Starting phenix.real_space_refine on Mon Apr 28 21:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2a_45152/04_2025/9c2a_45152_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2a_45152/04_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_45152/04_2025/9c2a_45152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2a_45152/04_2025/9c2a_45152.map" model { file = "/net/cci-nas-00/data/ceres_data/9c2a_45152/04_2025/9c2a_45152_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2a_45152/04_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-5669/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: 5.44, per 1000 atoms: 0.69 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=6, 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 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 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: 0.78 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: 1.85 Time building geometry restraints manager: 2.42 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: 4698 17.42 - 34.84: 276 34.84 - 52.26: 81 52.26 - 69.68: 24 69.68 - 87.09: 9 Dihedral angle restraints: 5088 sinusoidal: 2460 harmonic: 2628 Sorted by residual: dihedral pdb=" CB CYS C 217 " pdb=" SG CYS C 217 " pdb=" SG CYS C 227 " pdb=" CB CYS C 227 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS B 217 " pdb=" SG CYS B 217 " pdb=" SG CYS B 227 " pdb=" CB CYS B 227 " ideal model delta sinusoidal sigma weight residual 93.00 178.28 -85.28 1 1.00e+01 1.00e-02 8.81e+01 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 ... (remaining 5085 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: 2.21 - 2.75: 894 2.75 - 3.28: 7280 3.28 - 3.82: 12534 3.82 - 4.36: 16587 4.36 - 4.90: 27461 Nonbonded interactions: 64756 Sorted by model distance: nonbonded pdb=" O3 NAG C 401 " pdb=" O7 NAG C 401 " model vdw 2.207 3.040 nonbonded pdb=" O3 NAG B 401 " pdb=" O7 NAG B 401 " model vdw 2.208 3.040 nonbonded pdb=" O3 NAG A 401 " pdb=" O7 NAG A 401 " model vdw 2.208 3.040 nonbonded pdb=" O THR C 75 " pdb=" OG1 THR C 75 " model vdw 2.411 3.040 nonbonded pdb=" O THR A 75 " pdb=" OG1 THR A 75 " model vdw 2.411 3.040 ... (remaining 64751 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: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.250 Find NCS groups from input model: 0.150 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:15.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.530 ------------------------------------------------------------------------------- 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 7962 Z= 0.503 Angle : 0.946 7.315 10860 Z= 0.652 Chirality : 0.061 0.236 1257 Planarity : 0.008 0.098 1320 Dihedral : 12.743 87.094 3390 Min Nonbonded Distance : 2.207 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 12) link_NAG-ASN : angle 1.21655 ( 36) link_BETA1-4 : bond 0.00271 ( 3) link_BETA1-4 : angle 0.95180 ( 9) hydrogen bonds : bond 0.17974 ( 211) hydrogen bonds : angle 7.16002 ( 534) SS BOND : bond 0.00424 ( 6) SS BOND : angle 1.51380 ( 12) covalent geometry : bond 0.00841 ( 7941) covalent geometry : angle 0.94423 (10803) *********************** 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 : 0.838 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: 1.4464 time to fit residues: 241.3830 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 : 0.854 ------------------------------------------------------------------------------- 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: 0.7980 chunk 84 optimal weight: 1.9990 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 = 0.145322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120371 restraints weight = 9942.362| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.36 r_work: 0.3338 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7962 Z= 0.168 Angle : 0.543 4.791 10860 Z= 0.283 Chirality : 0.046 0.245 1257 Planarity : 0.004 0.038 1320 Dihedral : 8.478 59.872 1730 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.16 % Allowed : 9.47 % Favored : 87.37 % 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: 0.12 (0.28), residues: 915 helix: 0.00 (0.35), residues: 252 sheet: 0.70 (0.28), residues: 285 loop : -0.21 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 85 HIS 0.004 0.001 HIS C 120 PHE 0.013 0.002 PHE B 243 TYR 0.017 0.002 TYR A 90 ARG 0.003 0.000 ARG A 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 1.35655 ( 36) link_BETA1-4 : bond 0.00392 ( 3) link_BETA1-4 : angle 0.66792 ( 9) hydrogen bonds : bond 0.03806 ( 211) hydrogen bonds : angle 4.88864 ( 534) SS BOND : bond 0.00447 ( 6) SS BOND : angle 0.87929 ( 12) covalent geometry : bond 0.00403 ( 7941) covalent geometry : angle 0.53776 (10803) *********************** 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: 25 poor density : 151 time to evaluate : 0.873 Fit side-chains REVERT: A 36 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7975 (tp) REVERT: A 219 PHE cc_start: 0.8599 (t80) cc_final: 0.8282 (t80) REVERT: A 268 ARG cc_start: 0.8213 (ptm-80) cc_final: 0.7820 (ptm160) REVERT: B 114 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8354 (mt0) REVERT: B 188 PHE cc_start: 0.8755 (t80) cc_final: 0.8537 (t80) REVERT: B 268 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7866 (ptm160) outliers start: 25 outliers final: 8 residues processed: 160 average time/residue: 1.2846 time to fit residues: 217.0823 Evaluate side-chains 158 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120101 restraints weight = 10105.241| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.35 r_work: 0.3325 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 7962 Z= 0.166 Angle : 0.507 4.805 10860 Z= 0.265 Chirality : 0.045 0.211 1257 Planarity : 0.004 0.043 1320 Dihedral : 8.517 59.923 1728 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.90 % Allowed : 12.37 % Favored : 84.72 % 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: 0.30 (0.28), residues: 915 helix: 0.22 (0.35), residues: 252 sheet: 0.87 (0.29), residues: 285 loop : -0.21 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 259 HIS 0.004 0.001 HIS A 120 PHE 0.024 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.003 0.000 ARG A 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 12) link_NAG-ASN : angle 1.27425 ( 36) link_BETA1-4 : bond 0.00325 ( 3) link_BETA1-4 : angle 0.77464 ( 9) hydrogen bonds : bond 0.03582 ( 211) hydrogen bonds : angle 4.68754 ( 534) SS BOND : bond 0.00424 ( 6) SS BOND : angle 0.87367 ( 12) covalent geometry : bond 0.00405 ( 7941) covalent geometry : angle 0.50131 (10803) *********************** 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 179 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.797 Fit side-chains REVERT: A 36 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7949 (tp) REVERT: A 219 PHE cc_start: 0.8617 (t80) cc_final: 0.8328 (t80) REVERT: B 188 PHE cc_start: 0.8762 (t80) cc_final: 0.8557 (t80) REVERT: B 268 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7860 (ptm160) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 1.2577 time to fit residues: 218.1961 Evaluate side-chains 166 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 120 HIS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.142760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118020 restraints weight = 10003.572| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.32 r_work: 0.3296 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 7962 Z= 0.335 Angle : 0.611 5.418 10860 Z= 0.316 Chirality : 0.050 0.227 1257 Planarity : 0.005 0.050 1320 Dihedral : 8.757 59.027 1728 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.91 % Allowed : 13.64 % Favored : 82.45 % 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: 0.01 (0.28), residues: 915 helix: -0.08 (0.34), residues: 252 sheet: 0.65 (0.29), residues: 303 loop : -0.34 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 259 HIS 0.009 0.002 HIS C 220 PHE 0.023 0.003 PHE B 342 TYR 0.015 0.002 TYR A 304 ARG 0.004 0.000 ARG C 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 1.51040 ( 36) link_BETA1-4 : bond 0.00517 ( 3) link_BETA1-4 : angle 0.85502 ( 9) hydrogen bonds : bond 0.04407 ( 211) hydrogen bonds : angle 4.95085 ( 534) SS BOND : bond 0.00746 ( 6) SS BOND : angle 1.36926 ( 12) covalent geometry : bond 0.00818 ( 7941) covalent geometry : angle 0.60393 (10803) *********************** 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 177 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.884 Fit side-chains REVERT: A 36 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7942 (tp) REVERT: A 219 PHE cc_start: 0.8620 (t80) cc_final: 0.8273 (t80) REVERT: B 188 PHE cc_start: 0.8760 (t80) cc_final: 0.8519 (t80) REVERT: B 268 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7894 (ptm160) outliers start: 31 outliers final: 19 residues processed: 158 average time/residue: 1.2241 time to fit residues: 204.3146 Evaluate side-chains 167 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 70 LYS 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 69 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 57 optimal weight: 0.5980 chunk 28 optimal weight: 0.0060 chunk 18 optimal weight: 0.0000 chunk 72 optimal weight: 1.9990 overall best weight: 0.1556 ------------------------------------------------------------------------------- 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 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.145508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120613 restraints weight = 9924.007| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.36 r_work: 0.3339 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 7962 Z= 0.096 Angle : 0.466 4.882 10860 Z= 0.245 Chirality : 0.043 0.205 1257 Planarity : 0.003 0.044 1320 Dihedral : 8.261 59.408 1728 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.65 % Allowed : 15.78 % Favored : 81.57 % 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: 0.41 (0.35), residues: 258 sheet: 0.79 (0.29), residues: 303 loop : -0.14 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 85 HIS 0.005 0.001 HIS B 120 PHE 0.015 0.001 PHE B 342 TYR 0.014 0.001 TYR B 90 ARG 0.003 0.000 ARG B 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 12) link_NAG-ASN : angle 1.22925 ( 36) link_BETA1-4 : bond 0.00446 ( 3) link_BETA1-4 : angle 0.86326 ( 9) hydrogen bonds : bond 0.02901 ( 211) hydrogen bonds : angle 4.50777 ( 534) SS BOND : bond 0.00276 ( 6) SS BOND : angle 0.74100 ( 12) covalent geometry : bond 0.00223 ( 7941) covalent geometry : angle 0.46021 (10803) *********************** 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 178 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.867 Fit side-chains REVERT: A 36 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7825 (tp) REVERT: A 199 LYS cc_start: 0.8472 (mttt) cc_final: 0.8256 (mttt) REVERT: A 268 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7631 (ptm160) REVERT: B 188 PHE cc_start: 0.8735 (t80) cc_final: 0.8534 (t80) REVERT: B 292 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8356 (mtm180) outliers start: 21 outliers final: 9 residues processed: 163 average time/residue: 1.1949 time to fit residues: 206.3246 Evaluate side-chains 164 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 111 LYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A 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 342 PHE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 114 GLN B 120 HIS C 105 ASN C 120 HIS C 290 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120276 restraints weight = 9863.013| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.34 r_work: 0.3329 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7962 Z= 0.141 Angle : 0.483 4.889 10860 Z= 0.251 Chirality : 0.044 0.203 1257 Planarity : 0.003 0.044 1320 Dihedral : 8.024 59.705 1728 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.78 % Allowed : 17.05 % Favored : 80.18 % 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: 0.55 (0.28), residues: 915 helix: 0.84 (0.37), residues: 234 sheet: 0.84 (0.30), residues: 303 loop : -0.24 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 259 HIS 0.004 0.001 HIS A 120 PHE 0.020 0.001 PHE C 342 TYR 0.014 0.001 TYR A 90 ARG 0.004 0.000 ARG A 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.30510 ( 36) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 0.88919 ( 9) hydrogen bonds : bond 0.03224 ( 211) hydrogen bonds : angle 4.51465 ( 534) SS BOND : bond 0.00494 ( 6) SS BOND : angle 1.02105 ( 12) covalent geometry : bond 0.00348 ( 7941) covalent geometry : angle 0.47604 (10803) *********************** 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 173 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.769 Fit side-chains REVERT: A 36 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7844 (tp) REVERT: A 219 PHE cc_start: 0.8609 (t80) cc_final: 0.8318 (t80) REVERT: A 268 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7649 (ptm160) REVERT: B 188 PHE cc_start: 0.8742 (t80) cc_final: 0.8541 (t80) REVERT: B 268 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7889 (ptm160) REVERT: B 275 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7780 (tt0) REVERT: B 292 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8418 (mtm180) REVERT: C 275 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7849 (tt0) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 1.2032 time to fit residues: 203.6598 Evaluate side-chains 167 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 111 LYS 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 B residue 62 ILE Chi-restraints excluded: chain B residue 193 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119465 restraints weight = 9892.069| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.33 r_work: 0.3305 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 7962 Z= 0.188 Angle : 0.504 4.900 10860 Z= 0.264 Chirality : 0.045 0.204 1257 Planarity : 0.004 0.045 1320 Dihedral : 7.850 59.050 1728 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.16 % Allowed : 17.30 % Favored : 79.55 % 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: 0.83 (0.37), residues: 234 sheet: 0.85 (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 A 259 HIS 0.004 0.001 HIS C 220 PHE 0.017 0.002 PHE B 342 TYR 0.014 0.002 TYR A 90 ARG 0.005 0.000 ARG A 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 12) link_NAG-ASN : angle 1.37756 ( 36) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 0.87637 ( 9) hydrogen bonds : bond 0.03478 ( 211) hydrogen bonds : angle 4.61186 ( 534) SS BOND : bond 0.00501 ( 6) SS BOND : angle 1.02419 ( 12) covalent geometry : bond 0.00462 ( 7941) covalent geometry : angle 0.49742 (10803) *********************** 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: 25 poor density : 152 time to evaluate : 0.898 Fit side-chains REVERT: A 36 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7807 (tp) REVERT: A 219 PHE cc_start: 0.8624 (t80) cc_final: 0.8295 (t80) REVERT: A 268 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7617 (ptm160) REVERT: B 188 PHE cc_start: 0.8750 (t80) cc_final: 0.8547 (t80) REVERT: B 268 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7870 (ptm160) REVERT: B 275 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7787 (tt0) REVERT: B 292 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8443 (mtm180) REVERT: C 275 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7870 (tt0) outliers start: 25 outliers final: 14 residues processed: 162 average time/residue: 1.1958 time to fit residues: 205.0198 Evaluate side-chains 169 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 111 LYS 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 B residue 62 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 227 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.143946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119141 restraints weight = 9983.531| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.35 r_work: 0.3313 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 7962 Z= 0.201 Angle : 0.512 4.971 10860 Z= 0.268 Chirality : 0.045 0.206 1257 Planarity : 0.004 0.046 1320 Dihedral : 7.694 59.941 1728 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.16 % Allowed : 17.42 % Favored : 79.42 % 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: 0.49 (0.28), residues: 915 helix: 0.83 (0.37), residues: 234 sheet: 0.85 (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 A 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 0.005 0.000 ARG A 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 12) link_NAG-ASN : angle 1.42209 ( 36) link_BETA1-4 : bond 0.00382 ( 3) link_BETA1-4 : angle 0.88780 ( 9) hydrogen bonds : bond 0.03511 ( 211) hydrogen bonds : angle 4.64776 ( 534) SS BOND : bond 0.00479 ( 6) SS BOND : angle 0.83325 ( 12) covalent geometry : bond 0.00493 ( 7941) covalent geometry : angle 0.50546 (10803) *********************** 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 174 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.854 Fit side-chains REVERT: A 36 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 219 PHE cc_start: 0.8624 (t80) cc_final: 0.8282 (t80) REVERT: A 268 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7628 (ptm160) REVERT: B 188 PHE cc_start: 0.8752 (t80) cc_final: 0.8534 (t80) REVERT: B 268 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7880 (ptm160) REVERT: B 275 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7791 (tt0) REVERT: B 292 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8447 (mtm180) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 1.3154 time to fit residues: 221.4482 Evaluate side-chains 170 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 111 LYS 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 B residue 62 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 227 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.142740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118145 restraints weight = 10074.614| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.33 r_work: 0.3302 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.005 0.067 7962 Z= 0.188 Angle : 0.503 4.915 10860 Z= 0.263 Chirality : 0.045 0.204 1257 Planarity : 0.004 0.046 1320 Dihedral : 7.559 59.029 1728 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.54 % Allowed : 17.42 % Favored : 79.04 % 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: 0.51 (0.28), residues: 915 helix: 0.85 (0.37), residues: 234 sheet: 0.84 (0.28), residues: 330 loop : -0.42 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 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 A 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 12) link_NAG-ASN : angle 1.41367 ( 36) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 0.91237 ( 9) hydrogen bonds : bond 0.03459 ( 211) hydrogen bonds : angle 4.63306 ( 534) SS BOND : bond 0.00444 ( 6) SS BOND : angle 0.80488 ( 12) covalent geometry : bond 0.00461 ( 7941) covalent geometry : angle 0.49649 (10803) *********************** 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: 28 poor density : 151 time to evaluate : 1.047 Fit side-chains REVERT: A 219 PHE cc_start: 0.8638 (t80) cc_final: 0.8301 (t80) REVERT: A 268 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7596 (ptm160) REVERT: B 188 PHE cc_start: 0.8752 (t80) cc_final: 0.8545 (t80) REVERT: B 268 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7845 (ptm160) REVERT: B 275 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7842 (tt0) REVERT: B 292 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8448 (mtm180) REVERT: C 36 ILE cc_start: 0.8153 (tp) cc_final: 0.7780 (tp) outliers start: 28 outliers final: 18 residues processed: 163 average time/residue: 1.3894 time to fit residues: 240.9955 Evaluate side-chains 172 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 64 SER 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 227 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 114 GLN B 120 HIS C 105 ASN C 120 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118363 restraints weight = 9910.258| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.32 r_work: 0.3308 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 7962 Z= 0.171 Angle : 0.496 4.947 10860 Z= 0.260 Chirality : 0.045 0.203 1257 Planarity : 0.004 0.046 1320 Dihedral : 7.487 59.209 1728 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.03 % Allowed : 17.80 % Favored : 79.17 % 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: 0.51 (0.28), residues: 915 helix: 0.84 (0.37), residues: 234 sheet: 0.87 (0.29), residues: 330 loop : -0.43 (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 0.003 0.000 ARG C 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.39747 ( 36) link_BETA1-4 : bond 0.00381 ( 3) link_BETA1-4 : angle 0.93193 ( 9) hydrogen bonds : bond 0.03382 ( 211) hydrogen bonds : angle 4.59594 ( 534) SS BOND : bond 0.00436 ( 6) SS BOND : angle 0.72755 ( 12) covalent geometry : bond 0.00420 ( 7941) covalent geometry : angle 0.48987 (10803) ********************** 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 173 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.861 Fit side-chains REVERT: A 219 PHE cc_start: 0.8635 (t80) cc_final: 0.8290 (t80) REVERT: A 268 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7602 (ptm160) REVERT: B 188 PHE cc_start: 0.8750 (t80) cc_final: 0.8539 (t80) REVERT: B 268 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7862 (ptm160) REVERT: B 275 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7858 (tt0) REVERT: B 292 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8438 (mtm180) REVERT: C 36 ILE cc_start: 0.8153 (tp) cc_final: 0.7776 (tp) outliers start: 24 outliers final: 18 residues processed: 160 average time/residue: 1.3335 time to fit residues: 225.8770 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 : 1.032 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 64 SER 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 227 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 4 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119098 restraints weight = 9924.698| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.34 r_work: 0.3313 rms_B_bonded: 2.82 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: 0.7781 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7962 Z= 0.130 Angle : 0.470 4.925 10860 Z= 0.247 Chirality : 0.044 0.198 1257 Planarity : 0.003 0.045 1320 Dihedral : 7.334 59.491 1728 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.53 % Allowed : 18.56 % Favored : 78.91 % 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 (0.29), residues: 915 helix: 0.82 (0.36), residues: 240 sheet: 0.92 (0.29), residues: 330 loop : -0.34 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 259 HIS 0.006 0.001 HIS C 120 PHE 0.016 0.001 PHE B 342 TYR 0.014 0.001 TYR A 90 ARG 0.002 0.000 ARG B 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 1.34230 ( 36) link_BETA1-4 : bond 0.00424 ( 3) link_BETA1-4 : angle 0.98891 ( 9) hydrogen bonds : bond 0.03102 ( 211) hydrogen bonds : angle 4.49547 ( 534) SS BOND : bond 0.00324 ( 6) SS BOND : angle 0.67823 ( 12) covalent geometry : bond 0.00316 ( 7941) covalent geometry : angle 0.46344 (10803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7344.86 seconds wall clock time: 127 minutes 49.20 seconds (7669.20 seconds total)