Starting phenix.real_space_refine on Fri Jul 25 13:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgv_50430/07_2025/9fgv_50430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgv_50430/07_2025/9fgv_50430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgv_50430/07_2025/9fgv_50430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgv_50430/07_2025/9fgv_50430.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgv_50430/07_2025/9fgv_50430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgv_50430/07_2025/9fgv_50430.cif" } resolution = 3.39 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= 0.014 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4934 2.51 5 N 1252 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 366, 2842 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Conformer: "B" Number of residues, atoms: 366, 2842 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} bond proxies already assigned to first conformer: 2877 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 969 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 366, 2842 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} Conformer: "B" Number of residues, atoms: 366, 2842 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 21, 'TRANS': 344} bond proxies already assigned to first conformer: 2877 Chain: "D" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Conformer: "B" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} bond proxies already assigned to first conformer: 985 Time building chain proxies: 9.33, per 1000 atoms: 1.21 Number of scatterers: 7685 At special positions: 0 Unit cell: (82.49, 124.83, 72.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1475 8.00 N 1252 7.00 C 4934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS D 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 16 sheets defined 42.0% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 Processing helix chain 'A' and resid 42 through 52 Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.554A pdb=" N GLY A 68 " --> pdb=" O HIS A 64 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.711A pdb=" N VAL A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 4.638A pdb=" N ALA A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 185 through 201 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.215A pdb=" N GLU A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.543A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 42 through 52 Proline residue: C 48 - end of helix Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.675A pdb=" N GLY C 68 " --> pdb=" O HIS C 64 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.582A pdb=" N VAL C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 removed outlier: 4.628A pdb=" N ALA C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 286 through 297 removed outlier: 3.509A pdb=" N ASP C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 312 removed outlier: 4.169A pdb=" N GLU C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 327 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 356 through 366 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.543A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.528A pdb=" N TYR D 112 " --> pdb=" O GLN D 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.601A pdb=" N LEU A 7 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLU A 38 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 9 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 8 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE A 61 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP A 10 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA A 63 " --> pdb=" O TRP A 10 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE A 258 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA A 112 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 260 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 110 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A 262 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 301 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.601A pdb=" N LEU A 7 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLU A 38 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 9 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 8 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE A 61 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TRP A 10 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA A 63 " --> pdb=" O TRP A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 removed outlier: 6.244A pdb=" N ALA A 146 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE A 226 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 223 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.794A pdb=" N LYS A 170 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.256A pdb=" N ARG B 38 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLY B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 38 removed outlier: 6.620A pdb=" N LEU C 7 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLU C 38 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 9 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 8 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE C 61 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP C 10 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ALA C 63 " --> pdb=" O TRP C 10 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N PHE C 258 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA C 112 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY C 260 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL C 110 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 262 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 301 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 38 removed outlier: 6.620A pdb=" N LEU C 7 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLU C 38 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 9 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 8 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE C 61 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP C 10 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ALA C 63 " --> pdb=" O TRP C 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 147 removed outlier: 6.249A pdb=" N ALA C 146 " --> pdb=" O MET C 224 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE C 226 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA C 223 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.788A pdb=" N LYS C 170 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.280A pdb=" N ARG D 38 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLY D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 12 373 hydrogen bonds defined for protein. 1023 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: 2.36 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2456 1.34 - 1.46: 1644 1.46 - 1.58: 3741 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 7883 Sorted by residual: bond pdb=" CB LYS A 137 " pdb=" CG LYS A 137 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CG LYS A 137 " pdb=" CD LYS A 137 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CA GLY A 260 " pdb=" C GLY A 260 " ideal model delta sigma weight residual 1.520 1.513 0.008 7.30e-03 1.88e+04 1.07e+00 bond pdb=" CA GLY C 260 " pdb=" C GLY C 260 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 9.07e-01 bond pdb=" CA LYS C 239 " pdb=" CB LYS C 239 " ideal model delta sigma weight residual 1.529 1.543 -0.014 1.62e-02 3.81e+03 7.32e-01 ... (remaining 7878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 10573 1.60 - 3.20: 126 3.20 - 4.80: 17 4.80 - 6.40: 2 6.40 - 8.00: 1 Bond angle restraints: 10719 Sorted by residual: angle pdb=" CB LYS A 137 " pdb=" CG LYS A 137 " pdb=" CD LYS A 137 " ideal model delta sigma weight residual 111.30 119.30 -8.00 2.30e+00 1.89e-01 1.21e+01 angle pdb=" CA LYS C 239 " pdb=" CB LYS C 239 " pdb=" CG LYS C 239 " ideal model delta sigma weight residual 114.10 118.71 -4.61 2.00e+00 2.50e-01 5.32e+00 angle pdb=" CA MET A 336 " pdb=" CB MET A 336 " pdb=" CG MET A 336 " ideal model delta sigma weight residual 114.10 109.50 4.60 2.00e+00 2.50e-01 5.28e+00 angle pdb=" N ASN C 332 " pdb=" CA ASN C 332 " pdb=" C ASN C 332 " ideal model delta sigma weight residual 110.44 113.15 -2.71 1.20e+00 6.94e-01 5.12e+00 angle pdb=" C SER C 238 " pdb=" N LYS C 239 " pdb=" CA LYS C 239 " ideal model delta sigma weight residual 122.07 125.27 -3.20 1.43e+00 4.89e-01 5.00e+00 ... (remaining 10714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4335 17.29 - 34.58: 300 34.58 - 51.86: 66 51.86 - 69.15: 8 69.15 - 86.44: 3 Dihedral angle restraints: 4712 sinusoidal: 1836 harmonic: 2876 Sorted by residual: dihedral pdb=" CB CYS B 11 " pdb=" SG CYS B 11 " pdb=" SG CYS D 11 " pdb=" CB CYS D 11 " ideal model delta sinusoidal sigma weight residual -86.00 -34.95 -51.05 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA MET C 336 " pdb=" C MET C 336 " pdb=" N SER C 337 " pdb=" CA SER C 337 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA MET A 336 " pdb=" C MET A 336 " pdb=" N SER A 337 " pdb=" CA SER A 337 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 874 0.039 - 0.079: 178 0.079 - 0.118: 94 0.118 - 0.158: 4 0.158 - 0.197: 2 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA MET C 336 " pdb=" N MET C 336 " pdb=" C MET C 336 " pdb=" CB MET C 336 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA MET A 336 " pdb=" N MET A 336 " pdb=" C MET A 336 " pdb=" CB MET A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB ILE A 329 " pdb=" CA ILE A 329 " pdb=" CG1 ILE A 329 " pdb=" CG2 ILE A 329 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1149 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 330 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 331 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 330 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO C 331 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 331 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 331 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 333 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO A 334 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.019 5.00e-02 4.00e+02 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 841 2.75 - 3.29: 7435 3.29 - 3.83: 13115 3.83 - 4.36: 15727 4.36 - 4.90: 27034 Nonbonded interactions: 64152 Sorted by model distance: nonbonded pdb=" O GLU A 214 " pdb=" ND2 ASN A 218 " model vdw 2.217 3.120 nonbonded pdb=" NE2 HIS C 64 " pdb=" O MET C 330 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLN A 72 " pdb=" OH TYR A 99 " model vdw 2.301 3.040 nonbonded pdb=" NE2 HIS A 64 " pdb=" O MET A 330 " model vdw 2.302 3.120 nonbonded pdb=" O TYR C 90 " pdb=" OG1 THR C 93 " model vdw 2.308 3.040 ... (remaining 64147 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 21 or resid 23 through 81 or resid 83 through 21 \ 0 or resid 212 through 237 or resid 239 through 277 or resid 279 through 329 or \ resid 331 through 366)) selection = (chain 'C' and (resid 1 through 21 or resid 23 through 81 or resid 83 through 21 \ 0 or resid 212 through 237 or resid 239 through 277 or resid 279 through 329 or \ resid 331 through 366)) } ncs_group { reference = (chain 'B' and (resid 0 through 16 or resid 18 through 31 or resid 33 through 12 \ 4)) selection = (chain 'D' and (resid 0 through 16 or resid 18 through 31 or resid 33 through 12 \ 4)) } 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=0.00 max=1.00 mean=0.99 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: 5.750 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.730 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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 : 0.002 0.033 7886 Z= 0.095 Angle : 0.454 8.001 10725 Z= 0.244 Chirality : 0.041 0.197 1152 Planarity : 0.004 0.061 1388 Dihedral : 12.655 86.437 2883 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.89 (0.27), residues: 988 helix: 1.65 (0.28), residues: 352 sheet: 1.28 (0.37), residues: 188 loop : 1.12 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 62 HIS 0.008 0.002 HIS A 39 PHE 0.008 0.001 PHE C 149 TYR 0.009 0.001 TYR C 242 ARG 0.002 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.17306 ( 355) hydrogen bonds : angle 7.03074 ( 1023) SS BOND : bond 0.00135 ( 3) SS BOND : angle 1.15153 ( 6) covalent geometry : bond 0.00193 ( 7883) covalent geometry : angle 0.45351 (10719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.822 Fit side-chains REVERT: B 28 ILE cc_start: 0.6165 (pt) cc_final: 0.5744 (mm) REVERT: C 102 LYS cc_start: 0.7441 (mttm) cc_final: 0.7167 (pttt) REVERT: C 218 ASN cc_start: 0.8216 (m-40) cc_final: 0.7738 (m110) REVERT: C 239 LYS cc_start: 0.6095 (ptmm) cc_final: 0.5802 (ptpp) REVERT: D 28 ILE cc_start: 0.5954 (pt) cc_final: 0.5538 (mm) REVERT: D 122 MET cc_start: 0.6719 (mtt) cc_final: 0.6487 (mtp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1803 time to fit residues: 28.5227 Evaluate side-chains 86 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 72 GLN C 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.205557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158894 restraints weight = 40460.822| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 7.17 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3845 r_free = 0.3845 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7886 Z= 0.142 Angle : 0.537 5.502 10725 Z= 0.290 Chirality : 0.044 0.177 1152 Planarity : 0.004 0.055 1388 Dihedral : 3.713 18.682 1078 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.75 % Allowed : 5.76 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 988 helix: 1.44 (0.28), residues: 352 sheet: 1.33 (0.38), residues: 164 loop : 1.04 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 62 HIS 0.028 0.007 HIS A 39 PHE 0.016 0.002 PHE A 339 TYR 0.019 0.001 TYR C 99 ARG 0.002 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 355) hydrogen bonds : angle 5.34877 ( 1023) SS BOND : bond 0.00176 ( 3) SS BOND : angle 2.43877 ( 6) covalent geometry : bond 0.00328 ( 7883) covalent geometry : angle 0.53389 (10719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 1.169 Fit side-chains REVERT: A 170 LYS cc_start: 0.7897 (tppt) cc_final: 0.7417 (tppt) REVERT: C 102 LYS cc_start: 0.7766 (mttm) cc_final: 0.7018 (pttt) REVERT: C 170 LYS cc_start: 0.7860 (tppt) cc_final: 0.7387 (tppt) REVERT: C 218 ASN cc_start: 0.8063 (m-40) cc_final: 0.7654 (m110) REVERT: C 239 LYS cc_start: 0.6674 (ptmm) cc_final: 0.6327 (ptpt) outliers start: 6 outliers final: 3 residues processed: 100 average time/residue: 0.2301 time to fit residues: 31.8441 Evaluate side-chains 93 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS C 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.200149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.170481 restraints weight = 40773.098| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 9.64 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7886 Z= 0.163 Angle : 0.557 5.551 10725 Z= 0.298 Chirality : 0.044 0.189 1152 Planarity : 0.004 0.051 1388 Dihedral : 3.956 18.548 1078 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.75 % Allowed : 7.88 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.27), residues: 988 helix: 1.15 (0.27), residues: 352 sheet: 1.09 (0.37), residues: 164 loop : 1.02 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 62 HIS 0.011 0.003 HIS A 39 PHE 0.017 0.002 PHE D 111 TYR 0.008 0.001 TYR C 99 ARG 0.002 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 355) hydrogen bonds : angle 5.15745 ( 1023) SS BOND : bond 0.00415 ( 3) SS BOND : angle 2.90981 ( 6) covalent geometry : bond 0.00388 ( 7883) covalent geometry : angle 0.55268 (10719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 1.068 Fit side-chains REVERT: A 72 GLN cc_start: 0.8040 (tt0) cc_final: 0.7338 (tm-30) REVERT: A 170 LYS cc_start: 0.7970 (tppt) cc_final: 0.7603 (tppt) REVERT: C 102 LYS cc_start: 0.7481 (mttm) cc_final: 0.7140 (pttt) REVERT: C 170 LYS cc_start: 0.7937 (tppt) cc_final: 0.7573 (tppt) REVERT: C 218 ASN cc_start: 0.8210 (m-40) cc_final: 0.7800 (m110) REVERT: C 239 LYS cc_start: 0.6730 (ptmm) cc_final: 0.6420 (ptpp) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.2231 time to fit residues: 31.0661 Evaluate side-chains 92 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.196389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152746 restraints weight = 46129.384| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 9.68 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7886 Z= 0.181 Angle : 0.577 5.934 10725 Z= 0.306 Chirality : 0.045 0.207 1152 Planarity : 0.004 0.049 1388 Dihedral : 4.159 18.119 1078 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.13 % Allowed : 10.26 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 988 helix: 0.82 (0.27), residues: 362 sheet: 0.69 (0.37), residues: 166 loop : 0.93 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 62 HIS 0.006 0.002 HIS C 39 PHE 0.019 0.002 PHE D 111 TYR 0.009 0.001 TYR C 99 ARG 0.002 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 355) hydrogen bonds : angle 5.11422 ( 1023) SS BOND : bond 0.00363 ( 3) SS BOND : angle 2.94158 ( 6) covalent geometry : bond 0.00436 ( 7883) covalent geometry : angle 0.57317 (10719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.842 Fit side-chains REVERT: A 170 LYS cc_start: 0.8130 (tppt) cc_final: 0.7726 (tppt) REVERT: C 102 LYS cc_start: 0.7774 (mttm) cc_final: 0.7524 (mmtt) REVERT: C 170 LYS cc_start: 0.8172 (tppt) cc_final: 0.7744 (tppt) REVERT: C 239 LYS cc_start: 0.6796 (ptmm) cc_final: 0.6508 (ptpp) outliers start: 9 outliers final: 7 residues processed: 100 average time/residue: 0.1916 time to fit residues: 26.6174 Evaluate side-chains 94 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN C 218 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.197121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145686 restraints weight = 42954.304| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 8.11 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7886 Z= 0.141 Angle : 0.536 6.131 10725 Z= 0.286 Chirality : 0.044 0.195 1152 Planarity : 0.004 0.050 1388 Dihedral : 4.149 19.241 1078 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.00 % Allowed : 11.39 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 988 helix: 0.93 (0.27), residues: 362 sheet: 0.63 (0.36), residues: 166 loop : 0.83 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 62 HIS 0.004 0.001 HIS A 39 PHE 0.015 0.002 PHE D 111 TYR 0.008 0.001 TYR C 99 ARG 0.003 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 355) hydrogen bonds : angle 5.03882 ( 1023) SS BOND : bond 0.00233 ( 3) SS BOND : angle 2.45127 ( 6) covalent geometry : bond 0.00336 ( 7883) covalent geometry : angle 0.53284 (10719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.776 Fit side-chains REVERT: A 72 GLN cc_start: 0.8161 (tt0) cc_final: 0.6938 (tm-30) REVERT: A 137 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8466 (mtpt) REVERT: A 170 LYS cc_start: 0.8043 (tppt) cc_final: 0.7673 (tppt) REVERT: C 102 LYS cc_start: 0.7749 (mttm) cc_final: 0.7453 (mmtt) REVERT: C 170 LYS cc_start: 0.8018 (tppt) cc_final: 0.7678 (tppt) REVERT: C 239 LYS cc_start: 0.6729 (ptmm) cc_final: 0.6417 (ptpp) outliers start: 8 outliers final: 7 residues processed: 92 average time/residue: 0.2012 time to fit residues: 25.4414 Evaluate side-chains 84 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.196902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145301 restraints weight = 42971.113| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 8.09 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7886 Z= 0.142 Angle : 0.535 6.543 10725 Z= 0.284 Chirality : 0.043 0.211 1152 Planarity : 0.004 0.050 1388 Dihedral : 4.097 20.227 1078 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.88 % Allowed : 12.14 % Favored : 86.98 % 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: 1.02 (0.27), residues: 988 helix: 0.91 (0.27), residues: 364 sheet: 0.59 (0.36), residues: 166 loop : 0.72 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 62 HIS 0.003 0.001 HIS A 39 PHE 0.015 0.002 PHE D 111 TYR 0.007 0.001 TYR C 99 ARG 0.002 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 355) hydrogen bonds : angle 4.98518 ( 1023) SS BOND : bond 0.00264 ( 3) SS BOND : angle 1.87472 ( 6) covalent geometry : bond 0.00339 ( 7883) covalent geometry : angle 0.53306 (10719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.822 Fit side-chains REVERT: A 72 GLN cc_start: 0.8061 (tt0) cc_final: 0.6943 (tm-30) REVERT: A 170 LYS cc_start: 0.8128 (tppt) cc_final: 0.7746 (tppt) REVERT: C 102 LYS cc_start: 0.7794 (mttm) cc_final: 0.7512 (mmtt) REVERT: C 170 LYS cc_start: 0.8057 (tppt) cc_final: 0.7693 (tppt) REVERT: C 239 LYS cc_start: 0.6695 (ptmm) cc_final: 0.6422 (ptpp) REVERT: C 285 LEU cc_start: 0.5969 (mm) cc_final: 0.5737 (mm) REVERT: C 313 LYS cc_start: 0.7701 (ptpp) cc_final: 0.7303 (mmtm) outliers start: 7 outliers final: 6 residues processed: 90 average time/residue: 0.2115 time to fit residues: 25.8536 Evaluate side-chains 92 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.194389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141625 restraints weight = 50642.688| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 8.68 r_work: 0.3376 rms_B_bonded: 8.68 restraints_weight: 2.0000 r_work: 0.3552 rms_B_bonded: 5.36 restraints_weight: 4.0000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7886 Z= 0.170 Angle : 0.563 6.719 10725 Z= 0.299 Chirality : 0.044 0.226 1152 Planarity : 0.004 0.051 1388 Dihedral : 4.251 20.717 1078 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.00 % Allowed : 12.39 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 988 helix: 0.78 (0.27), residues: 364 sheet: 0.08 (0.34), residues: 190 loop : 0.76 (0.33), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 62 HIS 0.004 0.001 HIS A 39 PHE 0.019 0.002 PHE D 111 TYR 0.011 0.001 TYR D 114 ARG 0.001 0.000 ARG A 344 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 355) hydrogen bonds : angle 5.01832 ( 1023) SS BOND : bond 0.00315 ( 3) SS BOND : angle 2.38183 ( 6) covalent geometry : bond 0.00413 ( 7883) covalent geometry : angle 0.56053 (10719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.804 Fit side-chains REVERT: A 72 GLN cc_start: 0.7803 (tt0) cc_final: 0.6632 (tm-30) REVERT: A 103 LEU cc_start: 0.6366 (mp) cc_final: 0.6057 (tt) REVERT: A 137 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8481 (mtpt) REVERT: A 170 LYS cc_start: 0.8247 (tppt) cc_final: 0.7929 (tppt) REVERT: A 235 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 285 LEU cc_start: 0.6395 (mm) cc_final: 0.6004 (mm) REVERT: C 170 LYS cc_start: 0.8226 (tppt) cc_final: 0.7937 (tppt) REVERT: C 239 LYS cc_start: 0.6533 (ptmm) cc_final: 0.6332 (ptpt) REVERT: C 285 LEU cc_start: 0.6109 (mm) cc_final: 0.5888 (mm) REVERT: C 313 LYS cc_start: 0.7581 (ptpp) cc_final: 0.7349 (pttp) outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.2032 time to fit residues: 27.3612 Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 44 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 0.0040 chunk 43 optimal weight: 0.0060 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 overall best weight: 0.2406 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.198607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148030 restraints weight = 49882.960| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 8.56 r_work: 0.3466 rms_B_bonded: 7.98 restraints_weight: 2.0000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7886 Z= 0.105 Angle : 0.512 7.049 10725 Z= 0.272 Chirality : 0.042 0.218 1152 Planarity : 0.004 0.049 1388 Dihedral : 3.984 22.373 1078 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.00 % Allowed : 12.27 % Favored : 86.73 % 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: 1.10 (0.27), residues: 988 helix: 1.10 (0.28), residues: 364 sheet: 0.57 (0.36), residues: 170 loop : 0.69 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 62 HIS 0.002 0.001 HIS A 39 PHE 0.009 0.001 PHE D 111 TYR 0.019 0.001 TYR A 99 ARG 0.003 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 355) hydrogen bonds : angle 4.88356 ( 1023) SS BOND : bond 0.00112 ( 3) SS BOND : angle 1.46496 ( 6) covalent geometry : bond 0.00236 ( 7883) covalent geometry : angle 0.51136 (10719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7809 (tt0) cc_final: 0.6731 (tm-30) REVERT: A 103 LEU cc_start: 0.6352 (mp) cc_final: 0.6070 (tt) REVERT: A 137 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8455 (mtpt) REVERT: A 170 LYS cc_start: 0.8247 (tppt) cc_final: 0.7948 (tppt) REVERT: A 285 LEU cc_start: 0.6295 (mm) cc_final: 0.5938 (mm) REVERT: C 39 HIS cc_start: 0.7988 (p90) cc_final: 0.7683 (p-80) REVERT: C 137 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8513 (mtpt) REVERT: C 170 LYS cc_start: 0.8206 (tppt) cc_final: 0.7929 (tppt) REVERT: C 267 ASN cc_start: 0.7522 (t0) cc_final: 0.6960 (t0) REVERT: C 313 LYS cc_start: 0.7550 (ptpp) cc_final: 0.7318 (pttp) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.2119 time to fit residues: 29.0283 Evaluate side-chains 98 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 85 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.197575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153006 restraints weight = 35020.280| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 7.28 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7886 Z= 0.118 Angle : 0.525 9.004 10725 Z= 0.276 Chirality : 0.042 0.213 1152 Planarity : 0.004 0.049 1388 Dihedral : 3.925 22.831 1078 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.88 % Allowed : 11.89 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 988 helix: 1.17 (0.28), residues: 364 sheet: 0.61 (0.36), residues: 170 loop : 0.69 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 62 HIS 0.002 0.001 HIS A 39 PHE 0.012 0.001 PHE D 111 TYR 0.019 0.001 TYR A 99 ARG 0.003 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 355) hydrogen bonds : angle 4.80089 ( 1023) SS BOND : bond 0.00122 ( 3) SS BOND : angle 1.65695 ( 6) covalent geometry : bond 0.00275 ( 7883) covalent geometry : angle 0.52393 (10719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7832 (tt0) cc_final: 0.6865 (tm-30) REVERT: A 103 LEU cc_start: 0.6511 (mp) cc_final: 0.6256 (tt) REVERT: A 170 LYS cc_start: 0.8257 (tppt) cc_final: 0.7875 (tppt) REVERT: A 235 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 285 LEU cc_start: 0.6260 (mm) cc_final: 0.5930 (mm) REVERT: C 39 HIS cc_start: 0.7967 (p90) cc_final: 0.7646 (p-80) REVERT: C 170 LYS cc_start: 0.8208 (tppt) cc_final: 0.7851 (tppt) REVERT: C 313 LYS cc_start: 0.7604 (ptpp) cc_final: 0.7359 (pttp) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.3053 time to fit residues: 39.4705 Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 68 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.197048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.153330 restraints weight = 39140.462| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 8.25 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7886 Z= 0.125 Angle : 0.523 8.418 10725 Z= 0.277 Chirality : 0.042 0.215 1152 Planarity : 0.004 0.049 1388 Dihedral : 3.947 22.717 1078 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.00 % Allowed : 12.27 % Favored : 86.73 % 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: 1.15 (0.27), residues: 988 helix: 1.15 (0.27), residues: 364 sheet: 0.65 (0.36), residues: 170 loop : 0.68 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 62 HIS 0.003 0.001 HIS A 39 PHE 0.013 0.001 PHE D 111 TYR 0.019 0.001 TYR A 99 ARG 0.002 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 355) hydrogen bonds : angle 4.80769 ( 1023) SS BOND : bond 0.00134 ( 3) SS BOND : angle 1.63457 ( 6) covalent geometry : bond 0.00294 ( 7883) covalent geometry : angle 0.52180 (10719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7883 (tt0) cc_final: 0.6868 (tm-30) REVERT: A 103 LEU cc_start: 0.6515 (mp) cc_final: 0.6234 (tt) REVERT: A 170 LYS cc_start: 0.8275 (tppt) cc_final: 0.8052 (tppt) REVERT: A 235 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 267 ASN cc_start: 0.7452 (t0) cc_final: 0.6991 (t0) REVERT: A 285 LEU cc_start: 0.5875 (mm) cc_final: 0.5602 (mm) REVERT: C 170 LYS cc_start: 0.8235 (tppt) cc_final: 0.8019 (tppt) REVERT: C 267 ASN cc_start: 0.7465 (t0) cc_final: 0.6946 (t0) REVERT: C 313 LYS cc_start: 0.7627 (ptpp) cc_final: 0.7281 (mmtm) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.2142 time to fit residues: 28.5512 Evaluate side-chains 100 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 0.0770 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 35 optimal weight: 0.0270 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.203033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.173648 restraints weight = 36516.542| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 7.44 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7886 Z= 0.114 Angle : 0.531 8.333 10725 Z= 0.280 Chirality : 0.042 0.212 1152 Planarity : 0.004 0.049 1388 Dihedral : 3.902 22.850 1078 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.00 % Allowed : 13.02 % Favored : 85.98 % 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: 1.20 (0.27), residues: 988 helix: 1.17 (0.27), residues: 364 sheet: 0.75 (0.36), residues: 170 loop : 0.69 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 62 HIS 0.002 0.001 HIS A 39 PHE 0.010 0.001 PHE D 111 TYR 0.019 0.001 TYR A 99 ARG 0.002 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 355) hydrogen bonds : angle 4.79376 ( 1023) SS BOND : bond 0.00120 ( 3) SS BOND : angle 1.39635 ( 6) covalent geometry : bond 0.00265 ( 7883) covalent geometry : angle 0.52994 (10719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4223.55 seconds wall clock time: 75 minutes 32.86 seconds (4532.86 seconds total)