Starting phenix.real_space_refine on Wed Jan 15 06:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2a_45152/01_2025/9c2a_45152_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2a_45152/01_2025/9c2a_45152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c2a_45152/01_2025/9c2a_45152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2a_45152/01_2025/9c2a_45152.map" model { file = "/net/cci-nas-00/data/ceres_data/9c2a_45152/01_2025/9c2a_45152_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2a_45152/01_2025/9c2a_45152_trim.cif" } resolution = 2.74 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5058 2.51 5 N 1254 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7833 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2437 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'NAG': 3, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Restraints were copied for chains: D, F, C, B Time building chain proxies: 5.61, per 1000 atoms: 0.72 Number of scatterers: 7833 At special positions: 0 Unit cell: (85.6416, 87.588, 122.623, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1479 8.00 N 1254 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 401 " - " ASN A 242 " " NAG A 402 " - " ASN A 184 " " NAG A 403 " - " ASN A 300 " " NAG B 401 " - " ASN B 242 " " NAG B 402 " - " ASN B 184 " " NAG B 403 " - " ASN B 300 " " NAG C 401 " - " ASN C 242 " " NAG C 402 " - " ASN C 184 " " NAG C 403 " - " ASN C 300 " " NAG D 1 " - " ASN A 153 " " NAG E 1 " - " ASN B 153 " " NAG F 1 " - " ASN C 153 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 27.8% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.836A pdb=" N GLU A 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.516A pdb=" N LYS A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 354 removed outlier: 3.770A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.836A pdb=" N GLU B 183 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.517A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 354 removed outlier: 3.770A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.836A pdb=" N GLU C 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.516A pdb=" N LYS C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 354 removed outlier: 3.769A pdb=" N THR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 59 current: chain 'A' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 99 through 118 current: chain 'A' and resid 144 through 151 removed outlier: 9.229A pdb=" N ILE A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N TRP A 164 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 146 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 165 current: chain 'A' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 277 current: chain 'A' and resid 302 through 326 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 59 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 59 current: chain 'B' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 99 through 118 current: chain 'B' and resid 144 through 151 removed outlier: 9.229A pdb=" N ILE B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N TRP B 164 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR B 146 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 165 current: chain 'B' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 277 current: chain 'B' and resid 302 through 326 Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 59 current: chain 'C' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 99 through 118 current: chain 'C' and resid 144 through 151 removed outlier: 9.228A pdb=" N ILE C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N TRP C 164 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR C 146 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 165 current: chain 'C' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 277 current: chain 'C' and resid 302 through 326 Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 74 211 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1410 1.33 - 1.45: 2031 1.45 - 1.57: 4449 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7941 Sorted by residual: bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.96e+00 bond pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.89e+00 bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.82e+00 bond pdb=" N VAL B 156 " pdb=" CA VAL B 156 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.82e+00 bond pdb=" N VAL C 156 " pdb=" CA VAL C 156 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.82e+00 ... (remaining 7936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 9574 1.46 - 2.93: 1014 2.93 - 4.39: 196 4.39 - 5.85: 13 5.85 - 7.31: 6 Bond angle restraints: 10803 Sorted by residual: angle pdb=" C CYS A 117 " pdb=" CA CYS A 117 " pdb=" CB CYS A 117 " ideal model delta sigma weight residual 111.17 103.86 7.31 1.96e+00 2.60e-01 1.39e+01 angle pdb=" C CYS C 117 " pdb=" CA CYS C 117 " pdb=" CB CYS C 117 " ideal model delta sigma weight residual 111.17 103.88 7.29 1.96e+00 2.60e-01 1.38e+01 angle pdb=" C CYS B 117 " pdb=" CA CYS B 117 " pdb=" CB CYS B 117 " ideal model delta sigma weight residual 111.17 103.92 7.25 1.96e+00 2.60e-01 1.37e+01 angle pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" O VAL A 40 " ideal model delta sigma weight residual 121.17 117.27 3.90 1.06e+00 8.90e-01 1.35e+01 angle pdb=" CA VAL C 40 " pdb=" C VAL C 40 " pdb=" O VAL C 40 " ideal model delta sigma weight residual 121.17 117.28 3.89 1.06e+00 8.90e-01 1.34e+01 ... (remaining 10798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4696 17.42 - 34.84: 268 34.84 - 52.26: 81 52.26 - 69.68: 24 69.68 - 87.09: 7 Dihedral angle restraints: 5076 sinusoidal: 2448 harmonic: 2628 Sorted by residual: dihedral pdb=" CB CYS A 217 " pdb=" SG CYS A 217 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual 93.00 178.27 -85.27 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CA ARG B 175 " pdb=" C ARG B 175 " pdb=" N PRO B 176 " pdb=" CA PRO B 176 " ideal model delta harmonic sigma weight residual 0.00 19.83 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ARG C 175 " pdb=" C ARG C 175 " pdb=" N PRO C 176 " pdb=" CA PRO C 176 " ideal model delta harmonic sigma weight residual 0.00 19.81 -19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 801 0.047 - 0.094: 271 0.094 - 0.142: 149 0.142 - 0.189: 33 0.189 - 0.236: 3 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA CYS A 117 " pdb=" N CYS A 117 " pdb=" C CYS A 117 " pdb=" CB CYS A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA CYS B 117 " pdb=" N CYS B 117 " pdb=" C CYS B 117 " pdb=" CB CYS B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA CYS C 117 " pdb=" N CYS C 117 " pdb=" C CYS C 117 " pdb=" CB CYS C 117 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1254 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 37 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLN B 37 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN B 37 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 38 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 37 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C GLN C 37 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN C 37 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 38 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 37 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C GLN A 37 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN A 37 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 38 " 0.015 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 97 2.60 - 3.18: 6627 3.18 - 3.75: 11327 3.75 - 4.33: 17902 4.33 - 4.90: 28815 Nonbonded interactions: 64768 Sorted by model distance: nonbonded pdb=" SG CYS C 261 " pdb=" SG CYS C 270 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 261 " pdb=" SG CYS B 270 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 217 " pdb=" SG CYS B 227 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS C 217 " pdb=" SG CYS C 227 " model vdw 2.033 3.760 nonbonded pdb=" O3 NAG C 401 " pdb=" O7 NAG C 401 " model vdw 2.207 3.040 ... (remaining 64763 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: 0.05 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.990 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.008 0.047 7941 Z= 0.564 Angle : 0.944 7.315 10803 Z= 0.653 Chirality : 0.061 0.236 1257 Planarity : 0.008 0.098 1320 Dihedral : 12.743 87.094 3390 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -1.18 (0.27), residues: 915 helix: -1.70 (0.28), residues: 270 sheet: 0.36 (0.30), residues: 276 loop : -0.76 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 259 HIS 0.004 0.001 HIS C 224 PHE 0.021 0.002 PHE A 293 TYR 0.011 0.001 TYR B 90 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.999 Fit side-chains REVERT: A 68 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7725 (ttmt) REVERT: A 202 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8145 (mmm160) REVERT: A 268 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7392 (ptm160) REVERT: B 188 PHE cc_start: 0.8511 (t80) cc_final: 0.8285 (t80) outliers start: 0 outliers final: 1 residues processed: 158 average time/residue: 1.3296 time to fit residues: 221.7309 Evaluate side-chains 150 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 114 GLN B 105 ASN C 105 ASN C 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120321 restraints weight = 9906.466| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.35 r_work: 0.3341 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 7941 Z= 0.275 Angle : 0.545 5.477 10803 Z= 0.286 Chirality : 0.045 0.233 1257 Planarity : 0.004 0.038 1320 Dihedral : 8.503 59.264 1730 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.03 % Allowed : 8.96 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 915 helix: -0.02 (0.35), residues: 252 sheet: 0.67 (0.28), residues: 285 loop : -0.23 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 85 HIS 0.005 0.001 HIS C 220 PHE 0.013 0.002 PHE B 243 TYR 0.016 0.002 TYR A 90 ARG 0.002 0.000 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.787 Fit side-chains REVERT: A 36 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7991 (tp) REVERT: A 202 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8296 (mmm160) REVERT: A 219 PHE cc_start: 0.8603 (t80) cc_final: 0.8284 (t80) REVERT: A 268 ARG cc_start: 0.8217 (ptm-80) cc_final: 0.7827 (ptm160) REVERT: B 114 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8349 (mt0) REVERT: B 188 PHE cc_start: 0.8747 (t80) cc_final: 0.8502 (t80) REVERT: B 268 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7858 (ptm160) outliers start: 24 outliers final: 9 residues processed: 161 average time/residue: 1.3135 time to fit residues: 223.2166 Evaluate side-chains 160 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 114 GLN B 120 HIS C 114 GLN C 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.144799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119707 restraints weight = 10080.668| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.37 r_work: 0.3322 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7941 Z= 0.304 Angle : 0.516 4.837 10803 Z= 0.272 Chirality : 0.045 0.210 1257 Planarity : 0.004 0.045 1320 Dihedral : 8.599 59.861 1730 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.28 % Allowed : 12.25 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 915 helix: 0.19 (0.35), residues: 252 sheet: 0.85 (0.29), residues: 285 loop : -0.27 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 259 HIS 0.004 0.001 HIS C 220 PHE 0.025 0.002 PHE B 342 TYR 0.013 0.002 TYR A 90 ARG 0.003 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.904 Fit side-chains REVERT: A 36 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7938 (tp) REVERT: A 219 PHE cc_start: 0.8617 (t80) cc_final: 0.8331 (t80) REVERT: B 114 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: B 188 PHE cc_start: 0.8750 (t80) cc_final: 0.8532 (t80) outliers start: 26 outliers final: 15 residues processed: 162 average time/residue: 1.2713 time to fit residues: 217.7664 Evaluate side-chains 163 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 114 GLN A 120 HIS B 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118603 restraints weight = 9950.929| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.32 r_work: 0.3307 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 7941 Z= 0.453 Angle : 0.559 4.915 10803 Z= 0.293 Chirality : 0.047 0.221 1257 Planarity : 0.004 0.048 1320 Dihedral : 8.667 58.748 1730 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.91 % Allowed : 13.13 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.28), residues: 915 helix: 0.06 (0.34), residues: 252 sheet: 0.72 (0.29), residues: 303 loop : -0.29 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 259 HIS 0.007 0.001 HIS C 220 PHE 0.021 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.004 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.785 Fit side-chains REVERT: A 36 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A 219 PHE cc_start: 0.8621 (t80) cc_final: 0.8273 (t80) REVERT: B 188 PHE cc_start: 0.8749 (t80) cc_final: 0.8423 (t80) REVERT: B 268 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7925 (ptm160) outliers start: 31 outliers final: 18 residues processed: 156 average time/residue: 1.2876 time to fit residues: 211.9380 Evaluate side-chains 170 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 120 HIS B 120 HIS C 105 ASN C 120 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119496 restraints weight = 9918.454| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.30 r_work: 0.3317 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7941 Z= 0.330 Angle : 0.507 4.906 10803 Z= 0.267 Chirality : 0.045 0.214 1257 Planarity : 0.004 0.046 1320 Dihedral : 8.350 59.820 1730 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.28 % Allowed : 15.03 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 915 helix: 0.28 (0.35), residues: 252 sheet: 0.79 (0.30), residues: 285 loop : -0.25 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 259 HIS 0.005 0.001 HIS C 220 PHE 0.018 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.003 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.786 Fit side-chains REVERT: A 36 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7870 (tp) REVERT: A 219 PHE cc_start: 0.8624 (t80) cc_final: 0.8287 (t80) REVERT: A 268 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7634 (ptm160) REVERT: A 292 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8136 (mtm180) REVERT: B 188 PHE cc_start: 0.8734 (t80) cc_final: 0.8516 (t80) REVERT: B 268 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7907 (ptm160) REVERT: B 292 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8435 (mtm180) outliers start: 26 outliers final: 15 residues processed: 157 average time/residue: 1.2827 time to fit residues: 212.6998 Evaluate side-chains 166 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.0570 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 120 HIS C 120 HIS C 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.144592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119861 restraints weight = 9814.355| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.33 r_work: 0.3319 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7941 Z= 0.270 Angle : 0.483 4.932 10803 Z= 0.255 Chirality : 0.044 0.207 1257 Planarity : 0.004 0.045 1320 Dihedral : 8.006 58.850 1730 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.54 % Allowed : 15.28 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 915 helix: 0.80 (0.37), residues: 234 sheet: 0.82 (0.28), residues: 330 loop : -0.45 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.004 0.001 HIS A 120 PHE 0.016 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.004 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.654 Fit side-chains REVERT: A 36 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7825 (tp) REVERT: A 219 PHE cc_start: 0.8614 (t80) cc_final: 0.8291 (t80) REVERT: A 268 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7611 (ptm160) REVERT: A 292 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8067 (mtm180) REVERT: B 188 PHE cc_start: 0.8739 (t80) cc_final: 0.8521 (t80) REVERT: B 275 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7786 (tt0) REVERT: B 292 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8432 (mtm180) outliers start: 28 outliers final: 17 residues processed: 157 average time/residue: 1.2699 time to fit residues: 210.3533 Evaluate side-chains 168 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 105 ASN B 120 HIS C 105 ASN C 120 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120112 restraints weight = 9831.307| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.32 r_work: 0.3327 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7941 Z= 0.242 Angle : 0.469 4.898 10803 Z= 0.248 Chirality : 0.044 0.202 1257 Planarity : 0.003 0.044 1320 Dihedral : 7.720 58.687 1730 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.41 % Allowed : 15.91 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.28), residues: 915 helix: 0.79 (0.36), residues: 240 sheet: 0.86 (0.28), residues: 330 loop : -0.39 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 259 HIS 0.004 0.001 HIS A 120 PHE 0.015 0.001 PHE B 342 TYR 0.014 0.001 TYR A 90 ARG 0.004 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.816 Fit side-chains REVERT: A 36 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7790 (tp) REVERT: A 268 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7586 (ptm160) REVERT: A 292 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8056 (mtm180) REVERT: B 188 PHE cc_start: 0.8736 (t80) cc_final: 0.8524 (t80) REVERT: B 226 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7168 (mp) REVERT: B 268 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7900 (ptm160) REVERT: B 275 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7804 (tt0) REVERT: B 292 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8441 (mtm180) outliers start: 27 outliers final: 18 residues processed: 156 average time/residue: 1.2881 time to fit residues: 212.6093 Evaluate side-chains 168 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 114 GLN B 120 HIS C 120 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118670 restraints weight = 9940.799| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.34 r_work: 0.3312 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 7941 Z= 0.386 Angle : 0.520 5.037 10803 Z= 0.274 Chirality : 0.046 0.207 1257 Planarity : 0.004 0.046 1320 Dihedral : 7.750 59.595 1730 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.91 % Allowed : 15.40 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.28), residues: 915 helix: 0.75 (0.36), residues: 234 sheet: 0.80 (0.28), residues: 330 loop : -0.51 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 259 HIS 0.005 0.001 HIS C 220 PHE 0.019 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.004 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.775 Fit side-chains REVERT: A 36 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7797 (tp) REVERT: A 219 PHE cc_start: 0.8620 (t80) cc_final: 0.8287 (t80) REVERT: A 268 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7611 (ptm160) REVERT: A 292 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8230 (mtm180) REVERT: B 188 PHE cc_start: 0.8744 (t80) cc_final: 0.8528 (t80) REVERT: B 226 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7212 (mp) REVERT: B 268 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7915 (ptm160) REVERT: B 275 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7784 (tt0) REVERT: B 292 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8459 (mtm180) REVERT: C 275 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7912 (tt0) outliers start: 31 outliers final: 21 residues processed: 161 average time/residue: 1.2305 time to fit residues: 209.4769 Evaluate side-chains 178 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 54 optimal weight: 0.0470 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 120 HIS C 105 ASN C 120 HIS C 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118879 restraints weight = 9998.621| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.34 r_work: 0.3314 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7941 Z= 0.248 Angle : 0.476 4.910 10803 Z= 0.252 Chirality : 0.044 0.200 1257 Planarity : 0.003 0.045 1320 Dihedral : 7.529 59.340 1730 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.66 % Allowed : 16.41 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 915 helix: 0.77 (0.36), residues: 240 sheet: 0.85 (0.28), residues: 330 loop : -0.39 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 259 HIS 0.006 0.001 HIS C 120 PHE 0.017 0.001 PHE B 342 TYR 0.014 0.001 TYR A 90 ARG 0.005 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.841 Fit side-chains REVERT: A 36 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7794 (tp) REVERT: A 219 PHE cc_start: 0.8623 (t80) cc_final: 0.8306 (t80) REVERT: A 268 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7589 (ptm160) REVERT: A 292 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8095 (mtm180) REVERT: B 226 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7188 (mp) REVERT: B 268 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7860 (ptm160) REVERT: B 275 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7831 (tt0) outliers start: 29 outliers final: 21 residues processed: 163 average time/residue: 1.2244 time to fit residues: 211.0125 Evaluate side-chains 174 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 47 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 105 ASN B 120 HIS C 105 ASN C 120 HIS C 290 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119901 restraints weight = 9876.532| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.32 r_work: 0.3331 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7941 Z= 0.202 Angle : 0.456 4.887 10803 Z= 0.241 Chirality : 0.043 0.196 1257 Planarity : 0.003 0.044 1320 Dihedral : 7.324 59.748 1730 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 17.30 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 915 helix: 0.90 (0.36), residues: 240 sheet: 0.91 (0.29), residues: 330 loop : -0.36 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 259 HIS 0.006 0.001 HIS C 120 PHE 0.015 0.001 PHE B 342 TYR 0.014 0.001 TYR A 90 ARG 0.004 0.000 ARG B 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.819 Fit side-chains REVERT: A 36 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7733 (tp) REVERT: A 292 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8003 (mtm180) REVERT: B 226 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7133 (mp) REVERT: B 275 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7814 (tt0) outliers start: 22 outliers final: 15 residues processed: 162 average time/residue: 1.2235 time to fit residues: 209.5695 Evaluate side-chains 166 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 120 HIS C 105 ASN C 120 HIS C 290 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118843 restraints weight = 9881.808| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.33 r_work: 0.3310 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7941 Z= 0.299 Angle : 0.491 4.921 10803 Z= 0.260 Chirality : 0.044 0.200 1257 Planarity : 0.004 0.045 1320 Dihedral : 7.384 59.538 1730 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.03 % Allowed : 17.68 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 915 helix: 0.93 (0.37), residues: 234 sheet: 0.91 (0.28), residues: 330 loop : -0.38 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.005 0.001 HIS C 120 PHE 0.018 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.002 0.000 ARG C 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6751.92 seconds wall clock time: 119 minutes 54.77 seconds (7194.77 seconds total)