Starting phenix.real_space_refine on Thu Jun 26 00:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijk_35487/06_2025/8ijk_35487_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijk_35487/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ijk_35487/06_2025/8ijk_35487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijk_35487/06_2025/8ijk_35487.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijk_35487/06_2025/8ijk_35487_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijk_35487/06_2025/8ijk_35487_neut_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.33, per 1000 atoms: 0.47 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: 8.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.61 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: 12.55 Time building geometry restraints manager: 9.78 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: 0.14 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.840 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: 0.460 Extract box with map and model: 1.210 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 62.450 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (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 TRP 0.007 0.001 TRP C 146 HIS 0.002 0.001 HIS C 228 PHE 0.011 0.001 PHE D 548 TYR 0.012 0.001 TYR A 74 ARG 0.007 0.000 ARG E 87 Details of bonding type rmsd hydrogen bonds : bond 0.10811 ( 1228) hydrogen bonds : angle 5.69852 ( 3672) covalent geometry : bond 0.00642 (15664) covalent geometry : angle 0.63575 (21084) *********************** 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 : 2.378 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: 0.6717 time to fit residues: 229.9781 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 : 2.379 ------------------------------------------------------------------------------- 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 158 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.131487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.096318 restraints weight = 107332.373| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.94 r_work: 0.3477 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15664 Z= 0.143 Angle : 0.561 6.307 21084 Z= 0.303 Chirality : 0.033 0.125 2336 Planarity : 0.003 0.036 2664 Dihedral : 5.295 71.882 2058 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.18 % Allowed : 23.57 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.19), residues: 1888 helix: 2.10 (0.13), residues: 1556 sheet: None (None), residues: 0 loop : -0.59 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.002 0.001 HIS A 228 PHE 0.013 0.001 PHE B 240 TYR 0.010 0.001 TYR E 100 ARG 0.002 0.000 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 1228) hydrogen bonds : angle 4.86936 ( 3672) covalent geometry : bond 0.00296 (15664) covalent geometry : angle 0.56095 (21084) *********************** 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 233 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 3.354 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: A 174 MET cc_start: 0.7443 (ptt) cc_final: 0.7224 (ptp) REVERT: B 174 MET cc_start: 0.7452 (ptt) cc_final: 0.7235 (ptp) REVERT: C 140 GLU cc_start: 0.6776 (mm-30) cc_final: 0.5543 (tt0) REVERT: C 174 MET cc_start: 0.7560 (ptt) cc_final: 0.7349 (ptp) REVERT: D 140 GLU cc_start: 0.6782 (mm-30) cc_final: 0.5548 (tt0) REVERT: D 174 MET cc_start: 0.7468 (ptt) cc_final: 0.7249 (ptp) REVERT: E 20 PHE cc_start: 0.8985 (m-10) cc_final: 0.8784 (m-10) REVERT: E 52 MET cc_start: 0.7503 (mtt) cc_final: 0.7268 (mtt) REVERT: F 20 PHE cc_start: 0.8984 (m-10) cc_final: 0.8783 (m-10) REVERT: G 20 PHE cc_start: 0.8981 (m-10) cc_final: 0.8775 (m-10) REVERT: G 52 MET cc_start: 0.7546 (mtt) cc_final: 0.7334 (mtt) outliers start: 19 outliers final: 15 residues processed: 229 average time/residue: 0.8179 time to fit residues: 267.7782 Evaluate side-chains 208 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 139 TYR Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 92 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 139 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 174 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.129692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094679 restraints weight = 108281.239| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.93 r_work: 0.3435 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15664 Z= 0.186 Angle : 0.557 6.949 21084 Z= 0.309 Chirality : 0.032 0.138 2336 Planarity : 0.003 0.036 2664 Dihedral : 4.862 48.549 2044 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.49 % Allowed : 21.83 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.19), residues: 1888 helix: 2.02 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.003 0.001 HIS D 228 PHE 0.012 0.001 PHE C 240 TYR 0.014 0.001 TYR A 74 ARG 0.003 0.000 ARG C 332 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 1228) hydrogen bonds : angle 4.85526 ( 3672) covalent geometry : bond 0.00391 (15664) covalent geometry : angle 0.55671 (21084) *********************** 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 245 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 2.239 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 174 MET cc_start: 0.7506 (ptt) cc_final: 0.7283 (ptp) REVERT: B 174 MET cc_start: 0.7502 (ptt) cc_final: 0.7280 (ptp) REVERT: C 140 GLU cc_start: 0.6830 (mm-30) cc_final: 0.5643 (tt0) REVERT: C 174 MET cc_start: 0.7505 (ptt) cc_final: 0.7283 (ptp) REVERT: D 140 GLU cc_start: 0.6805 (mm-30) cc_final: 0.5609 (tt0) REVERT: D 174 MET cc_start: 0.7507 (ptt) cc_final: 0.7281 (ptp) REVERT: F 49 LEU cc_start: 0.8269 (mt) cc_final: 0.8064 (mt) REVERT: H 49 LEU cc_start: 0.8266 (mt) cc_final: 0.8063 (mt) outliers start: 40 outliers final: 24 residues processed: 241 average time/residue: 0.6490 time to fit residues: 227.0521 Evaluate side-chains 221 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 585 LEU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4228 r_free = 0.4228 target = 0.130420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.095462 restraints weight = 108372.905| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.92 r_work: 0.3455 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15664 Z= 0.148 Angle : 0.534 6.849 21084 Z= 0.293 Chirality : 0.032 0.130 2336 Planarity : 0.003 0.036 2664 Dihedral : 4.477 50.754 2044 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.49 % Allowed : 22.39 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.19), residues: 1888 helix: 2.13 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 344 HIS 0.002 0.001 HIS B 228 PHE 0.013 0.001 PHE C 240 TYR 0.010 0.001 TYR A 74 ARG 0.002 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 1228) hydrogen bonds : angle 4.70502 ( 3672) covalent geometry : bond 0.00311 (15664) covalent geometry : angle 0.53429 (21084) *********************** 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 255 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 2.464 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: A 174 MET cc_start: 0.7550 (ptt) cc_final: 0.7320 (ptp) REVERT: B 174 MET cc_start: 0.7550 (ptt) cc_final: 0.7330 (ptp) REVERT: C 140 GLU cc_start: 0.6811 (mm-30) cc_final: 0.5618 (tt0) REVERT: C 174 MET cc_start: 0.7559 (ptt) cc_final: 0.7342 (ptp) REVERT: D 140 GLU cc_start: 0.6820 (mm-30) cc_final: 0.5622 (tt0) REVERT: D 174 MET cc_start: 0.7561 (ptt) cc_final: 0.7347 (ptp) REVERT: E 49 LEU cc_start: 0.8441 (mt) cc_final: 0.8236 (mt) REVERT: F 52 MET cc_start: 0.7215 (mtt) cc_final: 0.6938 (mtt) REVERT: F 146 MET cc_start: 0.8019 (tmm) cc_final: 0.7630 (tmm) REVERT: G 49 LEU cc_start: 0.8438 (mt) cc_final: 0.8234 (mt) REVERT: H 52 MET cc_start: 0.7218 (mtt) cc_final: 0.6939 (mtt) outliers start: 40 outliers final: 31 residues processed: 240 average time/residue: 0.6562 time to fit residues: 230.2520 Evaluate side-chains 233 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 585 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.130250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.095524 restraints weight = 107897.305| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.87 r_work: 0.3443 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15664 Z= 0.166 Angle : 0.547 7.110 21084 Z= 0.302 Chirality : 0.032 0.133 2336 Planarity : 0.003 0.036 2664 Dihedral : 4.641 52.452 2044 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.99 % Allowed : 22.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 1888 helix: 2.06 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 344 HIS 0.002 0.001 HIS D 228 PHE 0.012 0.001 PHE C 240 TYR 0.012 0.001 TYR A 74 ARG 0.003 0.000 ARG C 332 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 1228) hydrogen bonds : angle 4.69171 ( 3672) covalent geometry : bond 0.00349 (15664) covalent geometry : angle 0.54740 (21084) *********************** 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 260 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 2.266 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 174 MET cc_start: 0.7612 (ptt) cc_final: 0.7398 (ptp) REVERT: B 174 MET cc_start: 0.7605 (ptt) cc_final: 0.7387 (ptp) REVERT: C 140 GLU cc_start: 0.6712 (mm-30) cc_final: 0.5544 (tt0) REVERT: C 174 MET cc_start: 0.7610 (ptt) cc_final: 0.7395 (ptp) REVERT: D 140 GLU cc_start: 0.6736 (mm-30) cc_final: 0.5567 (tt0) REVERT: D 174 MET cc_start: 0.7605 (ptt) cc_final: 0.7389 (ptp) REVERT: E 49 LEU cc_start: 0.8406 (mt) cc_final: 0.8138 (mt) REVERT: E 146 MET cc_start: 0.7894 (tmm) cc_final: 0.7494 (tmm) REVERT: G 49 LEU cc_start: 0.8405 (mt) cc_final: 0.8135 (mt) REVERT: G 75 ARG cc_start: 0.7551 (tpp80) cc_final: 0.7314 (tpp80) REVERT: H 146 MET cc_start: 0.7907 (tmm) cc_final: 0.7507 (tmm) outliers start: 48 outliers final: 41 residues processed: 249 average time/residue: 0.6937 time to fit residues: 242.5934 Evaluate side-chains 245 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 A residue 585 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 B residue 585 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 C residue 585 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 D residue 585 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 130 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.129979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.094652 restraints weight = 109687.040| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.90 r_work: 0.3447 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2472 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= 0.155 Angle : 0.530 7.463 21084 Z= 0.293 Chirality : 0.032 0.132 2336 Planarity : 0.003 0.035 2664 Dihedral : 4.624 55.197 2044 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.05 % Allowed : 22.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.19), residues: 1888 helix: 2.09 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 344 HIS 0.002 0.001 HIS A 228 PHE 0.012 0.001 PHE C 240 TYR 0.011 0.001 TYR A 74 ARG 0.002 0.000 ARG D 332 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 1228) hydrogen bonds : angle 4.61413 ( 3672) covalent geometry : bond 0.00323 (15664) covalent geometry : angle 0.53024 (21084) *********************** 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 263 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 3.503 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: 0.7602 (ptt) cc_final: 0.7390 (ptp) REVERT: A 546 MET cc_start: 0.8592 (tpp) cc_final: 0.8302 (tpp) REVERT: B 174 MET cc_start: 0.7594 (ptt) cc_final: 0.7381 (ptp) REVERT: C 140 GLU cc_start: 0.6771 (mm-30) cc_final: 0.5608 (tt0) REVERT: C 174 MET cc_start: 0.7629 (ptt) cc_final: 0.7408 (ptp) REVERT: C 546 MET cc_start: 0.8577 (tpp) cc_final: 0.8284 (tpp) REVERT: D 140 GLU cc_start: 0.6772 (mm-30) cc_final: 0.5611 (tt0) REVERT: D 174 MET cc_start: 0.7611 (ptt) cc_final: 0.7394 (ptp) REVERT: E 49 LEU cc_start: 0.8458 (mt) cc_final: 0.8233 (mt) REVERT: E 75 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7274 (tpp80) REVERT: E 146 MET cc_start: 0.7992 (tmm) cc_final: 0.7599 (tmm) REVERT: G 49 LEU cc_start: 0.8461 (mt) cc_final: 0.8236 (mt) REVERT: G 75 ARG cc_start: 0.7629 (tpp80) cc_final: 0.7346 (tpp80) REVERT: H 146 MET cc_start: 0.8007 (tmm) cc_final: 0.7620 (tmm) outliers start: 49 outliers final: 42 residues processed: 252 average time/residue: 0.9418 time to fit residues: 345.3617 Evaluate side-chains 248 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 585 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 B residue 585 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 C residue 585 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 D residue 585 LEU 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.127287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091644 restraints weight = 110873.989| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.85 r_work: 0.3382 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15664 Z= 0.268 Angle : 0.617 7.664 21084 Z= 0.350 Chirality : 0.035 0.156 2336 Planarity : 0.004 0.039 2664 Dihedral : 6.023 58.153 2044 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.92 % Allowed : 21.52 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.19), residues: 1888 helix: 1.76 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.43 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 344 HIS 0.004 0.001 HIS C 260 PHE 0.017 0.002 PHE C 548 TYR 0.020 0.002 TYR B 74 ARG 0.003 0.000 ARG B 581 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 1228) hydrogen bonds : angle 4.94620 ( 3672) covalent geometry : bond 0.00568 (15664) covalent geometry : angle 0.61716 (21084) *********************** 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 283 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 MET cc_start: 0.7568 (ptt) cc_final: 0.7368 (ptp) REVERT: C 140 GLU cc_start: 0.6612 (mm-30) cc_final: 0.5581 (tt0) REVERT: C 174 MET cc_start: 0.7568 (ptt) cc_final: 0.7367 (ptp) REVERT: D 140 GLU cc_start: 0.6611 (mm-30) cc_final: 0.5581 (tt0) REVERT: E 49 LEU cc_start: 0.8495 (mt) cc_final: 0.8279 (mt) REVERT: E 121 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: E 146 MET cc_start: 0.7958 (tmm) cc_final: 0.7491 (tmm) REVERT: F 121 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: F 146 MET cc_start: 0.8090 (tmm) cc_final: 0.7603 (tmm) REVERT: G 49 LEU cc_start: 0.8495 (mt) cc_final: 0.8281 (mt) REVERT: G 121 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: G 146 MET cc_start: 0.7964 (tmm) cc_final: 0.7461 (tmm) REVERT: H 121 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: H 146 MET cc_start: 0.7968 (tmm) cc_final: 0.7504 (tmm) outliers start: 63 outliers final: 51 residues processed: 273 average time/residue: 0.8102 time to fit residues: 325.3434 Evaluate side-chains 262 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 585 LEU 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 203 LEU Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 541 ARG Chi-restraints excluded: chain C residue 585 LEU 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 541 ARG Chi-restraints excluded: chain D residue 585 LEU 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 121 GLU 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 13 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.128666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.093297 restraints weight = 110334.316| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.85 r_work: 0.3414 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15664 Z= 0.180 Angle : 0.565 7.144 21084 Z= 0.312 Chirality : 0.033 0.138 2336 Planarity : 0.003 0.035 2664 Dihedral : 5.195 59.945 2044 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.23 % Allowed : 22.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 1888 helix: 1.89 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.44 (0.40), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.002 0.001 HIS A 228 PHE 0.011 0.001 PHE C 240 TYR 0.013 0.001 TYR A 74 ARG 0.005 0.000 ARG H 75 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 1228) hydrogen bonds : angle 4.76014 ( 3672) covalent geometry : bond 0.00377 (15664) covalent geometry : angle 0.56540 (21084) *********************** 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 266 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 4.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6614 (mm-30) cc_final: 0.5433 (tt0) REVERT: D 140 GLU cc_start: 0.6635 (mm-30) cc_final: 0.5463 (tt0) REVERT: E 49 LEU cc_start: 0.8508 (mt) cc_final: 0.8173 (mt) REVERT: E 121 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6357 (mp0) REVERT: F 121 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: G 49 LEU cc_start: 0.8501 (mt) cc_final: 0.8163 (mt) REVERT: G 121 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: H 121 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6327 (mp0) outliers start: 52 outliers final: 48 residues processed: 252 average time/residue: 0.6983 time to fit residues: 253.8008 Evaluate side-chains 258 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 541 ARG Chi-restraints excluded: chain A residue 585 LEU 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 203 LEU Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain B residue 585 LEU 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 C residue 585 LEU 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 D residue 585 LEU 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 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 117 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.129693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.094352 restraints weight = 109983.245| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.88 r_work: 0.3441 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15664 Z= 0.143 Angle : 0.543 7.936 21084 Z= 0.295 Chirality : 0.032 0.126 2336 Planarity : 0.003 0.036 2664 Dihedral : 4.599 58.860 2044 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.05 % Allowed : 23.32 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 1888 helix: 2.06 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.39 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.002 0.000 HIS A 228 PHE 0.012 0.001 PHE D 240 TYR 0.009 0.001 TYR A 74 ARG 0.004 0.000 ARG H 75 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 1228) hydrogen bonds : angle 4.59730 ( 3672) covalent geometry : bond 0.00299 (15664) covalent geometry : angle 0.54287 (21084) *********************** 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 266 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 140 GLU cc_start: 0.6531 (mm-30) cc_final: 0.5405 (tt0) REVERT: D 140 GLU cc_start: 0.6530 (mm-30) cc_final: 0.5400 (tt0) REVERT: E 49 LEU cc_start: 0.8368 (mt) cc_final: 0.8153 (mt) REVERT: E 121 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: F 121 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: G 49 LEU cc_start: 0.8378 (mt) cc_final: 0.8119 (mt) REVERT: G 121 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: H 121 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6379 (mp0) outliers start: 49 outliers final: 44 residues processed: 253 average time/residue: 0.7223 time to fit residues: 263.9957 Evaluate side-chains 259 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 A residue 585 LEU 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 B residue 585 LEU 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 C residue 585 LEU 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 D residue 585 LEU 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 38 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.127877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.092311 restraints weight = 110617.621| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.85 r_work: 0.3396 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15664 Z= 0.221 Angle : 0.603 8.063 21084 Z= 0.333 Chirality : 0.033 0.145 2336 Planarity : 0.004 0.037 2664 Dihedral : 5.284 58.656 2044 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.73 % Allowed : 23.45 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1888 helix: 1.91 (0.12), residues: 1552 sheet: None (None), residues: 0 loop : -0.61 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 344 HIS 0.002 0.001 HIS D 260 PHE 0.011 0.001 PHE C 548 TYR 0.015 0.001 TYR A 74 ARG 0.002 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 1228) hydrogen bonds : angle 4.75931 ( 3672) covalent geometry : bond 0.00467 (15664) covalent geometry : angle 0.60315 (21084) ********************** 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 270 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 4.478 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: C 140 GLU cc_start: 0.6687 (mm-30) cc_final: 0.5537 (tt0) REVERT: D 140 GLU cc_start: 0.6662 (mm-30) cc_final: 0.5504 (tt0) REVERT: E 49 LEU cc_start: 0.8408 (mt) cc_final: 0.8172 (mt) REVERT: E 121 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: E 146 MET cc_start: 0.8506 (tmm) cc_final: 0.7736 (tmm) REVERT: F 121 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: G 49 LEU cc_start: 0.8406 (mt) cc_final: 0.8162 (mt) REVERT: G 121 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: H 121 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6353 (mp0) outliers start: 60 outliers final: 46 residues processed: 254 average time/residue: 1.0229 time to fit residues: 385.2563 Evaluate side-chains 259 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 2.839 ------------------------------------------------------------------------------- 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 A residue 585 LEU 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 B residue 585 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 129 LEU 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 C residue 585 LEU 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 D residue 585 LEU 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 137 VAL 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 101 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.129700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094459 restraints weight = 109923.392| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.90 r_work: 0.3444 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15664 Z= 0.141 Angle : 0.562 8.236 21084 Z= 0.303 Chirality : 0.032 0.126 2336 Planarity : 0.003 0.034 2664 Dihedral : 4.656 58.150 2044 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.99 % Allowed : 24.32 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.19), residues: 1888 helix: 2.05 (0.12), residues: 1556 sheet: None (None), residues: 0 loop : -0.45 (0.39), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 344 HIS 0.002 0.000 HIS C 228 PHE 0.012 0.001 PHE B 168 TYR 0.009 0.001 TYR E 100 ARG 0.002 0.000 ARG D 332 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 1228) hydrogen bonds : angle 4.58810 ( 3672) covalent geometry : bond 0.00295 (15664) covalent geometry : angle 0.56178 (21084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16788.80 seconds wall clock time: 296 minutes 5.68 seconds (17765.68 seconds total)