Starting phenix.real_space_refine on Mon Aug 25 18:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijk_35487/08_2025/8ijk_35487_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijk_35487/08_2025/8ijk_35487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ijk_35487/08_2025/8ijk_35487_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijk_35487/08_2025/8ijk_35487_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ijk_35487/08_2025/8ijk_35487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijk_35487/08_2025/8ijk_35487.map" } resolution = 3.4 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 S 88 5.16 5 C 9972 2.51 5 N 2580 2.21 5 O 2696 1.98 5 F 4 1.80 5 H 15016 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30356 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} 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: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} 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: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} 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: "D" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5438 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 7, 'TRANS': 329} 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: "E" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7PN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.73, per 1000 atoms: 0.16 Number of scatterers: 30356 At special positions: 0 Unit cell: (129.27, 129.27, 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 F 4 9.00 O 2696 8.00 N 2580 7.00 C 9972 6.00 H 15016 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 681.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 4 sheets defined 85.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 115 removed outlier: 3.553A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 149 removed outlier: 3.892A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.944A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 161 " --> pdb=" O TRP A 157 " (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: 3.636A pdb=" N ASP A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 349 removed outlier: 4.429A 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 536 through 559 Processing helix chain 'A' and resid 563 through 600 removed outlier: 3.597A pdb=" N GLY A 574 " --> pdb=" O GLN A 570 " (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: 3.549A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 149 removed outlier: 3.893A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.945A pdb=" N ARG B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) 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 ASP B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 349 removed outlier: 4.428A 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 536 through 559 Processing helix chain 'B' and resid 563 through 600 removed outlier: 3.599A 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 71 through 86 Processing helix chain 'C' and resid 90 through 115 removed outlier: 3.551A pdb=" N ILE C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 149 removed outlier: 3.890A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.949A pdb=" N ARG C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 184 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 254 Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.634A pdb=" N ASP C 262 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 349 removed outlier: 4.428A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Proline residue: C 308 - end of helix Proline residue: C 335 - end of helix Processing helix chain 'C' and resid 536 through 559 Processing helix chain 'C' and resid 563 through 600 removed outlier: 3.598A pdb=" N GLY C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) Proline residue: C 597 - end of helix Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 90 through 115 removed outlier: 3.547A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 149 removed outlier: 3.893A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.950A pdb=" N ARG D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 161 " --> pdb=" O TRP D 157 " (cutoff:3.500A) 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: 3.631A pdb=" N ASP D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 349 removed outlier: 4.428A 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 536 through 559 Processing helix chain 'D' and resid 563 through 600 removed outlier: 3.599A pdb=" N GLY D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) Proline residue: D 597 - end of helix 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 66 through 75 Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.643A 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 113 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 148 Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 Processing helix chain 'F' and resid 76 through 81 removed outlier: 3.678A pdb=" N ASP F 81 " --> pdb=" O MET F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 66 through 74 Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.678A pdb=" N ASP G 81 " --> pdb=" O MET G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 102 through 113 Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 138 through 148 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 66 through 75 Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.643A pdb=" N ASP H 81 " --> pdb=" O MET H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 102 through 113 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 138 through 148 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 28 removed outlier: 3.528A pdb=" N ILE E 64 " --> pdb=" O ILE E 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 27 through 28 removed outlier: 3.527A pdb=" N ILE F 64 " --> pdb=" O ILE F 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 27 through 28 removed outlier: 3.573A pdb=" N ILE G 64 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 27 through 28 removed outlier: 3.530A pdb=" N ILE H 64 " --> pdb=" O ILE H 28 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3672 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: 6.08 Time building geometry restraints manager: 3.37 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: 14988 1.03 - 1.23: 146 1.23 - 1.43: 6530 1.43 - 1.62: 8868 1.62 - 1.82: 148 Bond restraints: 30680 Sorted by residual: bond pdb=" C16 7PN A 801 " pdb=" C17 7PN A 801 " ideal model delta sigma weight residual 1.382 1.524 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C16 7PN B 801 " pdb=" C17 7PN B 801 " ideal model delta sigma weight residual 1.382 1.523 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C16 7PN C 801 " pdb=" C17 7PN C 801 " ideal model delta sigma weight residual 1.382 1.522 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C16 7PN D 801 " pdb=" C17 7PN D 801 " ideal model delta sigma weight residual 1.382 1.522 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C18 7PN C 801 " pdb=" C19 7PN C 801 " ideal model delta sigma weight residual 1.387 1.520 -0.133 2.00e-02 2.50e+03 4.42e+01 ... (remaining 30675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 54607 1.86 - 3.72: 533 3.72 - 5.58: 44 5.58 - 7.44: 18 7.44 - 9.30: 10 Bond angle restraints: 55212 Sorted by residual: angle pdb=" CA PRO H 67 " pdb=" N PRO H 67 " pdb=" CD PRO H 67 " ideal model delta sigma weight residual 112.00 104.75 7.25 1.40e+00 5.10e-01 2.68e+01 angle pdb=" CA PRO E 67 " pdb=" N PRO E 67 " pdb=" CD PRO E 67 " ideal model delta sigma weight residual 112.00 104.75 7.25 1.40e+00 5.10e-01 2.68e+01 angle pdb=" CA PRO F 67 " pdb=" N PRO F 67 " pdb=" CD PRO F 67 " ideal model delta sigma weight residual 112.00 104.80 7.20 1.40e+00 5.10e-01 2.65e+01 angle pdb=" N PRO E 67 " pdb=" CD PRO E 67 " pdb=" CG PRO E 67 " ideal model delta sigma weight residual 103.20 97.15 6.05 1.50e+00 4.44e-01 1.63e+01 angle pdb=" N PRO H 67 " pdb=" CD PRO H 67 " pdb=" CG PRO H 67 " ideal model delta sigma weight residual 103.20 97.15 6.05 1.50e+00 4.44e-01 1.63e+01 ... (remaining 55207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12404 17.92 - 35.85: 1274 35.85 - 53.77: 409 53.77 - 71.70: 119 71.70 - 89.62: 30 Dihedral angle restraints: 14236 sinusoidal: 7576 harmonic: 6660 Sorted by residual: dihedral pdb=" CA TRP A 91 " pdb=" CB TRP A 91 " pdb=" CG TRP A 91 " pdb=" CD1 TRP A 91 " ideal model delta sinusoidal sigma weight residual 90.00 158.09 -68.09 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA TRP B 91 " pdb=" CB TRP B 91 " pdb=" CG TRP B 91 " pdb=" CD1 TRP B 91 " ideal model delta sinusoidal sigma weight residual 90.00 158.09 -68.09 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA TRP C 91 " pdb=" CB TRP C 91 " pdb=" CG TRP C 91 " pdb=" CD1 TRP C 91 " ideal model delta sinusoidal sigma weight residual 90.00 158.00 -68.00 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 14233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1521 0.027 - 0.054: 591 0.054 - 0.081: 162 0.081 - 0.108: 51 0.108 - 0.135: 11 Chirality restraints: 2336 Sorted by residual: 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 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA PRO C 308 " pdb=" N PRO C 308 " pdb=" C PRO C 308 " pdb=" CB PRO C 308 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA PRO D 308 " pdb=" N PRO D 308 " pdb=" C PRO D 308 " pdb=" CB PRO D 308 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2333 not shown) Planarity restraints: 4532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 66 " 0.053 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO E 67 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 66 " 0.053 5.00e-02 4.00e+02 7.60e-02 9.24e+00 pdb=" N PRO H 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO H 67 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 67 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 66 " 0.052 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO F 67 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 67 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 67 " 0.043 5.00e-02 4.00e+02 ... (remaining 4529 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1098 2.13 - 2.75: 56677 2.75 - 3.36: 93131 3.36 - 3.98: 108630 3.98 - 4.60: 172986 Nonbonded interactions: 432522 Sorted by model distance: nonbonded pdb=" OD1 ASN G 138 " pdb=" H GLU G 140 " model vdw 1.510 2.450 nonbonded pdb=" OD1 ASN H 138 " pdb=" H GLU H 140 " model vdw 1.511 2.450 nonbonded pdb=" OD1 ASN F 138 " pdb=" H GLU F 140 " model vdw 1.511 2.450 nonbonded pdb=" OD1 ASN E 138 " pdb=" H GLU E 140 " model vdw 1.512 2.450 nonbonded pdb="HH12 ARG G 38 " pdb=" O GLN G 42 " model vdw 1.566 2.450 ... (remaining 432517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 24.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.006 0.142 15664 Z= 0.314 Angle : 0.636 9.304 21084 Z= 0.344 Chirality : 0.033 0.135 2336 Planarity : 0.004 0.076 2664 Dihedral : 17.523 89.619 5624 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.75 % Allowed : 22.64 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.19), residues: 1888 helix: 1.83 (0.13), residues: 1548 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.012 0.001 TYR A 74 PHE 0.011 0.001 PHE D 548 TRP 0.007 0.001 TRP C 146 HIS 0.002 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00642 (15664) covalent geometry : angle 0.63575 (21084) hydrogen bonds : bond 0.10811 ( 1228) hydrogen bonds : angle 5.69852 ( 3672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 241 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6727 (mm-30) cc_final: 0.5452 (tt0) REVERT: D 140 GLU cc_start: 0.6718 (mm-30) cc_final: 0.5433 (tt0) REVERT: E 52 MET cc_start: 0.7630 (mtt) cc_final: 0.7401 (mtt) REVERT: G 52 MET cc_start: 0.7637 (mtt) cc_final: 0.7411 (mtt) outliers start: 12 outliers final: 10 residues processed: 241 average time/residue: 0.2893 time to fit residues: 98.9082 Evaluate side-chains 190 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 ASN F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.130211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094724 restraints weight = 108252.811| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.95 r_work: 0.3445 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15664 Z= 0.170 Angle : 0.575 6.362 21084 Z= 0.315 Chirality : 0.033 0.134 2336 Planarity : 0.003 0.037 2664 Dihedral : 5.549 73.385 2058 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.43 % Allowed : 23.69 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.19), residues: 1888 helix: 1.98 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -0.63 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 332 TYR 0.012 0.001 TYR A 74 PHE 0.012 0.001 PHE G 66 TRP 0.008 0.001 TRP B 344 HIS 0.003 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00358 (15664) covalent geometry : angle 0.57521 (21084) hydrogen bonds : bond 0.04859 ( 1228) hydrogen bonds : angle 4.97323 ( 3672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7434 (ptt) cc_final: 0.7229 (ptp) REVERT: B 174 MET cc_start: 0.7445 (ptt) cc_final: 0.7235 (ptp) REVERT: C 140 GLU cc_start: 0.6756 (mm-30) cc_final: 0.5523 (tt0) REVERT: D 140 GLU cc_start: 0.6764 (mm-30) cc_final: 0.5531 (tt0) REVERT: D 174 MET cc_start: 0.7436 (ptt) cc_final: 0.7230 (ptp) REVERT: E 52 MET cc_start: 0.7515 (mtt) cc_final: 0.7302 (mtt) REVERT: G 52 MET cc_start: 0.7522 (mtt) cc_final: 0.7310 (mtt) REVERT: H 52 MET cc_start: 0.7516 (mtt) cc_final: 0.7302 (mtt) outliers start: 23 outliers final: 19 residues processed: 220 average time/residue: 0.3278 time to fit residues: 101.7668 Evaluate side-chains 211 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.129531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.094769 restraints weight = 108598.579| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.90 r_work: 0.3437 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15664 Z= 0.178 Angle : 0.556 6.587 21084 Z= 0.307 Chirality : 0.032 0.136 2336 Planarity : 0.003 0.035 2664 Dihedral : 4.821 49.451 2046 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.74 % Allowed : 22.33 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.19), residues: 1888 helix: 1.99 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.57 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 332 TYR 0.012 0.001 TYR C 74 PHE 0.012 0.001 PHE B 240 TRP 0.007 0.001 TRP B 344 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00373 (15664) covalent geometry : angle 0.55617 (21084) hydrogen bonds : bond 0.04815 ( 1228) hydrogen bonds : angle 4.89229 ( 3672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 251 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7498 (ptt) cc_final: 0.7283 (ptp) REVERT: B 174 MET cc_start: 0.7497 (ptt) cc_final: 0.7281 (ptp) REVERT: C 140 GLU cc_start: 0.6858 (mm-30) cc_final: 0.5559 (tt0) REVERT: D 140 GLU cc_start: 0.6835 (mm-30) cc_final: 0.5525 (tt0) REVERT: D 174 MET cc_start: 0.7514 (ptt) cc_final: 0.7299 (ptp) REVERT: E 52 MET cc_start: 0.7588 (mtt) cc_final: 0.7211 (mtt) REVERT: F 52 MET cc_start: 0.7457 (mtt) cc_final: 0.7083 (mtt) REVERT: G 52 MET cc_start: 0.7611 (mtt) cc_final: 0.7239 (mtt) REVERT: H 52 MET cc_start: 0.7455 (mtt) cc_final: 0.7083 (mtt) outliers start: 44 outliers final: 26 residues processed: 243 average time/residue: 0.3166 time to fit residues: 111.5548 Evaluate side-chains 222 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 286 GLN B 258 ASN B 286 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN D 286 GLN E 112 ASN F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.130316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095872 restraints weight = 107138.939| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.82 r_work: 0.3442 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15664 Z= 0.171 Angle : 0.554 6.822 21084 Z= 0.306 Chirality : 0.032 0.135 2336 Planarity : 0.003 0.036 2664 Dihedral : 4.698 50.568 2044 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.36 % Allowed : 21.77 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.19), residues: 1888 helix: 2.01 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.012 0.001 TYR A 74 PHE 0.012 0.001 PHE B 240 TRP 0.008 0.001 TRP D 344 HIS 0.002 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00356 (15664) covalent geometry : angle 0.55443 (21084) hydrogen bonds : bond 0.04753 ( 1228) hydrogen bonds : angle 4.82230 ( 3672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 258 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7519 (ptt) cc_final: 0.7317 (ptp) REVERT: B 174 MET cc_start: 0.7525 (ptt) cc_final: 0.7319 (ptp) REVERT: C 140 GLU cc_start: 0.6792 (mm-30) cc_final: 0.5510 (tt0) REVERT: D 140 GLU cc_start: 0.6798 (mm-30) cc_final: 0.5515 (tt0) REVERT: D 174 MET cc_start: 0.7538 (ptt) cc_final: 0.7331 (ptp) REVERT: E 52 MET cc_start: 0.7517 (mtt) cc_final: 0.7303 (mtt) REVERT: F 52 MET cc_start: 0.7406 (mtt) cc_final: 0.7206 (mtt) REVERT: F 146 MET cc_start: 0.8046 (tmm) cc_final: 0.7644 (tmm) REVERT: G 52 MET cc_start: 0.7521 (mtt) cc_final: 0.7305 (mtt) REVERT: G 75 ARG cc_start: 0.7643 (tpp80) cc_final: 0.7362 (tpp80) outliers start: 54 outliers final: 41 residues processed: 250 average time/residue: 0.3270 time to fit residues: 117.1595 Evaluate side-chains 234 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 150 CYS Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 258 ASN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 286 GLN C 258 ASN C 286 GLN D 286 GLN E 112 ASN F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.130526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.096211 restraints weight = 107022.742| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.84 r_work: 0.3446 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15664 Z= 0.154 Angle : 0.542 7.252 21084 Z= 0.299 Chirality : 0.032 0.131 2336 Planarity : 0.003 0.035 2664 Dihedral : 4.601 52.425 2044 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.23 % Allowed : 22.70 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.19), residues: 1888 helix: 2.05 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 332 TYR 0.011 0.001 TYR A 74 PHE 0.013 0.001 PHE C 240 TRP 0.009 0.001 TRP D 344 HIS 0.004 0.001 HIS E 108 Details of bonding type rmsd covalent geometry : bond 0.00322 (15664) covalent geometry : angle 0.54164 (21084) hydrogen bonds : bond 0.04666 ( 1228) hydrogen bonds : angle 4.70203 ( 3672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6721 (mm-30) cc_final: 0.5534 (tt0) REVERT: D 140 GLU cc_start: 0.6725 (mm-30) cc_final: 0.5535 (tt0) REVERT: E 146 MET cc_start: 0.7922 (tmm) cc_final: 0.7537 (tmm) REVERT: G 75 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7304 (tpp80) REVERT: H 146 MET cc_start: 0.7936 (tmm) cc_final: 0.7552 (tmm) outliers start: 52 outliers final: 40 residues processed: 250 average time/residue: 0.3391 time to fit residues: 120.9125 Evaluate side-chains 237 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 GLN E 112 ASN F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.130226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.096635 restraints weight = 109624.541| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.82 r_work: 0.3469 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15664 Z= 0.151 Angle : 0.548 7.482 21084 Z= 0.299 Chirality : 0.032 0.129 2336 Planarity : 0.003 0.035 2664 Dihedral : 4.579 53.717 2044 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.30 % Allowed : 22.33 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.19), residues: 1888 helix: 2.07 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 332 TYR 0.010 0.001 TYR A 74 PHE 0.013 0.001 PHE B 240 TRP 0.009 0.001 TRP D 344 HIS 0.002 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00317 (15664) covalent geometry : angle 0.54789 (21084) hydrogen bonds : bond 0.04615 ( 1228) hydrogen bonds : angle 4.64939 ( 3672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 257 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8510 (tpp) cc_final: 0.8207 (tpp) REVERT: B 286 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8656 (mt0) REVERT: C 140 GLU cc_start: 0.6773 (mm-30) cc_final: 0.5578 (tt0) REVERT: D 140 GLU cc_start: 0.6785 (mm-30) cc_final: 0.5595 (tt0) REVERT: D 546 MET cc_start: 0.8545 (tpp) cc_final: 0.8249 (tpp) REVERT: E 121 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: E 146 MET cc_start: 0.8005 (tmm) cc_final: 0.7616 (tmm) REVERT: F 121 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: F 146 MET cc_start: 0.8611 (tmm) cc_final: 0.8115 (tmm) REVERT: G 75 ARG cc_start: 0.7553 (tpp80) cc_final: 0.7294 (tpp80) REVERT: G 121 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: H 121 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: H 146 MET cc_start: 0.8025 (tmm) cc_final: 0.7637 (tmm) outliers start: 53 outliers final: 41 residues processed: 249 average time/residue: 0.3351 time to fit residues: 118.3640 Evaluate side-chains 244 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.129516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.095894 restraints weight = 109383.265| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.74 r_work: 0.3452 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15664 Z= 0.178 Angle : 0.554 7.589 21084 Z= 0.306 Chirality : 0.032 0.137 2336 Planarity : 0.003 0.036 2664 Dihedral : 4.911 55.621 2044 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.86 % Allowed : 22.14 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.19), residues: 1888 helix: 2.02 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.51 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.013 0.001 TYR A 74 PHE 0.012 0.001 PHE C 240 TRP 0.009 0.001 TRP C 344 HIS 0.002 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00374 (15664) covalent geometry : angle 0.55378 (21084) hydrogen bonds : bond 0.04684 ( 1228) hydrogen bonds : angle 4.68111 ( 3672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 269 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.8152 (mt0) cc_final: 0.7910 (mt0) REVERT: B 286 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8724 (mt0) REVERT: C 140 GLU cc_start: 0.6857 (mm-30) cc_final: 0.5589 (tt0) REVERT: D 140 GLU cc_start: 0.6852 (mm-30) cc_final: 0.5587 (tt0) REVERT: D 204 GLN cc_start: 0.8120 (mt0) cc_final: 0.7914 (mt0) REVERT: E 75 ARG cc_start: 0.7679 (tpp80) cc_final: 0.7334 (tpp80) REVERT: E 78 LYS cc_start: 0.8668 (tppt) cc_final: 0.8428 (tppt) REVERT: E 121 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: E 146 MET cc_start: 0.7956 (tmm) cc_final: 0.7523 (tmm) REVERT: F 75 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7258 (tpp80) REVERT: F 121 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: G 121 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: H 146 MET cc_start: 0.7893 (tmm) cc_final: 0.7459 (tmm) outliers start: 62 outliers final: 48 residues processed: 261 average time/residue: 0.3265 time to fit residues: 122.1463 Evaluate side-chains 251 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 163 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.127215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.092968 restraints weight = 110881.291| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.76 r_work: 0.3406 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15664 Z= 0.258 Angle : 0.617 7.801 21084 Z= 0.349 Chirality : 0.034 0.154 2336 Planarity : 0.004 0.038 2664 Dihedral : 5.805 58.557 2044 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.67 % Allowed : 22.64 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.19), residues: 1888 helix: 1.77 (0.12), residues: 1552 sheet: None (None), residues: 0 loop : -0.45 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 75 TYR 0.019 0.002 TYR A 74 PHE 0.015 0.002 PHE C 548 TRP 0.010 0.001 TRP C 344 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00547 (15664) covalent geometry : angle 0.61698 (21084) hydrogen bonds : bond 0.05126 ( 1228) hydrogen bonds : angle 4.94430 ( 3672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLN cc_start: 0.8202 (mt0) cc_final: 0.7955 (mt0) REVERT: C 140 GLU cc_start: 0.6626 (mm-30) cc_final: 0.5590 (tt0) REVERT: D 140 GLU cc_start: 0.6627 (mm-30) cc_final: 0.5589 (tt0) REVERT: D 204 GLN cc_start: 0.8206 (mt0) cc_final: 0.7981 (mt0) REVERT: E 78 LYS cc_start: 0.8655 (tppt) cc_final: 0.8445 (tppt) REVERT: E 146 MET cc_start: 0.7990 (tmm) cc_final: 0.7537 (tmm) REVERT: F 121 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: G 121 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: G 146 MET cc_start: 0.8006 (tmm) cc_final: 0.7488 (tmm) REVERT: H 121 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: H 146 MET cc_start: 0.7920 (tmm) cc_final: 0.7401 (tmm) outliers start: 59 outliers final: 48 residues processed: 263 average time/residue: 0.3398 time to fit residues: 125.6514 Evaluate side-chains 254 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 74 TYR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.129438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094054 restraints weight = 109815.204| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.89 r_work: 0.3437 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15664 Z= 0.141 Angle : 0.554 7.910 21084 Z= 0.301 Chirality : 0.032 0.128 2336 Planarity : 0.003 0.034 2664 Dihedral : 4.827 59.948 2044 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.17 % Allowed : 23.01 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.19), residues: 1888 helix: 2.01 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 75 TYR 0.010 0.001 TYR A 74 PHE 0.012 0.001 PHE B 168 TRP 0.010 0.001 TRP C 344 HIS 0.002 0.000 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00294 (15664) covalent geometry : angle 0.55433 (21084) hydrogen bonds : bond 0.04626 ( 1228) hydrogen bonds : angle 4.65930 ( 3672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 269 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6484 (mm-30) cc_final: 0.5412 (tt0) REVERT: D 140 GLU cc_start: 0.6483 (mm-30) cc_final: 0.5411 (tt0) REVERT: E 121 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: E 146 MET cc_start: 0.8105 (tmm) cc_final: 0.7628 (tmm) REVERT: F 121 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: G 121 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: H 121 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6302 (mp0) outliers start: 51 outliers final: 43 residues processed: 254 average time/residue: 0.3120 time to fit residues: 112.8208 Evaluate side-chains 250 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.129522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.094172 restraints weight = 108938.344| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.87 r_work: 0.3440 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 15664 Z= 0.225 Angle : 1.054 59.124 21084 Z= 0.638 Chirality : 0.033 0.148 2336 Planarity : 0.003 0.035 2664 Dihedral : 4.841 59.950 2044 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.92 % Allowed : 23.82 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.19), residues: 1888 helix: 2.00 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.44 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 75 TYR 0.010 0.001 TYR A 74 PHE 0.012 0.001 PHE B 240 TRP 0.009 0.001 TRP C 344 HIS 0.002 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00464 (15664) covalent geometry : angle 1.05434 (21084) hydrogen bonds : bond 0.04653 ( 1228) hydrogen bonds : angle 4.66917 ( 3672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 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 LYS 537 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 LYS 537 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 LYS 537 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 LYS 537 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. 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 247 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5422 (tt0) REVERT: D 140 GLU cc_start: 0.6500 (mm-30) cc_final: 0.5424 (tt0) REVERT: E 121 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6258 (mp0) REVERT: E 146 MET cc_start: 0.8143 (tmm) cc_final: 0.7636 (tmm) REVERT: F 121 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: G 121 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: H 121 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6299 (mp0) outliers start: 47 outliers final: 42 residues processed: 235 average time/residue: 0.3474 time to fit residues: 114.9568 Evaluate side-chains 245 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 321 GLN Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 139 TYR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 139 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 139 TYR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 177 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN G 112 ASN H 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.129588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.094124 restraints weight = 109795.567| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.88 r_work: 0.3436 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 15664 Z= 0.223 Angle : 1.054 59.200 21084 Z= 0.636 Chirality : 0.033 0.147 2336 Planarity : 0.003 0.035 2664 Dihedral : 4.841 59.950 2044 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.86 % Allowed : 23.82 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.19), residues: 1888 helix: 2.00 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.44 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 75 TYR 0.010 0.001 TYR A 74 PHE 0.012 0.001 PHE B 240 TRP 0.009 0.001 TRP C 344 HIS 0.002 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00461 (15664) covalent geometry : angle 1.05409 (21084) hydrogen bonds : bond 0.04654 ( 1228) hydrogen bonds : angle 4.66902 ( 3672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.65 seconds wall clock time: 131 minutes 59.27 seconds (7919.27 seconds total)