Starting phenix.real_space_refine on Fri Nov 15 02:33:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2a_45152/11_2024/9c2a_45152_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2a_45152/11_2024/9c2a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2a_45152/11_2024/9c2a_45152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2a_45152/11_2024/9c2a_45152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2a_45152/11_2024/9c2a_45152_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c2a_45152/11_2024/9c2a_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-5513/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: 5.88, per 1000 atoms: 0.75 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: 2.21 Conformation dependent library (CDL) restraints added in 978.6 milliseconds 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: 0.94 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: 2.29 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.530 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- 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 : 1.045 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: 1.2596 time to fit residues: 210.7006 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 : 0.813 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.790 Fit side-chains REVERT: A 36 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7880 (tp) REVERT: A 202 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8118 (mmm160) REVERT: A 219 PHE cc_start: 0.8374 (t80) cc_final: 0.8066 (t80) REVERT: A 268 ARG cc_start: 0.7743 (ptm-80) cc_final: 0.7399 (ptm160) REVERT: A 332 MET cc_start: 0.7662 (mmt) cc_final: 0.7409 (mmt) REVERT: B 114 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: B 188 PHE cc_start: 0.8542 (t80) cc_final: 0.8255 (t80) REVERT: B 268 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7459 (ptm160) outliers start: 24 outliers final: 9 residues processed: 161 average time/residue: 1.2957 time to fit residues: 220.4785 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 : 0.809 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 84 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 28 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 7941 Z= 0.222 Angle : 0.488 4.813 10803 Z= 0.258 Chirality : 0.044 0.206 1257 Planarity : 0.004 0.043 1320 Dihedral : 8.454 59.599 1730 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.90 % Allowed : 11.87 % Favored : 85.23 % 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: 0.28 (0.28), residues: 915 helix: 0.20 (0.35), residues: 258 sheet: 0.88 (0.29), residues: 285 loop : -0.23 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.004 0.001 HIS A 120 PHE 0.021 0.001 PHE B 342 TYR 0.014 0.001 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 180 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.869 Fit side-chains REVERT: A 36 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7844 (tp) REVERT: A 202 ARG cc_start: 0.8488 (mmm160) cc_final: 0.8042 (mmm160) REVERT: A 219 PHE cc_start: 0.8387 (t80) cc_final: 0.8111 (t80) REVERT: B 114 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: B 188 PHE cc_start: 0.8537 (t80) cc_final: 0.8300 (t80) REVERT: B 268 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7461 (ptm160) outliers start: 23 outliers final: 13 residues processed: 167 average time/residue: 1.2397 time to fit residues: 219.0451 Evaluate side-chains 164 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 268 ARG 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 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.0000 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.4742 ------------------------------------------------------------------------------- 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 C 105 ASN C 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7941 Z= 0.229 Angle : 0.479 5.558 10803 Z= 0.252 Chirality : 0.044 0.207 1257 Planarity : 0.003 0.044 1320 Dihedral : 8.395 59.531 1728 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.17 % Allowed : 12.63 % Favored : 83.21 % 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: 0.41 (0.28), residues: 915 helix: 0.26 (0.35), residues: 258 sheet: 0.92 (0.29), residues: 303 loop : -0.14 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 259 HIS 0.004 0.001 HIS A 120 PHE 0.017 0.001 PHE B 342 TYR 0.013 0.001 TYR A 90 ARG 0.003 0.000 ARG B 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 180 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.900 Fit side-chains REVERT: A 36 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 114 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: B 188 PHE cc_start: 0.8550 (t80) cc_final: 0.8327 (t80) REVERT: B 261 CYS cc_start: 0.7612 (p) cc_final: 0.7370 (m) outliers start: 33 outliers final: 16 residues processed: 160 average time/residue: 1.2519 time to fit residues: 211.4879 Evaluate side-chains 164 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 318 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7941 Z= 0.252 Angle : 0.477 4.872 10803 Z= 0.251 Chirality : 0.044 0.205 1257 Planarity : 0.003 0.044 1320 Dihedral : 8.301 58.593 1728 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 15.15 % Favored : 82.07 % 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: 0.43 (0.28), residues: 915 helix: 0.31 (0.35), residues: 258 sheet: 0.96 (0.30), residues: 285 loop : -0.13 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 259 HIS 0.004 0.001 HIS A 120 PHE 0.016 0.001 PHE B 342 TYR 0.013 0.001 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 172 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.750 Fit side-chains REVERT: A 36 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7803 (tp) REVERT: B 114 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: B 188 PHE cc_start: 0.8555 (t80) cc_final: 0.8328 (t80) outliers start: 22 outliers final: 16 residues processed: 158 average time/residue: 1.2225 time to fit residues: 204.3324 Evaluate side-chains 167 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 318 LEU 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 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 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2127 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 : 0.496 4.889 10803 Z= 0.261 Chirality : 0.045 0.204 1257 Planarity : 0.004 0.044 1320 Dihedral : 8.123 59.343 1728 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.28 % Allowed : 15.66 % Favored : 81.06 % 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: 0.45 (0.28), residues: 915 helix: 0.41 (0.35), residues: 252 sheet: 0.88 (0.29), residues: 303 loop : -0.15 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 259 HIS 0.005 0.001 HIS C 220 PHE 0.017 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 174 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.863 Fit side-chains REVERT: A 36 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7770 (tp) REVERT: A 268 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7181 (ptm160) REVERT: B 114 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: B 144 ILE cc_start: 0.8453 (mt) cc_final: 0.8148 (mm) REVERT: B 188 PHE cc_start: 0.8558 (t80) cc_final: 0.8324 (t80) REVERT: B 268 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7464 (ptm160) outliers start: 26 outliers final: 17 residues processed: 155 average time/residue: 1.2620 time to fit residues: 206.7116 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 : 0.950 ------------------------------------------------------------------------------- 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 268 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 103 MET 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 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 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.3610 ------------------------------------------------------------------------------- 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 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7941 Z= 0.197 Angle : 0.452 4.925 10803 Z= 0.239 Chirality : 0.043 0.198 1257 Planarity : 0.003 0.042 1320 Dihedral : 7.800 59.856 1728 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.90 % Allowed : 16.67 % Favored : 80.43 % 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: 0.64 (0.29), residues: 915 helix: 0.82 (0.36), residues: 240 sheet: 0.98 (0.29), residues: 330 loop : -0.31 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 259 HIS 0.004 0.001 HIS C 120 PHE 0.015 0.001 PHE B 342 TYR 0.014 0.001 TYR A 90 ARG 0.003 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 177 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.843 Fit side-chains REVERT: A 36 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7734 (tp) REVERT: A 292 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7479 (mtm180) REVERT: B 144 ILE cc_start: 0.8443 (mt) cc_final: 0.8169 (mm) REVERT: B 188 PHE cc_start: 0.8548 (t80) cc_final: 0.8315 (t80) REVERT: B 226 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.7010 (mp) REVERT: B 292 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8102 (mtm180) outliers start: 23 outliers final: 13 residues processed: 161 average time/residue: 1.2618 time to fit residues: 215.2817 Evaluate side-chains 167 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 193 ILE Chi-restraints excluded: chain B residue 226 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2293 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= 0.380 Angle : 0.519 4.979 10803 Z= 0.272 Chirality : 0.046 0.205 1257 Planarity : 0.004 0.045 1320 Dihedral : 7.786 59.235 1728 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.54 % Allowed : 16.79 % Favored : 79.67 % 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: 0.45 (0.28), residues: 915 helix: 0.46 (0.35), residues: 252 sheet: 0.92 (0.28), residues: 330 loop : -0.34 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 259 HIS 0.006 0.001 HIS C 220 PHE 0.020 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.005 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 181 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.881 Fit side-chains REVERT: A 36 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7718 (tp) REVERT: A 268 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7170 (ptm160) REVERT: B 144 ILE cc_start: 0.8418 (mt) cc_final: 0.8119 (mm) REVERT: B 188 PHE cc_start: 0.8566 (t80) cc_final: 0.8326 (t80) REVERT: B 226 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7058 (mp) REVERT: B 268 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7486 (ptm160) REVERT: B 292 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8149 (mtm180) outliers start: 28 outliers final: 15 residues processed: 162 average time/residue: 1.2693 time to fit residues: 217.3156 Evaluate side-chains 169 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 268 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 41 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 88 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 120 HIS C 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2385 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= 0.241 Angle : 0.466 4.918 10803 Z= 0.246 Chirality : 0.044 0.197 1257 Planarity : 0.003 0.044 1320 Dihedral : 7.520 59.834 1728 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.78 % Allowed : 17.42 % Favored : 79.80 % 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: 0.57 (0.28), residues: 915 helix: 0.78 (0.36), residues: 240 sheet: 0.96 (0.28), residues: 330 loop : -0.39 (0.34), residues: 345 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 0.016 0.001 PHE B 342 TYR 0.014 0.001 TYR A 90 ARG 0.003 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 173 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.918 Fit side-chains REVERT: B 144 ILE cc_start: 0.8404 (mt) cc_final: 0.8139 (mm) REVERT: B 188 PHE cc_start: 0.8562 (t80) cc_final: 0.8329 (t80) REVERT: B 226 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7043 (mp) REVERT: B 268 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7468 (ptm160) REVERT: B 292 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8114 (mtm180) outliers start: 22 outliers final: 16 residues processed: 160 average time/residue: 1.2661 time to fit residues: 214.5650 Evaluate side-chains 168 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 193 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 41 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 B residue 318 LEU 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 53 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7941 Z= 0.283 Angle : 0.482 4.930 10803 Z= 0.254 Chirality : 0.044 0.198 1257 Planarity : 0.003 0.045 1320 Dihedral : 7.442 59.272 1728 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.90 % Allowed : 17.42 % Favored : 79.67 % 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: 0.84 (0.37), residues: 234 sheet: 0.95 (0.28), residues: 330 loop : -0.37 (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 0.005 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 171 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.972 Fit side-chains REVERT: B 144 ILE cc_start: 0.8417 (mt) cc_final: 0.8142 (mm) REVERT: B 188 PHE cc_start: 0.8567 (t80) cc_final: 0.8330 (t80) REVERT: B 226 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7043 (mp) REVERT: B 268 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7496 (ptm160) REVERT: B 292 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8144 (mtm180) REVERT: C 202 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7837 (mtp180) outliers start: 23 outliers final: 18 residues processed: 157 average time/residue: 1.2714 time to fit residues: 211.0533 Evaluate side-chains 169 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 318 LEU Chi-restraints excluded: chain B residue 41 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 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 B residue 318 LEU 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 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 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 = 0.3781 r_free = 0.3781 target = 0.143414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119359 restraints weight = 9847.861| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.28 r_work: 0.3318 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7941 Z= 0.289 Angle : 0.480 4.985 10803 Z= 0.253 Chirality : 0.044 0.197 1257 Planarity : 0.003 0.045 1320 Dihedral : 7.373 59.278 1728 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.03 % Allowed : 17.17 % Favored : 79.80 % 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: 0.86 (0.37), residues: 234 sheet: 0.92 (0.28), residues: 330 loop : -0.34 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.006 0.001 HIS C 120 PHE 0.018 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.004 0.000 ARG A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.97 seconds wall clock time: 71 minutes 16.20 seconds (4276.20 seconds total)