Starting phenix.real_space_refine on Fri Aug 22 16:52:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p6h_71309/08_2025/9p6h_71309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p6h_71309/08_2025/9p6h_71309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p6h_71309/08_2025/9p6h_71309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p6h_71309/08_2025/9p6h_71309.map" model { file = "/net/cci-nas-00/data/ceres_data/9p6h_71309/08_2025/9p6h_71309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p6h_71309/08_2025/9p6h_71309.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.036 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 21 5.16 5 C 3768 2.51 5 N 981 2.21 5 O 1192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5963 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2121 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 13, 'TRANS': 240} Chain: "B" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3611 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 27, 'TRANS': 419} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BGC': 1, 'FUL': 1, 'GCU': 1, 'MAN': 1, 'NGA': 2, 'RAM': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BGC': 1, 'FUL': 1, 'GCU': 1, 'MAN': 1, 'NGA': 2, 'RAM': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {'BGC': 1, 'GCU': 1, 'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BMA': 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.61, per 1000 atoms: 0.27 Number of scatterers: 5963 At special positions: 0 Unit cell: (93.72, 105.6, 91.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 21 16.00 O 1192 8.00 N 981 7.00 C 3768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 469 " distance=2.04 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=2, symmetry=0 Links applied ALPHA1-2 " MAN C 1 " - " GCU C 2 " " MAN D 1 " - " GCU D 2 " " MAN E 1 " - " GCU E 2 " ALPHA1-4 " BGC C 3 " - " FUL C 4 " ~> Even though FUL is a beta isomer, an alpha linkage is required... " BGC D 3 " - " FUL D 4 " BETA1-3 " NGA C 5 " - " NGA C 6 " " NGA D 5 " - " NGA D 6 " BETA1-4 " MAN C 1 " - " RAM C 7 " ~> Even though RAM is an alpha isomer, a beta linkage is required... " GCU C 2 " - " BGC C 3 " " FUL C 4 " - " NGA C 5 " " MAN D 1 " - " RAM D 7 " " GCU D 2 " - " BGC D 3 " " FUL D 4 " - " NGA D 5 " " MAN E 1 " - " RAM E 4 " " GCU E 2 " - " BGC E 3 " MAN-SER " MAN D 1 " - " SER B 106 " " MAN E 1 " - " SER B 68 " MAN-THR " MAN C 1 " - " THR B 222 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 396.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 9 sheets defined 29.2% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.694A pdb=" N LEU A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.525A pdb=" N LYS A 131 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 216 through 224 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.643A pdb=" N ARG A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 92 through 114 removed outlier: 3.644A pdb=" N PHE B 99 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 192 through 196 Processing helix chain 'B' and resid 198 through 203 removed outlier: 4.041A pdb=" N ASN B 203 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 245 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.662A pdb=" N THR B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.744A pdb=" N ASP B 284 " --> pdb=" O PRO B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 428 through 431 Processing helix chain 'B' and resid 444 through 449 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 118 removed outlier: 4.072A pdb=" N PHE A 212 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE A 188 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR A 178 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE A 190 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A 176 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 170 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 256 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A 77 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE A 254 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 228 removed outlier: 3.722A pdb=" N SER A 239 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.544A pdb=" N PHE B 84 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 61 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 127 removed outlier: 8.281A pdb=" N LYS B 124 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR B 126 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 164 Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 185 Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 225 Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 457 removed outlier: 5.404A pdb=" N THR B 402 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG B 437 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR B 400 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA B 397 " --> pdb=" O GLY B 466 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 432 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: 0.94 Time building geometry restraints manager: 0.92 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: 1219 1.33 - 1.46: 1888 1.46 - 1.59: 2971 1.59 - 1.72: 0 1.72 - 1.84: 36 Bond restraints: 6114 Sorted by residual: bond pdb=" C1 FUL C 4 " pdb=" O5 FUL C 4 " ideal model delta sigma weight residual 1.392 1.507 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C1 FUL D 4 " pdb=" O5 FUL D 4 " ideal model delta sigma weight residual 1.392 1.498 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C1 RAM E 4 " pdb=" O5 RAM E 4 " ideal model delta sigma weight residual 1.401 1.506 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 RAM D 7 " pdb=" O5 RAM D 7 " ideal model delta sigma weight residual 1.401 1.501 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASP B 211 " pdb=" CA ASP B 211 " ideal model delta sigma weight residual 1.453 1.491 -0.037 1.16e-02 7.43e+03 1.02e+01 ... (remaining 6109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 7782 1.80 - 3.60: 427 3.60 - 5.41: 74 5.41 - 7.21: 13 7.21 - 9.01: 5 Bond angle restraints: 8301 Sorted by residual: angle pdb=" CA THR B 222 " pdb=" CB THR B 222 " pdb=" OG1 THR B 222 " ideal model delta sigma weight residual 109.60 102.21 7.39 1.50e+00 4.44e-01 2.43e+01 angle pdb=" N MET A 302 " pdb=" CA MET A 302 " pdb=" C MET A 302 " ideal model delta sigma weight residual 112.38 106.60 5.78 1.22e+00 6.72e-01 2.24e+01 angle pdb=" N VAL B 215 " pdb=" CA VAL B 215 " pdb=" CB VAL B 215 " ideal model delta sigma weight residual 110.99 116.47 -5.48 1.20e+00 6.94e-01 2.08e+01 angle pdb=" N TYR A 90 " pdb=" CA TYR A 90 " pdb=" CB TYR A 90 " ideal model delta sigma weight residual 110.37 118.15 -7.78 1.78e+00 3.16e-01 1.91e+01 angle pdb=" N GLU A 167 " pdb=" CA GLU A 167 " pdb=" C GLU A 167 " ideal model delta sigma weight residual 113.41 108.55 4.86 1.22e+00 6.72e-01 1.59e+01 ... (remaining 8296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 3603 24.66 - 49.31: 174 49.31 - 73.96: 33 73.96 - 98.62: 58 98.62 - 123.27: 41 Dihedral angle restraints: 3909 sinusoidal: 1841 harmonic: 2068 Sorted by residual: dihedral pdb=" C2 FUL D 4 " pdb=" C1 FUL D 4 " pdb=" O5 FUL D 4 " pdb=" C5 FUL D 4 " ideal model delta sinusoidal sigma weight residual 61.43 -61.84 123.27 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O2 FUL D 4 " pdb=" C1 FUL D 4 " pdb=" C2 FUL D 4 " pdb=" O5 FUL D 4 " ideal model delta sinusoidal sigma weight residual 181.32 63.47 117.85 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" O2 BMA A 401 " pdb=" C1 BMA A 401 " pdb=" C2 BMA A 401 " pdb=" O5 BMA A 401 " ideal model delta sinusoidal sigma weight residual 60.15 177.47 -117.32 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 3906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 701 0.054 - 0.107: 165 0.107 - 0.161: 38 0.161 - 0.214: 12 0.214 - 0.268: 6 Chirality restraints: 922 Sorted by residual: chirality pdb=" C1 BGC C 3 " pdb=" O4 GCU C 2 " pdb=" C2 BGC C 3 " pdb=" O5 BGC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.39e+02 chirality pdb=" C1 FUL C 4 " pdb=" O4 BGC C 3 " pdb=" C2 FUL C 4 " pdb=" O5 FUL C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-02 2.50e+03 7.15e+01 chirality pdb=" C5 BMA A 402 " pdb=" C4 BMA A 402 " pdb=" C6 BMA A 402 " pdb=" O5 BMA A 402 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 919 not shown) Planarity restraints: 1057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NGA C 6 " 0.344 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NGA C 6 " -0.090 2.00e-02 2.50e+03 pdb=" C8 NGA C 6 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NGA C 6 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NGA C 6 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NGA D 5 " 0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NGA D 5 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NGA D 5 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NGA D 5 " -0.517 2.00e-02 2.50e+03 pdb=" O7 NGA D 5 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NGA C 5 " 0.343 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NGA C 5 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NGA C 5 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NGA C 5 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NGA C 5 " 0.083 2.00e-02 2.50e+03 ... (remaining 1054 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 793 2.75 - 3.29: 5921 3.29 - 3.83: 10197 3.83 - 4.36: 12430 4.36 - 4.90: 20201 Nonbonded interactions: 49542 Sorted by model distance: nonbonded pdb=" OG1 THR A 271 " pdb=" OD1 ASP A 273 " model vdw 2.215 3.040 nonbonded pdb=" ND2 ASN B 174 " pdb=" OD1 ASP B 176 " model vdw 2.226 3.120 nonbonded pdb=" NE1 TRP B 330 " pdb=" OE1 GLU B 398 " model vdw 2.261 3.120 nonbonded pdb=" OE2 GLU B 327 " pdb=" NH2 ARG B 437 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLU A 175 " pdb=" OH TYR A 250 " model vdw 2.306 3.040 ... (remaining 49537 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 'C' selection = chain 'D' } 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: 0.450 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.960 Find NCS groups from input model: 0.030 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 6135 Z= 0.432 Angle : 1.013 20.821 8354 Z= 0.558 Chirality : 0.055 0.268 922 Planarity : 0.019 0.292 1057 Dihedral : 23.350 123.275 2578 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 0.32 % Allowed : 1.29 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.32), residues: 697 helix: 0.82 (0.44), residues: 155 sheet: -1.48 (0.47), residues: 89 loop : -0.73 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 354 TYR 0.019 0.001 TYR A 90 PHE 0.017 0.001 PHE A 102 TRP 0.012 0.001 TRP B 399 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 6114) covalent geometry : angle 0.93133 ( 8301) SS BOND : bond 0.00781 ( 1) SS BOND : angle 3.16627 ( 2) hydrogen bonds : bond 0.18419 ( 160) hydrogen bonds : angle 7.28977 ( 432) Misc. bond : bond 0.07619 ( 2) link_ALPHA1-2 : bond 0.02840 ( 3) link_ALPHA1-2 : angle 4.09775 ( 9) link_ALPHA1-4 : bond 0.02301 ( 2) link_ALPHA1-4 : angle 8.89269 ( 6) link_BETA1-3 : bond 0.00483 ( 2) link_BETA1-3 : angle 1.24901 ( 6) link_BETA1-4 : bond 0.02558 ( 8) link_BETA1-4 : angle 3.45888 ( 24) link_MAN-SER : bond 0.05194 ( 2) link_MAN-SER : angle 9.56518 ( 4) link_MAN-THR : bond 0.05215 ( 1) link_MAN-THR : angle 5.99737 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.239 Fit side-chains REVERT: B 188 ARG cc_start: 0.8104 (tpt-90) cc_final: 0.7075 (mmp-170) REVERT: B 276 MET cc_start: 0.8366 (mmt) cc_final: 0.8117 (mmm) outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 0.8464 time to fit residues: 71.7340 Evaluate side-chains 52 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 174 ASN B 248 ASN B 267 ASN B 385 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085602 restraints weight = 9657.136| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.73 r_work: 0.2997 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6135 Z= 0.140 Angle : 0.722 9.366 8354 Z= 0.331 Chirality : 0.050 0.424 922 Planarity : 0.005 0.051 1057 Dihedral : 22.567 104.702 1176 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.30 % Favored : 96.41 % Rotamer: Outliers : 1.61 % Allowed : 8.06 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.32), residues: 697 helix: 0.86 (0.43), residues: 165 sheet: -1.03 (0.59), residues: 63 loop : -0.56 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 354 TYR 0.019 0.001 TYR A 90 PHE 0.025 0.001 PHE A 102 TRP 0.010 0.001 TRP B 399 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6114) covalent geometry : angle 0.69448 ( 8301) SS BOND : bond 0.00913 ( 1) SS BOND : angle 3.14269 ( 2) hydrogen bonds : bond 0.03942 ( 160) hydrogen bonds : angle 5.78403 ( 432) Misc. bond : bond 0.00271 ( 2) link_ALPHA1-2 : bond 0.00652 ( 3) link_ALPHA1-2 : angle 2.06232 ( 9) link_ALPHA1-4 : bond 0.01345 ( 2) link_ALPHA1-4 : angle 2.64298 ( 6) link_BETA1-3 : bond 0.00280 ( 2) link_BETA1-3 : angle 4.72987 ( 6) link_BETA1-4 : bond 0.01373 ( 8) link_BETA1-4 : angle 2.06802 ( 24) link_MAN-SER : bond 0.00532 ( 2) link_MAN-SER : angle 1.80936 ( 4) link_MAN-THR : bond 0.00354 ( 1) link_MAN-THR : angle 1.17105 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.208 Fit side-chains REVERT: A 146 GLN cc_start: 0.8396 (pp30) cc_final: 0.7684 (pp30) REVERT: B 188 ARG cc_start: 0.8538 (tpt-90) cc_final: 0.6930 (mmp-170) REVERT: B 276 MET cc_start: 0.8790 (mmt) cc_final: 0.8449 (mmm) REVERT: B 459 ASN cc_start: 0.8969 (t0) cc_final: 0.8749 (t0) outliers start: 10 outliers final: 3 residues processed: 68 average time/residue: 0.8370 time to fit residues: 58.9495 Evaluate side-chains 53 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain B residue 305 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 93 ASN B 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.081733 restraints weight = 9603.292| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.75 r_work: 0.2950 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6135 Z= 0.215 Angle : 0.726 8.407 8354 Z= 0.334 Chirality : 0.049 0.323 922 Planarity : 0.005 0.055 1057 Dihedral : 19.065 105.350 1174 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.27 % Rotamer: Outliers : 1.61 % Allowed : 11.13 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.32), residues: 697 helix: 0.87 (0.43), residues: 167 sheet: -1.35 (0.48), residues: 88 loop : -0.47 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 354 TYR 0.011 0.001 TYR B 429 PHE 0.021 0.002 PHE A 102 TRP 0.007 0.001 TRP B 345 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 6114) covalent geometry : angle 0.69525 ( 8301) SS BOND : bond 0.00471 ( 1) SS BOND : angle 4.29653 ( 2) hydrogen bonds : bond 0.03863 ( 160) hydrogen bonds : angle 5.58528 ( 432) Misc. bond : bond 0.00039 ( 2) link_ALPHA1-2 : bond 0.00581 ( 3) link_ALPHA1-2 : angle 2.22431 ( 9) link_ALPHA1-4 : bond 0.01104 ( 2) link_ALPHA1-4 : angle 3.37212 ( 6) link_BETA1-3 : bond 0.00563 ( 2) link_BETA1-3 : angle 4.20381 ( 6) link_BETA1-4 : bond 0.01257 ( 8) link_BETA1-4 : angle 2.11488 ( 24) link_MAN-SER : bond 0.00257 ( 2) link_MAN-SER : angle 2.21911 ( 4) link_MAN-THR : bond 0.00353 ( 1) link_MAN-THR : angle 1.87420 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.265 Fit side-chains REVERT: A 146 GLN cc_start: 0.8427 (pp30) cc_final: 0.7686 (pp30) REVERT: B 188 ARG cc_start: 0.8583 (tpt-90) cc_final: 0.6968 (mmp-170) outliers start: 10 outliers final: 3 residues processed: 61 average time/residue: 0.8472 time to fit residues: 53.5895 Evaluate side-chains 56 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.0370 chunk 12 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084965 restraints weight = 9576.229| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.76 r_work: 0.2994 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6135 Z= 0.115 Angle : 0.671 9.188 8354 Z= 0.303 Chirality : 0.046 0.291 922 Planarity : 0.005 0.055 1057 Dihedral : 16.388 102.290 1174 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.27 % Rotamer: Outliers : 0.97 % Allowed : 12.58 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.32), residues: 697 helix: 1.10 (0.43), residues: 166 sheet: -1.54 (0.59), residues: 64 loop : -0.36 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 354 TYR 0.011 0.001 TYR A 90 PHE 0.017 0.001 PHE A 102 TRP 0.010 0.001 TRP B 399 HIS 0.002 0.000 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6114) covalent geometry : angle 0.63937 ( 8301) SS BOND : bond 0.01303 ( 1) SS BOND : angle 3.15958 ( 2) hydrogen bonds : bond 0.03176 ( 160) hydrogen bonds : angle 5.21748 ( 432) Misc. bond : bond 0.00056 ( 2) link_ALPHA1-2 : bond 0.00509 ( 3) link_ALPHA1-2 : angle 1.98303 ( 9) link_ALPHA1-4 : bond 0.01286 ( 2) link_ALPHA1-4 : angle 3.36740 ( 6) link_BETA1-3 : bond 0.00620 ( 2) link_BETA1-3 : angle 4.64150 ( 6) link_BETA1-4 : bond 0.01144 ( 8) link_BETA1-4 : angle 2.07666 ( 24) link_MAN-SER : bond 0.00298 ( 2) link_MAN-SER : angle 1.62255 ( 4) link_MAN-THR : bond 0.00071 ( 1) link_MAN-THR : angle 1.09722 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8584 (p90) cc_final: 0.7877 (p90) REVERT: A 146 GLN cc_start: 0.8434 (pp30) cc_final: 0.7658 (pp30) REVERT: A 297 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8516 (pp30) REVERT: B 65 GLU cc_start: 0.7563 (pp20) cc_final: 0.7356 (pp20) REVERT: B 128 ASN cc_start: 0.7983 (t0) cc_final: 0.7525 (t0) REVERT: B 188 ARG cc_start: 0.8613 (tpt-90) cc_final: 0.6994 (mmp-170) REVERT: B 319 MET cc_start: 0.8202 (tpp) cc_final: 0.7802 (tpt) REVERT: B 420 GLU cc_start: 0.8932 (tt0) cc_final: 0.8622 (tm-30) REVERT: B 442 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8540 (pttp) REVERT: B 459 ASN cc_start: 0.8930 (t0) cc_final: 0.8680 (t0) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 0.7974 time to fit residues: 57.1330 Evaluate side-chains 61 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 442 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.084294 restraints weight = 9671.663| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.76 r_work: 0.3019 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6135 Z= 0.150 Angle : 0.686 9.211 8354 Z= 0.310 Chirality : 0.046 0.253 922 Planarity : 0.005 0.058 1057 Dihedral : 14.979 100.834 1174 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.44 % Favored : 96.41 % Rotamer: Outliers : 1.29 % Allowed : 13.06 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.32), residues: 697 helix: 1.38 (0.44), residues: 159 sheet: -1.63 (0.50), residues: 82 loop : -0.17 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 354 TYR 0.007 0.001 TYR A 171 PHE 0.016 0.001 PHE A 102 TRP 0.007 0.001 TRP A 301 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6114) covalent geometry : angle 0.65098 ( 8301) SS BOND : bond 0.00743 ( 1) SS BOND : angle 3.79204 ( 2) hydrogen bonds : bond 0.03241 ( 160) hydrogen bonds : angle 5.21643 ( 432) Misc. bond : bond 0.00096 ( 2) link_ALPHA1-2 : bond 0.00509 ( 3) link_ALPHA1-2 : angle 2.12800 ( 9) link_ALPHA1-4 : bond 0.01211 ( 2) link_ALPHA1-4 : angle 3.52845 ( 6) link_BETA1-3 : bond 0.00442 ( 2) link_BETA1-3 : angle 4.97711 ( 6) link_BETA1-4 : bond 0.01127 ( 8) link_BETA1-4 : angle 2.06596 ( 24) link_MAN-SER : bond 0.00226 ( 2) link_MAN-SER : angle 1.84230 ( 4) link_MAN-THR : bond 0.00160 ( 1) link_MAN-THR : angle 1.31131 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8642 (p90) cc_final: 0.7987 (p90) REVERT: A 140 ARG cc_start: 0.7620 (ptm-80) cc_final: 0.7062 (tmt-80) REVERT: A 146 GLN cc_start: 0.8491 (pp30) cc_final: 0.7718 (pp30) REVERT: A 258 GLU cc_start: 0.8832 (tt0) cc_final: 0.7573 (pm20) REVERT: A 297 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8631 (pp30) REVERT: B 128 ASN cc_start: 0.8009 (t0) cc_final: 0.7522 (t0) REVERT: B 188 ARG cc_start: 0.8570 (tpt-90) cc_final: 0.7132 (mmp-170) REVERT: B 319 MET cc_start: 0.8302 (tpp) cc_final: 0.7926 (tpt) REVERT: B 442 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8684 (pttp) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.8441 time to fit residues: 58.6963 Evaluate side-chains 62 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.085047 restraints weight = 9710.279| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.77 r_work: 0.3000 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6135 Z= 0.122 Angle : 0.676 9.799 8354 Z= 0.304 Chirality : 0.046 0.252 922 Planarity : 0.005 0.055 1057 Dihedral : 13.094 96.682 1174 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.29 % Allowed : 14.35 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.32), residues: 697 helix: 1.23 (0.43), residues: 166 sheet: -1.64 (0.56), residues: 64 loop : -0.18 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 354 TYR 0.007 0.001 TYR B 368 PHE 0.013 0.001 PHE A 102 TRP 0.012 0.001 TRP A 301 HIS 0.002 0.001 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6114) covalent geometry : angle 0.63917 ( 8301) SS BOND : bond 0.00426 ( 1) SS BOND : angle 3.42691 ( 2) hydrogen bonds : bond 0.03012 ( 160) hydrogen bonds : angle 5.01394 ( 432) Misc. bond : bond 0.00201 ( 2) link_ALPHA1-2 : bond 0.00444 ( 3) link_ALPHA1-2 : angle 1.97646 ( 9) link_ALPHA1-4 : bond 0.01279 ( 2) link_ALPHA1-4 : angle 3.82176 ( 6) link_BETA1-3 : bond 0.00536 ( 2) link_BETA1-3 : angle 5.16371 ( 6) link_BETA1-4 : bond 0.01165 ( 8) link_BETA1-4 : angle 2.05840 ( 24) link_MAN-SER : bond 0.00196 ( 2) link_MAN-SER : angle 1.64621 ( 4) link_MAN-THR : bond 0.00025 ( 1) link_MAN-THR : angle 1.02064 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8571 (p90) cc_final: 0.7874 (p90) REVERT: A 140 ARG cc_start: 0.7552 (ptm-80) cc_final: 0.7134 (tmt-80) REVERT: A 146 GLN cc_start: 0.8474 (pp30) cc_final: 0.7704 (pp30) REVERT: A 258 GLU cc_start: 0.8830 (tt0) cc_final: 0.7443 (pm20) REVERT: A 297 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8554 (pp30) REVERT: B 128 ASN cc_start: 0.8022 (t0) cc_final: 0.7504 (t0) REVERT: B 160 SER cc_start: 0.8609 (m) cc_final: 0.8351 (p) REVERT: B 188 ARG cc_start: 0.8556 (tpt-90) cc_final: 0.6997 (mmp-170) REVERT: B 442 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8478 (pttp) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.8368 time to fit residues: 59.9268 Evaluate side-chains 63 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 442 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086339 restraints weight = 9745.748| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.77 r_work: 0.3019 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6135 Z= 0.110 Angle : 0.662 10.765 8354 Z= 0.296 Chirality : 0.045 0.238 922 Planarity : 0.005 0.053 1057 Dihedral : 12.071 92.836 1174 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer: Outliers : 1.45 % Allowed : 15.32 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.32), residues: 697 helix: 1.22 (0.43), residues: 167 sheet: -1.70 (0.49), residues: 82 loop : -0.06 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 354 TYR 0.007 0.001 TYR B 368 PHE 0.012 0.001 PHE A 102 TRP 0.012 0.001 TRP A 301 HIS 0.002 0.000 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6114) covalent geometry : angle 0.62340 ( 8301) SS BOND : bond 0.00831 ( 1) SS BOND : angle 3.65979 ( 2) hydrogen bonds : bond 0.02903 ( 160) hydrogen bonds : angle 4.88246 ( 432) Misc. bond : bond 0.00009 ( 2) link_ALPHA1-2 : bond 0.00450 ( 3) link_ALPHA1-2 : angle 1.95126 ( 9) link_ALPHA1-4 : bond 0.01396 ( 2) link_ALPHA1-4 : angle 4.05632 ( 6) link_BETA1-3 : bond 0.00601 ( 2) link_BETA1-3 : angle 5.16583 ( 6) link_BETA1-4 : bond 0.01116 ( 8) link_BETA1-4 : angle 2.04035 ( 24) link_MAN-SER : bond 0.00209 ( 2) link_MAN-SER : angle 1.45741 ( 4) link_MAN-THR : bond 0.00009 ( 1) link_MAN-THR : angle 0.96991 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8617 (p90) cc_final: 0.7942 (p90) REVERT: A 140 ARG cc_start: 0.7520 (ptm-80) cc_final: 0.7095 (tmt-80) REVERT: A 146 GLN cc_start: 0.8478 (pp30) cc_final: 0.7698 (pp30) REVERT: A 258 GLU cc_start: 0.8863 (tt0) cc_final: 0.7498 (pm20) REVERT: A 297 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8518 (pp30) REVERT: B 128 ASN cc_start: 0.8126 (t0) cc_final: 0.7633 (t0) REVERT: B 149 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8514 (mmm160) REVERT: B 160 SER cc_start: 0.8556 (m) cc_final: 0.8270 (p) REVERT: B 188 ARG cc_start: 0.8398 (tpt-90) cc_final: 0.6818 (mmp-170) REVERT: B 319 MET cc_start: 0.8084 (tpp) cc_final: 0.7770 (tpt) REVERT: B 442 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8433 (pttp) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 0.8239 time to fit residues: 55.6168 Evaluate side-chains 62 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 442 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086457 restraints weight = 9706.991| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.76 r_work: 0.3025 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6135 Z= 0.118 Angle : 0.673 11.074 8354 Z= 0.302 Chirality : 0.045 0.272 922 Planarity : 0.005 0.055 1057 Dihedral : 11.336 87.304 1174 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 15.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.32), residues: 697 helix: 1.34 (0.43), residues: 161 sheet: -1.63 (0.50), residues: 82 loop : 0.03 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 354 TYR 0.007 0.001 TYR A 171 PHE 0.013 0.001 PHE A 102 TRP 0.012 0.001 TRP A 301 HIS 0.001 0.000 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6114) covalent geometry : angle 0.63560 ( 8301) SS BOND : bond 0.01630 ( 1) SS BOND : angle 3.06289 ( 2) hydrogen bonds : bond 0.02905 ( 160) hydrogen bonds : angle 4.88030 ( 432) Misc. bond : bond 0.00028 ( 2) link_ALPHA1-2 : bond 0.00460 ( 3) link_ALPHA1-2 : angle 1.96361 ( 9) link_ALPHA1-4 : bond 0.01408 ( 2) link_ALPHA1-4 : angle 4.28349 ( 6) link_BETA1-3 : bond 0.00836 ( 2) link_BETA1-3 : angle 5.07514 ( 6) link_BETA1-4 : bond 0.01191 ( 8) link_BETA1-4 : angle 2.05691 ( 24) link_MAN-SER : bond 0.00174 ( 2) link_MAN-SER : angle 1.43108 ( 4) link_MAN-THR : bond 0.00054 ( 1) link_MAN-THR : angle 0.91126 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8596 (p90) cc_final: 0.7916 (p90) REVERT: A 129 GLN cc_start: 0.8898 (tt0) cc_final: 0.8684 (pt0) REVERT: A 140 ARG cc_start: 0.7504 (ptm-80) cc_final: 0.7085 (tmt-80) REVERT: A 146 GLN cc_start: 0.8520 (pp30) cc_final: 0.7753 (pp30) REVERT: A 258 GLU cc_start: 0.8845 (tt0) cc_final: 0.7497 (pm20) REVERT: A 297 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8537 (pp30) REVERT: B 128 ASN cc_start: 0.8107 (t0) cc_final: 0.7679 (t0) REVERT: B 149 ARG cc_start: 0.8902 (mmm160) cc_final: 0.7395 (mmm160) REVERT: B 160 SER cc_start: 0.8565 (m) cc_final: 0.8280 (p) REVERT: B 188 ARG cc_start: 0.8487 (tpt-90) cc_final: 0.6831 (mmp-170) REVERT: B 319 MET cc_start: 0.8080 (tpp) cc_final: 0.7781 (tpt) REVERT: B 420 GLU cc_start: 0.9038 (tt0) cc_final: 0.8719 (tm-30) REVERT: B 442 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8472 (pttp) outliers start: 13 outliers final: 8 residues processed: 70 average time/residue: 0.7749 time to fit residues: 56.3365 Evaluate side-chains 68 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.0020 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.120865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087483 restraints weight = 9660.275| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.77 r_work: 0.3066 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6135 Z= 0.116 Angle : 0.678 11.469 8354 Z= 0.304 Chirality : 0.045 0.258 922 Planarity : 0.005 0.061 1057 Dihedral : 11.065 82.429 1174 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.61 % Allowed : 16.29 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.32), residues: 697 helix: 1.38 (0.43), residues: 161 sheet: -1.61 (0.50), residues: 82 loop : 0.02 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 354 TYR 0.007 0.001 TYR A 171 PHE 0.013 0.001 PHE A 102 TRP 0.009 0.001 TRP A 301 HIS 0.001 0.000 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6114) covalent geometry : angle 0.64045 ( 8301) SS BOND : bond 0.00787 ( 1) SS BOND : angle 3.31089 ( 2) hydrogen bonds : bond 0.02892 ( 160) hydrogen bonds : angle 4.84447 ( 432) Misc. bond : bond 0.00017 ( 2) link_ALPHA1-2 : bond 0.00446 ( 3) link_ALPHA1-2 : angle 1.95317 ( 9) link_ALPHA1-4 : bond 0.01395 ( 2) link_ALPHA1-4 : angle 4.43563 ( 6) link_BETA1-3 : bond 0.00762 ( 2) link_BETA1-3 : angle 5.08023 ( 6) link_BETA1-4 : bond 0.01153 ( 8) link_BETA1-4 : angle 2.03860 ( 24) link_MAN-SER : bond 0.00168 ( 2) link_MAN-SER : angle 1.40284 ( 4) link_MAN-THR : bond 0.00058 ( 1) link_MAN-THR : angle 0.88075 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8542 (p90) cc_final: 0.7959 (p90) REVERT: A 132 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7975 (tp) REVERT: A 140 ARG cc_start: 0.7403 (ptm-80) cc_final: 0.6972 (tmt-80) REVERT: A 146 GLN cc_start: 0.8559 (pp30) cc_final: 0.7777 (pp30) REVERT: A 258 GLU cc_start: 0.8789 (tt0) cc_final: 0.7591 (pm20) REVERT: A 297 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8608 (pp30) REVERT: B 128 ASN cc_start: 0.8095 (t0) cc_final: 0.7669 (t0) REVERT: B 148 LYS cc_start: 0.9251 (pptt) cc_final: 0.8848 (pptt) REVERT: B 160 SER cc_start: 0.8583 (m) cc_final: 0.8347 (p) REVERT: B 188 ARG cc_start: 0.8557 (tpt-90) cc_final: 0.6974 (mmp-170) REVERT: B 319 MET cc_start: 0.8151 (tpp) cc_final: 0.7903 (tpt) REVERT: B 420 GLU cc_start: 0.8964 (tt0) cc_final: 0.8712 (tm-30) REVERT: B 442 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8635 (pttp) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.8156 time to fit residues: 55.0261 Evaluate side-chains 64 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.087077 restraints weight = 9700.582| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.76 r_work: 0.3033 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6135 Z= 0.117 Angle : 0.688 11.552 8354 Z= 0.308 Chirality : 0.045 0.260 922 Planarity : 0.005 0.069 1057 Dihedral : 10.463 70.558 1174 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.13 % Allowed : 16.61 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.32), residues: 697 helix: 1.39 (0.43), residues: 161 sheet: -1.63 (0.50), residues: 82 loop : 0.03 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 354 TYR 0.007 0.001 TYR B 368 PHE 0.012 0.001 PHE A 102 TRP 0.012 0.001 TRP A 301 HIS 0.001 0.000 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6114) covalent geometry : angle 0.64919 ( 8301) SS BOND : bond 0.00825 ( 1) SS BOND : angle 3.12407 ( 2) hydrogen bonds : bond 0.02863 ( 160) hydrogen bonds : angle 4.80511 ( 432) Misc. bond : bond 0.00011 ( 2) link_ALPHA1-2 : bond 0.00451 ( 3) link_ALPHA1-2 : angle 1.93571 ( 9) link_ALPHA1-4 : bond 0.01407 ( 2) link_ALPHA1-4 : angle 4.81402 ( 6) link_BETA1-3 : bond 0.00767 ( 2) link_BETA1-3 : angle 5.04034 ( 6) link_BETA1-4 : bond 0.01198 ( 8) link_BETA1-4 : angle 2.04301 ( 24) link_MAN-SER : bond 0.00161 ( 2) link_MAN-SER : angle 1.34950 ( 4) link_MAN-THR : bond 0.00047 ( 1) link_MAN-THR : angle 0.86488 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.8470 (p90) cc_final: 0.7850 (p90) REVERT: A 132 ILE cc_start: 0.8256 (tt) cc_final: 0.7898 (tp) REVERT: A 140 ARG cc_start: 0.7346 (ptm-80) cc_final: 0.6901 (tmt-80) REVERT: A 146 GLN cc_start: 0.8525 (pp30) cc_final: 0.7750 (pp30) REVERT: A 258 GLU cc_start: 0.8820 (tt0) cc_final: 0.7411 (pm20) REVERT: A 297 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8563 (pp30) REVERT: B 128 ASN cc_start: 0.8095 (t0) cc_final: 0.7659 (t0) REVERT: B 160 SER cc_start: 0.8442 (m) cc_final: 0.8174 (p) REVERT: B 188 ARG cc_start: 0.8471 (tpt-90) cc_final: 0.6814 (mmp-170) REVERT: B 319 MET cc_start: 0.8189 (tpp) cc_final: 0.7891 (tpt) REVERT: B 442 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8454 (pttp) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 0.8032 time to fit residues: 51.7006 Evaluate side-chains 63 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.084685 restraints weight = 9764.969| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.76 r_work: 0.2995 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6135 Z= 0.157 Angle : 0.694 11.607 8354 Z= 0.314 Chirality : 0.046 0.259 922 Planarity : 0.005 0.063 1057 Dihedral : 9.814 68.950 1174 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.61 % Allowed : 16.29 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.32), residues: 697 helix: 1.46 (0.44), residues: 160 sheet: -1.50 (0.46), residues: 98 loop : -0.01 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 354 TYR 0.007 0.001 TYR B 250 PHE 0.012 0.001 PHE A 102 TRP 0.007 0.001 TRP A 301 HIS 0.002 0.000 HIS B 455 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6114) covalent geometry : angle 0.65169 ( 8301) SS BOND : bond 0.01018 ( 1) SS BOND : angle 3.64695 ( 2) hydrogen bonds : bond 0.03058 ( 160) hydrogen bonds : angle 4.92301 ( 432) Misc. bond : bond 0.00014 ( 2) link_ALPHA1-2 : bond 0.00476 ( 3) link_ALPHA1-2 : angle 2.06162 ( 9) link_ALPHA1-4 : bond 0.01409 ( 2) link_ALPHA1-4 : angle 5.04256 ( 6) link_BETA1-3 : bond 0.00817 ( 2) link_BETA1-3 : angle 4.96862 ( 6) link_BETA1-4 : bond 0.01121 ( 8) link_BETA1-4 : angle 2.18296 ( 24) link_MAN-SER : bond 0.00138 ( 2) link_MAN-SER : angle 1.66216 ( 4) link_MAN-THR : bond 0.00235 ( 1) link_MAN-THR : angle 1.06729 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2640.37 seconds wall clock time: 45 minutes 47.74 seconds (2747.74 seconds total)