 242 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.5239 (OUTLIER) cc_final: 0.4179 (mmm160) REVERT: A 158 ARG cc_start: 0.5129 (mtt180) cc_final: 0.4528 (tpt170) REVERT: B 78 GLN cc_start: 0.4309 (OUTLIER) cc_final: 0.3036 (tt0) REVERT: B 137 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.4461 (t80) REVERT: B 155 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.4176 (mmm160) REVERT: B 158 ARG cc_start: 0.5166 (mtt180) cc_final: 0.4570 (tpt170) REVERT: B 231 GLU cc_start: 0.8688 (mp0) cc_final: 0.8302 (mp0) REVERT: C 40 LEU cc_start: 0.8720 (mm) cc_final: 0.8399 (tp) REVERT: C 144 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8695 (tm-30) REVERT: D 158 ARG cc_start: 0.4782 (mtt180) cc_final: 0.4126 (tpt170) REVERT: F 121 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: G 131 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7333 (tp) REVERT: G 158 ARG cc_start: 0.4786 (mtt180) cc_final: 0.4109 (tpt170) REVERT: H 40 LEU cc_start: 0.8505 (mm) cc_final: 0.8177 (tp) REVERT: H 51 ASP cc_start: 0.8717 (t0) cc_final: 0.8156 (m-30) REVERT: E 110 MET cc_start: 0.8835 (mmm) cc_final: 0.8581 (mmp) outliers start: 58 outliers final: 46 residues processed: 226 average time/residue: 0.2721 time to fit residues: 91.8091 Evaluate side-chains 225 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 587 SER Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 124 optimal weight: 0.0980 chunk 187 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.159155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104774 restraints weight = 78672.684| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.32 r_work: 0.3306 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16576 Z= 0.169 Angle : 0.751 59.184 22324 Z= 0.418 Chirality : 0.033 0.213 2472 Planarity : 0.004 0.160 2780 Dihedral : 6.744 79.956 2358 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.04 % Allowed : 22.79 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1956 helix: 1.81 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG G 87 TYR 0.011 0.001 TYR B 74 PHE 0.014 0.001 PHE C 66 TRP 0.021 0.002 TRP B 146 HIS 0.002 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (16572) covalent geometry : angle 0.75094 / 0.42 (22324) hydrogen bonds : bond 0.04687 / 3.12 ( 1241) hydrogen bonds : angle 4.36676 / 3.26 ( 3723) Misc. bond : bond 0.01686 / 0.84 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 TYR 74 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue TYR 98 is missing expected H atoms. Skipping. Residue TYR 118 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 154 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue TYR 226 is missing expected H atoms. Skipping. Residue TYR 237 is missing expected H atoms. Skipping. Residue TYR 251 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Residue TYR 284 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue TYR 571 is missing expected H atoms. Skipping. Residue LYS 583 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 224 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4155 (mmm160) REVERT: A 158 ARG cc_start: 0.5141 (mtt180) cc_final: 0.4547 (tpt170) REVERT: B 137 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.4488 (t80) REVERT: B 155 ARG cc_start: 0.5098 (OUTLIER) cc_final: 0.4198 (mmm160) REVERT: B 158 ARG cc_start: 0.5172 (mtt180) cc_final: 0.4590 (tpt170) REVERT: B 231 GLU cc_start: 0.8668 (mp0) cc_final: 0.8276 (mp0) REVERT: C 40 LEU cc_start: 0.8718 (mm) cc_final: 0.8404 (tp) REVERT: C 144 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8691 (tm-30) REVERT: D 158 ARG cc_start: 0.4802 (mtt180) cc_final: 0.4153 (tpt170) REVERT: D 231 GLU cc_start: 0.8668 (mp0) cc_final: 0.8268 (mp0) REVERT: F 121 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: G 131 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7337 (tp) REVERT: G 158 ARG cc_start: 0.4805 (mtt180) cc_final: 0.4216 (tpp-160) REVERT: H 40 LEU cc_start: 0.8497 (mm) cc_final: 0.8174 (tp) REVERT: H 51 ASP cc_start: 0.8709 (t0) cc_final: 0.8158 (m-30) REVERT: E 110 MET cc_start: 0.8846 (mmm) cc_final: 0.8589 (mmp) outliers start: 51 outliers final: 46 residues processed: 210 average time/residue: 0.3017 time to fit residues: 94.2268 Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 571 TYR Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 100 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 543 VAL Chi-restraints excluded: chain G residue 587 SER Chi-restraints excluded: chain G residue 592 ILE Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 79 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.159072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104603 restraints weight = 78467.392| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.32 r_work: 0.3307 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 16576 Z= 0.168 Angle : 0.750 58.997 22324 Z= 0.418 Chirality : 0.033 0.193 2472 Planarity : 0.004 0.162 2780 Dihedral : 6.744 79.956 2358 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.04 % Allowed : 22.67 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.19), residues: 1956 helix: 1.81 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG G 87 TYR 0.011 0.001 TYR B 74 PHE 0.014 0.001 PHE C 66 TRP 0.021 0.002 TRP B 146 HIS 0.002 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (16572) covalent geometry : angle 0.74973 / 0.42 (22324) hydrogen bonds : bond 0.04687 / 3.12 ( 1241) hydrogen bonds : angle 4.36665 / 3.26 ( 3723) Misc. bond : bond 0.01515 / 0.76 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10068.48 seconds wall clock time: 170 minutes 57.21 seconds (10257.21 seconds total)