Starting phenix.real_space_refine on Fri Jan 17 01:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjv_39351/01_2025/8yjv_39351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjv_39351/01_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_39351/01_2025/8yjv_39351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjv_39351/01_2025/8yjv_39351.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjv_39351/01_2025/8yjv_39351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjv_39351/01_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.53, 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.87 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: 3.73 Time building geometry restraints manager: 2.78 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.080 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- 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 10220 Z= 0.455 Angle : 1.084 15.960 14068 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 *********************** 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 : 1.057 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: 0.2215 time to fit residues: 49.5053 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 : 1.152 ------------------------------------------------------------------------------- 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 = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121534 restraints weight = 13046.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125187 restraints weight = 7663.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127652 restraints weight = 5409.183| |-----------------------------------------------------------------------------| 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 10220 Z= 0.232 Angle : 0.615 7.309 14068 Z= 0.344 Chirality : 0.043 0.160 1619 Planarity : 0.005 0.078 1591 Dihedral : 21.605 168.205 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 *********************** 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 : 0.977 Fit side-chains REVERT: C 97 ASP cc_start: 0.5094 (p0) cc_final: 0.4419 (p0) REVERT: C 214 PHE cc_start: 0.8672 (m-10) cc_final: 0.8392 (m-10) REVERT: C 225 VAL cc_start: 0.8495 (t) cc_final: 0.8248 (p) REVERT: D 21 ASN cc_start: 0.8205 (m110) cc_final: 0.7966 (m110) REVERT: D 92 LEU cc_start: 0.7906 (mp) cc_final: 0.7698 (mp) REVERT: B 131 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.5904 (mm110) REVERT: B 143 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 146 ARG cc_start: 0.7139 (ttt90) cc_final: 0.6869 (ttt90) outliers start: 12 outliers final: 10 residues processed: 140 average time/residue: 0.2289 time to fit residues: 45.8806 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 : 1.017 ------------------------------------------------------------------------------- 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: 0.0770 chunk 30 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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** D 280 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120479 restraints weight = 13282.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124200 restraints weight = 7749.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126689 restraints weight = 5449.828| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10220 Z= 0.214 Angle : 0.568 6.252 14068 Z= 0.317 Chirality : 0.042 0.149 1619 Planarity : 0.004 0.074 1591 Dihedral : 21.428 168.302 1939 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.45 % Allowed : 10.70 % Favored : 87.85 % 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: -2.02 (0.24), residues: 1103 helix: 0.40 (0.30), residues: 313 sheet: -1.90 (0.27), residues: 325 loop : -2.05 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.006 0.001 HIS D 143 PHE 0.026 0.002 PHE B 214 TYR 0.010 0.001 TYR D 83 ARG 0.004 0.000 ARG D 70 *********************** 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: 14 poor density : 132 time to evaluate : 1.104 Fit side-chains REVERT: C 28 TRP cc_start: 0.8292 (m100) cc_final: 0.8049 (m100) REVERT: C 53 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7614 (mtm180) REVERT: C 97 ASP cc_start: 0.5101 (p0) cc_final: 0.4230 (p0) REVERT: C 214 PHE cc_start: 0.8672 (m-10) cc_final: 0.8340 (m-10) REVERT: D 21 ASN cc_start: 0.8300 (m110) cc_final: 0.8039 (m110) REVERT: B 75 MET cc_start: 0.8170 (ttt) cc_final: 0.7945 (ttt) REVERT: B 146 ARG cc_start: 0.7165 (ttt90) cc_final: 0.6959 (ttt90) outliers start: 14 outliers final: 12 residues processed: 139 average time/residue: 0.2065 time to fit residues: 41.2889 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 111 VAL 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: 1.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118092 restraints weight = 13301.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121777 restraints weight = 7810.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124252 restraints weight = 5514.422| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10220 Z= 0.263 Angle : 0.587 6.140 14068 Z= 0.323 Chirality : 0.043 0.146 1619 Planarity : 0.004 0.072 1591 Dihedral : 21.665 166.531 1939 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.97 % Allowed : 12.36 % Favored : 85.67 % 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 (0.24), residues: 1103 helix: 0.67 (0.30), residues: 318 sheet: -1.96 (0.27), residues: 321 loop : -2.03 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.006 0.001 HIS C 44 PHE 0.027 0.002 PHE B 214 TYR 0.013 0.002 TYR D 83 ARG 0.003 0.000 ARG D 70 *********************** 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 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.085 Fit side-chains REVERT: C 36 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: C 50 LEU cc_start: 0.8802 (tp) cc_final: 0.8596 (tp) REVERT: C 53 ARG cc_start: 0.8069 (mtm180) cc_final: 0.7551 (mtm180) REVERT: C 97 ASP cc_start: 0.5087 (p0) cc_final: 0.4182 (p0) REVERT: C 214 PHE cc_start: 0.8652 (m-10) cc_final: 0.8207 (m-10) REVERT: D 21 ASN cc_start: 0.8335 (m110) cc_final: 0.8118 (m110) REVERT: B 75 MET cc_start: 0.8163 (ttt) cc_final: 0.7942 (ttt) outliers start: 19 outliers final: 14 residues processed: 140 average time/residue: 0.2346 time to fit residues: 46.5640 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 86 ASP Chi-restraints excluded: chain D residue 110 GLN 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 216 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118179 restraints weight = 13273.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121693 restraints weight = 7763.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124106 restraints weight = 5456.222| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10220 Z= 0.228 Angle : 0.558 6.069 14068 Z= 0.308 Chirality : 0.042 0.144 1619 Planarity : 0.004 0.072 1591 Dihedral : 21.736 166.597 1939 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.49 % Allowed : 12.98 % Favored : 84.53 % 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: -1.78 (0.24), residues: 1103 helix: 0.77 (0.30), residues: 321 sheet: -1.94 (0.27), residues: 317 loop : -1.95 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 28 HIS 0.005 0.001 HIS D 143 PHE 0.023 0.002 PHE B 214 TYR 0.011 0.001 TYR D 83 ARG 0.004 0.000 ARG B 146 *********************** 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 161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.012 Fit side-chains REVERT: C 28 TRP cc_start: 0.8309 (m100) cc_final: 0.8034 (m100) REVERT: C 53 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7600 (mtm180) REVERT: C 97 ASP cc_start: 0.5234 (p0) cc_final: 0.4316 (p0) REVERT: C 214 PHE cc_start: 0.8647 (m-10) cc_final: 0.8278 (m-10) REVERT: D 327 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6491 (ptt180) REVERT: B 131 GLN cc_start: 0.6667 (mm-40) cc_final: 0.6443 (mm-40) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 0.2260 time to fit residues: 48.8612 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 86 ASP Chi-restraints excluded: chain D residue 110 GLN 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 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 70 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 110 GLN D 137 HIS D 208 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116490 restraints weight = 13461.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119916 restraints weight = 7949.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122298 restraints weight = 5656.571| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10220 Z= 0.281 Angle : 0.591 6.548 14068 Z= 0.321 Chirality : 0.043 0.146 1619 Planarity : 0.004 0.065 1591 Dihedral : 21.764 166.051 1939 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.01 % Allowed : 13.91 % 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: -1.79 (0.24), residues: 1103 helix: 0.82 (0.30), residues: 320 sheet: -2.01 (0.27), residues: 318 loop : -1.94 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.005 0.001 HIS D 143 PHE 0.023 0.002 PHE B 214 TYR 0.013 0.002 TYR D 83 ARG 0.004 0.000 ARG B 146 *********************** 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 153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.051 Fit side-chains REVERT: C 53 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7639 (mtm180) REVERT: C 214 PHE cc_start: 0.8650 (m-10) cc_final: 0.8299 (m-10) REVERT: D 327 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6523 (ptt180) REVERT: B 131 GLN cc_start: 0.6676 (mm-40) cc_final: 0.6432 (mm-40) REVERT: B 143 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7215 (mt-10) outliers start: 29 outliers final: 25 residues processed: 143 average time/residue: 0.2205 time to fit residues: 44.6917 Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 110 GLN 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 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 70 VAL Chi-restraints excluded: chain A residue 137 VAL 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 66 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 54 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 110 GLN D 137 HIS ** D 253 HIS ** 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 = 0.3942 r_free = 0.3942 target = 0.154257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.117549 restraints weight = 13419.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121121 restraints weight = 7854.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123484 restraints weight = 5522.410| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10220 Z= 0.231 Angle : 0.569 6.464 14068 Z= 0.309 Chirality : 0.042 0.156 1619 Planarity : 0.003 0.064 1591 Dihedral : 21.689 166.013 1939 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.22 % Allowed : 14.54 % 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: -1.73 (0.24), residues: 1103 helix: 0.87 (0.30), residues: 321 sheet: -2.00 (0.26), residues: 317 loop : -1.89 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 274 HIS 0.006 0.001 HIS C 44 PHE 0.022 0.002 PHE B 214 TYR 0.010 0.001 TYR D 83 ARG 0.003 0.000 ARG B 146 *********************** 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 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: C 53 ARG cc_start: 0.8036 (mtm180) cc_final: 0.7609 (mtm180) REVERT: C 97 ASP cc_start: 0.5320 (p0) cc_final: 0.4416 (p0) REVERT: C 214 PHE cc_start: 0.8628 (m-10) cc_final: 0.8251 (m-10) REVERT: D 182 CYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7756 (t) REVERT: D 327 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6502 (ptt180) REVERT: A 40 MET cc_start: 0.7673 (ttt) cc_final: 0.7352 (ttm) REVERT: B 131 GLN cc_start: 0.6562 (mm-40) cc_final: 0.6317 (mm-40) REVERT: B 143 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7209 (mt-10) outliers start: 31 outliers final: 24 residues processed: 146 average time/residue: 0.2278 time to fit residues: 47.4385 Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 182 CYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 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 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 182 LEU 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 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: 1.9990 chunk 80 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 110 GLN ** 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 = 0.3916 r_free = 0.3916 target = 0.152038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115181 restraints weight = 13442.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118655 restraints weight = 7918.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120997 restraints weight = 5625.992| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10220 Z= 0.306 Angle : 0.617 6.842 14068 Z= 0.331 Chirality : 0.044 0.148 1619 Planarity : 0.004 0.064 1591 Dihedral : 21.720 165.074 1939 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.12 % Allowed : 14.75 % Favored : 82.14 % 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: -1.83 (0.24), residues: 1103 helix: 0.83 (0.29), residues: 320 sheet: -2.19 (0.26), residues: 321 loop : -1.85 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 274 HIS 0.011 0.001 HIS C 44 PHE 0.024 0.002 PHE B 214 TYR 0.014 0.002 TYR D 83 ARG 0.006 0.000 ARG B 146 *********************** 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 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: C 53 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7565 (mtm180) REVERT: C 68 MET cc_start: 0.8315 (pmm) cc_final: 0.8095 (ptp) REVERT: C 214 PHE cc_start: 0.8676 (m-10) cc_final: 0.8322 (m-10) REVERT: D 74 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7030 (mmt) REVERT: D 327 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6538 (ptt180) REVERT: A 40 MET cc_start: 0.7745 (ttt) cc_final: 0.7429 (ttm) REVERT: B 131 GLN cc_start: 0.6547 (mm-40) cc_final: 0.6291 (mm-40) outliers start: 30 outliers final: 24 residues processed: 141 average time/residue: 0.2229 time to fit residues: 44.5540 Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 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 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 182 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.155075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118536 restraints weight = 13307.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122096 restraints weight = 7753.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124514 restraints weight = 5457.170| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10220 Z= 0.198 Angle : 0.563 10.784 14068 Z= 0.302 Chirality : 0.042 0.150 1619 Planarity : 0.003 0.063 1591 Dihedral : 21.553 164.656 1939 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 16.10 % Favored : 81.72 % 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: 0.95 (0.30), residues: 322 sheet: -2.02 (0.26), residues: 317 loop : -1.88 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.008 0.001 HIS C 44 PHE 0.022 0.002 PHE B 214 TYR 0.009 0.001 TYR C 211 ARG 0.007 0.000 ARG B 146 *********************** 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 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.127 Fit side-chains REVERT: C 28 TRP cc_start: 0.8305 (m100) cc_final: 0.8015 (m100) REVERT: C 53 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7581 (mtm180) REVERT: C 97 ASP cc_start: 0.5240 (p0) cc_final: 0.4401 (p0) REVERT: C 214 PHE cc_start: 0.8618 (m-10) cc_final: 0.8275 (m-10) REVERT: D 120 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5399 (mp0) REVERT: D 327 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6506 (ptt180) REVERT: A 40 MET cc_start: 0.7662 (ttt) cc_final: 0.7378 (ttm) REVERT: B 131 GLN cc_start: 0.6474 (mm-40) cc_final: 0.5976 (mm-40) outliers start: 21 outliers final: 18 residues processed: 140 average time/residue: 0.2241 time to fit residues: 44.7097 Evaluate side-chains 138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 79 ILE 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 321 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 70 VAL Chi-restraints excluded: chain A residue 182 LEU 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 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.154496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117052 restraints weight = 13315.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120652 restraints weight = 7781.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123143 restraints weight = 5488.259| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10220 Z= 0.260 Angle : 0.597 10.697 14068 Z= 0.317 Chirality : 0.043 0.153 1619 Planarity : 0.003 0.062 1591 Dihedral : 21.560 162.732 1939 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.28 % Allowed : 16.10 % 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: -1.69 (0.24), residues: 1103 helix: 0.95 (0.29), residues: 321 sheet: -2.05 (0.26), residues: 317 loop : -1.84 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 274 HIS 0.007 0.001 HIS C 44 PHE 0.024 0.002 PHE B 214 TYR 0.012 0.001 TYR B 250 ARG 0.007 0.000 ARG B 146 ********************** 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 : 1.066 Fit side-chains REVERT: C 53 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7614 (mtm180) REVERT: C 68 MET cc_start: 0.8273 (pmm) cc_final: 0.8053 (ptp) REVERT: C 97 ASP cc_start: 0.5424 (p0) cc_final: 0.4570 (p0) REVERT: C 214 PHE cc_start: 0.8650 (m-10) cc_final: 0.8275 (m-10) REVERT: D 120 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5401 (mp0) REVERT: D 327 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6470 (ptt180) REVERT: A 40 MET cc_start: 0.7715 (ttt) cc_final: 0.7411 (ttm) REVERT: A 115 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7326 (mt-10) REVERT: B 131 GLN cc_start: 0.6449 (mm-40) cc_final: 0.5952 (mm-40) outliers start: 22 outliers final: 18 residues processed: 137 average time/residue: 0.2241 time to fit residues: 43.2021 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 70 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 182 LEU 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 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 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 94 optimal weight: 0.3980 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 25 optimal weight: 0.2980 chunk 91 optimal weight: 0.0050 chunk 66 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- 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 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.122149 restraints weight = 13271.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.125354 restraints weight = 7633.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126262 restraints weight = 5731.975| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10220 Z= 0.173 Angle : 0.554 10.634 14068 Z= 0.297 Chirality : 0.041 0.143 1619 Planarity : 0.003 0.063 1591 Dihedral : 21.375 161.301 1939 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.77 % Allowed : 16.61 % 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: -1.48 (0.24), residues: 1103 helix: 1.12 (0.30), residues: 321 sheet: -1.87 (0.26), residues: 320 loop : -1.76 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.008 0.001 HIS C 44 PHE 0.019 0.001 PHE B 214 TYR 0.010 0.001 TYR C 211 ARG 0.008 0.000 ARG B 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3279.58 seconds wall clock time: 59 minutes 49.70 seconds (3589.70 seconds total)