Starting phenix.real_space_refine on Thu May 1 03:39:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjv_39351/05_2025/8yjv_39351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjv_39351/05_2025/8yjv_39351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjv_39351/05_2025/8yjv_39351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjv_39351/05_2025/8yjv_39351.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjv_39351/05_2025/8yjv_39351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjv_39351/05_2025/8yjv_39351.cif" } resolution = 3.51 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 404 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 61 5.16 5 C 6057 2.51 5 N 1667 2.21 5 O 2089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9938 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "D" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2779 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1946 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "B" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1938 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 6.54, per 1000 atoms: 0.66 Number of scatterers: 9938 At special positions: 0 Unit cell: (108.73, 107.07, 105.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 64 15.00 O 2089 8.00 N 1667 7.00 C 6057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " 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: 2.26 Conformation dependent library (CDL) restraints added in 996.4 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 31.9% alpha, 24.2% beta 12 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.243A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.132A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.796A pdb=" N TYR D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 27' Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.536A pdb=" N ASN D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 118 Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 134 through 149 Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.698A pdb=" N SER D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.894A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 256 through 262 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 317 through 334 removed outlier: 3.802A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.818A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 222 Proline residue: A 220 - end of helix No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.096A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.682A pdb=" N ALA B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 61 removed outlier: 4.924A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG C 5 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.779A pdb=" N MET C 68 " --> pdb=" O TRP C 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.527A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.027A pdb=" N LYS D 345 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 204 through 208 Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 21 Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.755A pdb=" N ALA D 174 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AB1, first strand: chain 'A' and resid 66 through 71 removed outlier: 7.288A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 251 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.735A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 160 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.904A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 30 Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 40 removed outlier: 3.728A pdb=" N LEU B 251 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 235 " --> pdb=" O LEU B 251 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2315 1.33 - 1.45: 2144 1.45 - 1.57: 5536 1.57 - 1.69: 127 1.69 - 1.81: 98 Bond restraints: 10220 Sorted by residual: bond pdb=" N THR C 219 " pdb=" CA THR C 219 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.80e+00 bond pdb=" C3' DT E 3 " pdb=" O3' DT E 3 " ideal model delta sigma weight residual 1.422 1.496 -0.074 3.00e-02 1.11e+03 6.12e+00 bond pdb=" N THR C 216 " pdb=" CA THR C 216 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.44e-02 4.82e+03 5.57e+00 bond pdb=" N LEU C 221 " pdb=" CA LEU C 221 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.30e+00 bond pdb=" N THR C 224 " pdb=" CA THR C 224 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.23e-02 6.61e+03 5.21e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 13775 3.19 - 6.38: 245 6.38 - 9.58: 39 9.58 - 12.77: 7 12.77 - 15.96: 2 Bond angle restraints: 14068 Sorted by residual: angle pdb=" C ALA C 242 " pdb=" N ASP C 243 " pdb=" CA ASP C 243 " ideal model delta sigma weight residual 121.54 135.01 -13.47 1.91e+00 2.74e-01 4.97e+01 angle pdb=" CA PRO B 106 " pdb=" N PRO B 106 " pdb=" CD PRO B 106 " ideal model delta sigma weight residual 112.00 104.02 7.98 1.40e+00 5.10e-01 3.25e+01 angle pdb=" C ALA B 242 " pdb=" N ASP B 243 " pdb=" CA ASP B 243 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" CA LEU D 275 " pdb=" CB LEU D 275 " pdb=" CG LEU D 275 " ideal model delta sigma weight residual 116.30 132.26 -15.96 3.50e+00 8.16e-02 2.08e+01 angle pdb=" N LYS C 217 " pdb=" CA LYS C 217 " pdb=" C LYS C 217 " ideal model delta sigma weight residual 113.28 107.73 5.55 1.22e+00 6.72e-01 2.07e+01 ... (remaining 14063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 5746 35.35 - 70.69: 402 70.69 - 106.04: 17 106.04 - 141.39: 1 141.39 - 176.73: 1 Dihedral angle restraints: 6167 sinusoidal: 2933 harmonic: 3234 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual 93.00 153.33 -60.33 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASP A 150 " pdb=" C ASP A 150 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ILE B 241 " pdb=" C ILE B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1317 0.073 - 0.145: 255 0.145 - 0.218: 38 0.218 - 0.290: 6 0.290 - 0.363: 3 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CG LEU B 72 " pdb=" CB LEU B 72 " pdb=" CD1 LEU B 72 " pdb=" CD2 LEU B 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU B 235 " pdb=" CB LEU B 235 " pdb=" CD1 LEU B 235 " pdb=" CD2 LEU B 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1616 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 234 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 214 " -0.019 2.00e-02 2.50e+03 2.60e-02 1.18e+01 pdb=" CG PHE B 214 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE B 214 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 214 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE B 214 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 214 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 214 " 0.018 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE C 214 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE C 214 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE C 214 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 214 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 214 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 214 " 0.001 2.00e-02 2.50e+03 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2804 2.83 - 3.35: 8286 3.35 - 3.87: 17788 3.87 - 4.38: 19625 4.38 - 4.90: 33050 Nonbonded interactions: 81553 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.317 3.040 nonbonded pdb=" O THR B 216 " pdb=" OG1 THR B 219 " model vdw 2.338 3.040 nonbonded pdb=" OG SER D 197 " pdb=" OP2 DA E 14 " model vdw 2.342 3.040 nonbonded pdb=" O ASN B 71 " pdb=" OG SER B 74 " model vdw 2.355 3.040 nonbonded pdb=" N GLY D 2 " pdb=" OD1 ASP D 179 " model vdw 2.383 3.120 ... (remaining 81548 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 2 through 253) selection = chain 'B' selection = (chain 'C' and resid 2 through 253) } 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 group one per residue 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.700 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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 : 0.007 0.099 10222 Z= 0.305 Angle : 1.084 15.960 14072 Z= 0.567 Chirality : 0.060 0.363 1619 Planarity : 0.008 0.103 1591 Dihedral : 20.737 176.732 4063 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 0.73 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.21), residues: 1103 helix: -2.47 (0.22), residues: 308 sheet: -2.02 (0.26), residues: 335 loop : -2.42 (0.22), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP D 274 HIS 0.016 0.002 HIS D 143 PHE 0.059 0.005 PHE B 214 TYR 0.030 0.003 TYR A 249 ARG 0.016 0.001 ARG B 5 Details of bonding type rmsd hydrogen bonds : bond 0.20225 ( 449) hydrogen bonds : angle 10.17809 ( 1230) SS BOND : bond 0.00067 ( 2) SS BOND : angle 1.35529 ( 4) covalent geometry : bond 0.00707 (10220) covalent geometry : angle 1.08369 (14068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.966 Fit side-chains REVERT: C 53 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7393 (mtm180) REVERT: C 97 ASP cc_start: 0.4939 (p0) cc_final: 0.4469 (p0) REVERT: C 244 MET cc_start: 0.8524 (mtp) cc_final: 0.8227 (mtp) REVERT: D 21 ASN cc_start: 0.7825 (m110) cc_final: 0.7594 (m110) REVERT: A 199 MET cc_start: 0.5303 (ttm) cc_final: 0.4907 (ttm) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.2048 time to fit residues: 46.1631 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.0050 chunk 59 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 153 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.158835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121527 restraints weight = 13046.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125196 restraints weight = 7669.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127668 restraints weight = 5405.395| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10222 Z= 0.164 Angle : 0.615 7.309 14072 Z= 0.344 Chirality : 0.043 0.160 1619 Planarity : 0.005 0.078 1591 Dihedral : 21.605 168.206 1939 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.25 % Allowed : 7.79 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1103 helix: -0.49 (0.28), residues: 313 sheet: -2.03 (0.26), residues: 329 loop : -2.12 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 274 HIS 0.006 0.001 HIS D 143 PHE 0.031 0.002 PHE B 214 TYR 0.010 0.001 TYR D 83 ARG 0.003 0.000 ARG D 192 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 449) hydrogen bonds : angle 6.93602 ( 1230) SS BOND : bond 0.00383 ( 2) SS BOND : angle 1.18954 ( 4) covalent geometry : bond 0.00367 (10220) covalent geometry : angle 0.61494 (14068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.920 Fit side-chains REVERT: C 97 ASP cc_start: 0.5090 (p0) cc_final: 0.4414 (p0) REVERT: C 214 PHE cc_start: 0.8671 (m-10) cc_final: 0.8390 (m-10) REVERT: C 225 VAL cc_start: 0.8496 (t) cc_final: 0.8248 (p) REVERT: D 21 ASN cc_start: 0.8204 (m110) cc_final: 0.7964 (m110) REVERT: D 92 LEU cc_start: 0.7903 (mp) cc_final: 0.7695 (mp) REVERT: B 131 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.5905 (mm110) REVERT: B 143 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7281 (mt-10) REVERT: B 146 ARG cc_start: 0.7144 (ttt90) cc_final: 0.6865 (ttt90) outliers start: 12 outliers final: 10 residues processed: 140 average time/residue: 0.2050 time to fit residues: 41.1276 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118749 restraints weight = 13295.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122443 restraints weight = 7771.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124925 restraints weight = 5471.714| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10222 Z= 0.180 Angle : 0.601 6.272 14072 Z= 0.332 Chirality : 0.043 0.150 1619 Planarity : 0.004 0.075 1591 Dihedral : 21.478 167.629 1939 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.77 % Allowed : 10.59 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.13 (0.24), residues: 1103 helix: 0.27 (0.29), residues: 315 sheet: -1.96 (0.27), residues: 327 loop : -2.09 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.006 0.001 HIS D 143 PHE 0.028 0.002 PHE B 214 TYR 0.013 0.002 TYR D 83 ARG 0.004 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 449) hydrogen bonds : angle 6.54891 ( 1230) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.83402 ( 4) covalent geometry : bond 0.00410 (10220) covalent geometry : angle 0.60104 (14068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.114 Fit side-chains REVERT: C 36 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7726 (m-40) REVERT: C 53 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7585 (mtm180) REVERT: C 214 PHE cc_start: 0.8681 (m-10) cc_final: 0.8300 (m-10) REVERT: D 21 ASN cc_start: 0.8309 (m110) cc_final: 0.8079 (m110) REVERT: A 239 TYR cc_start: 0.8368 (m-80) cc_final: 0.8148 (m-80) REVERT: B 75 MET cc_start: 0.8191 (ttt) cc_final: 0.7940 (ttt) REVERT: B 131 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6032 (mm-40) REVERT: B 146 ARG cc_start: 0.7157 (ttt90) cc_final: 0.6934 (ttt90) outliers start: 17 outliers final: 12 residues processed: 140 average time/residue: 0.2160 time to fit residues: 43.1611 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 0.0870 chunk 33 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 102 optimal weight: 0.0970 overall best weight: 0.2770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.158996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121792 restraints weight = 13259.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125621 restraints weight = 7699.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128184 restraints weight = 5378.198| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10222 Z= 0.123 Angle : 0.539 5.963 14072 Z= 0.301 Chirality : 0.042 0.144 1619 Planarity : 0.004 0.071 1591 Dihedral : 21.566 167.132 1939 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.14 % Allowed : 12.67 % Favored : 86.19 % 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: -1.79 (0.24), residues: 1103 helix: 0.72 (0.30), residues: 319 sheet: -1.80 (0.27), residues: 307 loop : -2.05 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 28 HIS 0.005 0.001 HIS D 143 PHE 0.023 0.001 PHE B 214 TYR 0.009 0.001 TYR A 114 ARG 0.003 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 449) hydrogen bonds : angle 6.14888 ( 1230) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.69613 ( 4) covalent geometry : bond 0.00274 (10220) covalent geometry : angle 0.53881 (14068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.033 Fit side-chains REVERT: C 53 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7603 (mtm180) REVERT: C 97 ASP cc_start: 0.5162 (p0) cc_final: 0.4287 (p0) REVERT: C 214 PHE cc_start: 0.8628 (m-10) cc_final: 0.8276 (m-10) REVERT: B 36 ASN cc_start: 0.7642 (m-40) cc_final: 0.7402 (m-40) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 0.2144 time to fit residues: 44.3007 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114231 restraints weight = 13340.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117694 restraints weight = 7864.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.120018 restraints weight = 5561.131| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10222 Z= 0.246 Angle : 0.649 7.188 14072 Z= 0.350 Chirality : 0.045 0.145 1619 Planarity : 0.004 0.073 1591 Dihedral : 21.832 165.700 1939 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.60 % Allowed : 13.29 % Favored : 84.11 % 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: -1.93 (0.24), residues: 1103 helix: 0.64 (0.30), residues: 319 sheet: -2.07 (0.27), residues: 319 loop : -1.98 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 28 HIS 0.004 0.001 HIS D 143 PHE 0.029 0.002 PHE B 214 TYR 0.018 0.002 TYR D 83 ARG 0.005 0.001 ARG D 320 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 449) hydrogen bonds : angle 6.41694 ( 1230) SS BOND : bond 0.00149 ( 2) SS BOND : angle 1.14421 ( 4) covalent geometry : bond 0.00575 (10220) covalent geometry : angle 0.64851 (14068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.991 Fit side-chains REVERT: C 53 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7598 (mtm180) REVERT: C 214 PHE cc_start: 0.8688 (m-10) cc_final: 0.8286 (m-10) REVERT: D 92 LEU cc_start: 0.7789 (mp) cc_final: 0.7545 (mp) REVERT: A 40 MET cc_start: 0.7664 (ttt) cc_final: 0.7334 (ttm) REVERT: B 75 MET cc_start: 0.8203 (ttt) cc_final: 0.7955 (ttt) REVERT: B 131 GLN cc_start: 0.6899 (mp10) cc_final: 0.6613 (mm-40) outliers start: 25 outliers final: 19 residues processed: 147 average time/residue: 0.2184 time to fit residues: 45.7620 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 0.0050 chunk 30 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118803 restraints weight = 13343.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122413 restraints weight = 7749.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124851 restraints weight = 5398.962| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10222 Z= 0.138 Angle : 0.555 6.660 14072 Z= 0.304 Chirality : 0.042 0.144 1619 Planarity : 0.003 0.066 1591 Dihedral : 21.704 166.394 1939 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.18 % Allowed : 14.75 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.24), residues: 1103 helix: 0.90 (0.30), residues: 320 sheet: -1.96 (0.27), residues: 313 loop : -1.88 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 28 HIS 0.008 0.001 HIS C 44 PHE 0.020 0.002 PHE B 214 TYR 0.008 0.001 TYR C 211 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 449) hydrogen bonds : angle 6.06645 ( 1230) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.64894 ( 4) covalent geometry : bond 0.00318 (10220) covalent geometry : angle 0.55533 (14068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.086 Fit side-chains REVERT: C 53 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7625 (mtm180) REVERT: C 97 ASP cc_start: 0.5263 (p0) cc_final: 0.4340 (p0) REVERT: C 214 PHE cc_start: 0.8639 (m-10) cc_final: 0.8296 (m-10) REVERT: D 92 LEU cc_start: 0.7753 (mp) cc_final: 0.7517 (mp) REVERT: D 327 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6473 (ptt180) REVERT: A 40 MET cc_start: 0.7661 (ttt) cc_final: 0.7353 (ttm) outliers start: 21 outliers final: 15 residues processed: 142 average time/residue: 0.2200 time to fit residues: 44.4686 Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** 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 = 0.3923 r_free = 0.3923 target = 0.152582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115028 restraints weight = 13368.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118628 restraints weight = 7855.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121035 restraints weight = 5555.744| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10222 Z= 0.227 Angle : 0.637 6.574 14072 Z= 0.341 Chirality : 0.044 0.155 1619 Planarity : 0.004 0.064 1591 Dihedral : 21.781 165.028 1939 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.70 % Allowed : 15.06 % Favored : 82.24 % 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: -1.85 (0.24), residues: 1103 helix: 0.76 (0.30), residues: 319 sheet: -2.15 (0.26), residues: 322 loop : -1.87 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 28 HIS 0.010 0.001 HIS C 44 PHE 0.024 0.002 PHE B 214 TYR 0.016 0.002 TYR D 83 ARG 0.007 0.001 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 449) hydrogen bonds : angle 6.35031 ( 1230) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.01048 ( 4) covalent geometry : bond 0.00532 (10220) covalent geometry : angle 0.63674 (14068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: C 53 ARG cc_start: 0.8057 (mtm180) cc_final: 0.7594 (mtm180) REVERT: C 68 MET cc_start: 0.8338 (pmm) cc_final: 0.8111 (ptp) REVERT: C 214 PHE cc_start: 0.8683 (m-10) cc_final: 0.8337 (m-10) REVERT: D 92 LEU cc_start: 0.7786 (mp) cc_final: 0.7549 (mp) REVERT: D 327 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6473 (ptt180) REVERT: B 75 MET cc_start: 0.8205 (ttt) cc_final: 0.7959 (ttt) outliers start: 26 outliers final: 22 residues processed: 137 average time/residue: 0.2188 time to fit residues: 42.3924 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 106 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118527 restraints weight = 13298.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122232 restraints weight = 7693.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124704 restraints weight = 5383.279| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10222 Z= 0.145 Angle : 0.569 7.159 14072 Z= 0.308 Chirality : 0.042 0.155 1619 Planarity : 0.003 0.063 1591 Dihedral : 21.614 164.952 1939 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.39 % Allowed : 15.99 % Favored : 81.62 % 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: -1.71 (0.24), residues: 1103 helix: 0.90 (0.30), residues: 321 sheet: -2.01 (0.26), residues: 317 loop : -1.87 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 28 HIS 0.012 0.001 HIS C 44 PHE 0.022 0.002 PHE B 214 TYR 0.010 0.001 TYR C 211 ARG 0.007 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 449) hydrogen bonds : angle 6.11304 ( 1230) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.70147 ( 4) covalent geometry : bond 0.00336 (10220) covalent geometry : angle 0.56924 (14068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.038 Fit side-chains REVERT: C 53 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7597 (mtm180) REVERT: C 97 ASP cc_start: 0.5342 (p0) cc_final: 0.4480 (p0) REVERT: C 214 PHE cc_start: 0.8634 (m-10) cc_final: 0.8304 (m-10) REVERT: D 74 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7089 (mmt) REVERT: D 92 LEU cc_start: 0.7771 (mp) cc_final: 0.7531 (mp) REVERT: D 120 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5479 (mp0) REVERT: D 327 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6477 (ptt180) REVERT: A 40 MET cc_start: 0.7636 (ttt) cc_final: 0.7203 (ttm) REVERT: A 115 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7254 (mt-10) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.2184 time to fit residues: 42.8890 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 30 optimal weight: 0.0470 chunk 77 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116979 restraints weight = 13292.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121060 restraints weight = 9355.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121804 restraints weight = 5686.671| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10222 Z= 0.169 Angle : 0.597 11.005 14072 Z= 0.317 Chirality : 0.043 0.143 1619 Planarity : 0.003 0.062 1591 Dihedral : 21.588 162.986 1939 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.39 % Allowed : 16.20 % Favored : 81.41 % 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: -1.66 (0.24), residues: 1103 helix: 0.98 (0.30), residues: 319 sheet: -2.00 (0.26), residues: 319 loop : -1.85 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 28 HIS 0.006 0.001 HIS D 143 PHE 0.023 0.002 PHE B 214 TYR 0.012 0.001 TYR D 83 ARG 0.008 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 449) hydrogen bonds : angle 6.15286 ( 1230) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.81130 ( 4) covalent geometry : bond 0.00397 (10220) covalent geometry : angle 0.59659 (14068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.137 Fit side-chains REVERT: C 53 ARG cc_start: 0.8045 (mtm180) cc_final: 0.7551 (mtm180) REVERT: C 68 MET cc_start: 0.8258 (pmm) cc_final: 0.8041 (ptp) REVERT: C 97 ASP cc_start: 0.5468 (p0) cc_final: 0.4610 (p0) REVERT: C 214 PHE cc_start: 0.8650 (m-10) cc_final: 0.8292 (m-10) REVERT: D 74 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7034 (mmt) REVERT: D 92 LEU cc_start: 0.7759 (mp) cc_final: 0.7540 (mp) REVERT: D 120 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5373 (mp0) REVERT: D 327 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6508 (ptt180) REVERT: A 115 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7307 (mt-10) outliers start: 23 outliers final: 17 residues processed: 136 average time/residue: 0.2202 time to fit residues: 42.7317 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117823 restraints weight = 13243.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121464 restraints weight = 7708.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123959 restraints weight = 5432.762| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10222 Z= 0.155 Angle : 0.587 10.669 14072 Z= 0.311 Chirality : 0.042 0.142 1619 Planarity : 0.003 0.062 1591 Dihedral : 21.482 160.399 1939 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.28 % Allowed : 16.61 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.67 (0.24), residues: 1103 helix: 0.96 (0.30), residues: 321 sheet: -2.04 (0.26), residues: 324 loop : -1.81 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 28 HIS 0.008 0.001 HIS C 44 PHE 0.022 0.002 PHE B 214 TYR 0.011 0.001 TYR B 250 ARG 0.008 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 449) hydrogen bonds : angle 6.08974 ( 1230) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.73585 ( 4) covalent geometry : bond 0.00362 (10220) covalent geometry : angle 0.58668 (14068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: C 53 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7580 (mtm180) REVERT: C 68 MET cc_start: 0.8210 (pmm) cc_final: 0.7991 (ptp) REVERT: C 97 ASP cc_start: 0.5349 (p0) cc_final: 0.4501 (p0) REVERT: C 214 PHE cc_start: 0.8629 (m-10) cc_final: 0.8283 (m-10) REVERT: D 74 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.6989 (mmt) REVERT: D 92 LEU cc_start: 0.7821 (mp) cc_final: 0.7592 (mp) REVERT: D 120 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5463 (mt-10) REVERT: D 327 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6471 (ptt180) REVERT: A 115 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7250 (mt-10) outliers start: 22 outliers final: 19 residues processed: 135 average time/residue: 0.2366 time to fit residues: 44.6058 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 25 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 30 optimal weight: 0.0770 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119474 restraints weight = 13242.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123220 restraints weight = 7697.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125649 restraints weight = 5387.438| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10222 Z= 0.129 Angle : 0.571 10.708 14072 Z= 0.304 Chirality : 0.042 0.141 1619 Planarity : 0.003 0.062 1591 Dihedral : 21.418 160.552 1939 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.08 % Allowed : 16.93 % Favored : 81.00 % 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: -1.56 (0.24), residues: 1103 helix: 1.07 (0.30), residues: 321 sheet: -1.94 (0.26), residues: 320 loop : -1.81 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 274 HIS 0.007 0.001 HIS C 44 PHE 0.021 0.001 PHE B 214 TYR 0.009 0.001 TYR C 211 ARG 0.007 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 449) hydrogen bonds : angle 5.98192 ( 1230) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.56789 ( 4) covalent geometry : bond 0.00299 (10220) covalent geometry : angle 0.57128 (14068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3681.74 seconds wall clock time: 64 minutes 58.24 seconds (3898.24 seconds total)