Starting phenix.real_space_refine on Sun Apr 27 22:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8urt_42500/04_2025/8urt_42500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8urt_42500/04_2025/8urt_42500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8urt_42500/04_2025/8urt_42500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8urt_42500/04_2025/8urt_42500.map" model { file = "/net/cci-nas-00/data/ceres_data/8urt_42500/04_2025/8urt_42500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8urt_42500/04_2025/8urt_42500.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 42 5.16 5 C 4474 2.51 5 N 956 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6622 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Unusual residues: {'ACE': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369} Chain: "B" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Unusual residues: {'ACE': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369} Chain: "A" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 244 Unusual residues: {' MG': 2, 'CTI': 1, 'PCW': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 136 Unusual residues: {' MG': 2, 'CTI': 1, 'PCW': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.02, per 1000 atoms: 0.76 Number of scatterers: 6622 At special positions: 0 Unit cell: (89.64, 103.68, 76.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Mg 4 11.99 O 1140 8.00 N 956 7.00 C 4474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 903.7 milliseconds 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1460 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 79.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 removed outlier: 4.757A pdb=" N GLY A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 14 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 30 through 39 removed outlier: 4.302A pdb=" N PHE A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 4.099A pdb=" N PHE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 removed outlier: 3.721A pdb=" N PHE A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 86 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 106 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.713A pdb=" N GLU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 141 through 165 removed outlier: 3.905A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.793A pdb=" N ILE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 217 through 250 Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.649A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 removed outlier: 3.904A pdb=" N ILE A 289 " --> pdb=" O PRO A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 290 through 314 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 326 through 341 Processing helix chain 'A' and resid 349 through 381 removed outlier: 4.284A pdb=" N TRP A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 removed outlier: 4.753A pdb=" N GLY B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 14 " --> pdb=" O GLY B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 30 through 39 removed outlier: 4.403A pdb=" N PHE B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 50 through 70 Processing helix chain 'B' and resid 78 through 107 removed outlier: 3.972A pdb=" N TYR B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 137 removed outlier: 3.704A pdb=" N GLU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.870A pdb=" N ILE B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 217 through 252 removed outlier: 4.142A pdb=" N ASN B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.504A pdb=" N THR B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 285 Processing helix chain 'B' and resid 286 through 289 removed outlier: 3.984A pdb=" N ILE B 289 " --> pdb=" O PRO B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 290 through 315 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.587A pdb=" N LEU B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 381 removed outlier: 3.833A pdb=" N ILE B 349 " --> pdb=" O GLN B 345 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 204 removed outlier: 7.146A pdb=" N VAL A 215 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 205 removed outlier: 7.370A pdb=" N VAL B 215 " --> pdb=" O VAL B 203 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1293 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: 1.99 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 932 1.31 - 1.43: 2069 1.43 - 1.56: 3727 1.56 - 1.68: 22 1.68 - 1.81: 68 Bond restraints: 6818 Sorted by residual: bond pdb=" C11 PCW A1003 " pdb=" O3 PCW A1003 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C11 PCW A1004 " pdb=" O3 PCW A1004 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C11 PCW A1006 " pdb=" O3 PCW A1006 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C11 PCW B 401 " pdb=" O3 PCW B 401 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C11 PCW A1007 " pdb=" O3 PCW A1007 " ideal model delta sigma weight residual 1.326 1.420 -0.094 2.00e-02 2.50e+03 2.19e+01 ... (remaining 6813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 9144 5.03 - 10.07: 58 10.07 - 15.10: 15 15.10 - 20.14: 9 20.14 - 25.17: 12 Bond angle restraints: 9238 Sorted by residual: angle pdb=" C19 PCW A1007 " pdb=" C20 PCW A1007 " pdb=" C21 PCW A1007 " ideal model delta sigma weight residual 127.82 152.99 -25.17 3.00e+00 1.11e-01 7.04e+01 angle pdb=" C19 PCW B 404 " pdb=" C20 PCW B 404 " pdb=" C21 PCW B 404 " ideal model delta sigma weight residual 127.82 152.99 -25.17 3.00e+00 1.11e-01 7.04e+01 angle pdb=" C19 PCW B 401 " pdb=" C20 PCW B 401 " pdb=" C21 PCW B 401 " ideal model delta sigma weight residual 127.82 152.75 -24.93 3.00e+00 1.11e-01 6.91e+01 angle pdb=" C19 PCW A1004 " pdb=" C20 PCW A1004 " pdb=" C21 PCW A1004 " ideal model delta sigma weight residual 127.82 152.71 -24.89 3.00e+00 1.11e-01 6.89e+01 angle pdb=" C19 PCW A1006 " pdb=" C20 PCW A1006 " pdb=" C21 PCW A1006 " ideal model delta sigma weight residual 127.82 152.58 -24.76 3.00e+00 1.11e-01 6.81e+01 ... (remaining 9233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.25: 3634 31.25 - 62.50: 279 62.50 - 93.75: 34 93.75 - 125.00: 2 125.00 - 156.25: 5 Dihedral angle restraints: 3954 sinusoidal: 1676 harmonic: 2278 Sorted by residual: dihedral pdb=" N PCW A1003 " pdb=" C4 PCW A1003 " pdb=" C5 PCW A1003 " pdb=" O4P PCW A1003 " ideal model delta sinusoidal sigma weight residual 293.34 137.09 156.25 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" N PCW B 404 " pdb=" C4 PCW B 404 " pdb=" C5 PCW B 404 " pdb=" O4P PCW B 404 " ideal model delta sinusoidal sigma weight residual 293.34 148.19 145.15 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" N PCW B 401 " pdb=" C4 PCW B 401 " pdb=" C5 PCW B 401 " pdb=" O4P PCW B 401 " ideal model delta sinusoidal sigma weight residual 293.34 158.33 135.01 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 755 0.044 - 0.088: 199 0.088 - 0.133: 38 0.133 - 0.177: 0 0.177 - 0.221: 6 Chirality restraints: 998 Sorted by residual: chirality pdb=" C2 PCW A1003 " pdb=" C1 PCW A1003 " pdb=" C3 PCW A1003 " pdb=" O2 PCW A1003 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C2 PCW B 404 " pdb=" C1 PCW B 404 " pdb=" C3 PCW B 404 " pdb=" O2 PCW B 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C2 PCW A1006 " pdb=" C1 PCW A1006 " pdb=" C3 PCW A1006 " pdb=" O2 PCW A1006 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 995 not shown) Planarity restraints: 1102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 47 " -0.037 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO A 48 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " 0.012 2.00e-02 2.50e+03 8.36e-03 1.75e+00 pdb=" CG TRP B 160 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 169 " 0.008 2.00e-02 2.50e+03 8.93e-03 1.60e+00 pdb=" CG TYR A 169 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 169 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 169 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 169 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 169 " 0.000 2.00e-02 2.50e+03 ... (remaining 1099 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 35 2.58 - 3.16: 5157 3.16 - 3.74: 9936 3.74 - 4.32: 13508 4.32 - 4.90: 23579 Nonbonded interactions: 52215 Sorted by model distance: nonbonded pdb=" OH TYR B 92 " pdb="MG MG B 403 " model vdw 1.995 2.170 nonbonded pdb=" OD2 ASP A 117 " pdb="MG MG A1001 " model vdw 2.047 2.170 nonbonded pdb=" OD2 ASP B 117 " pdb="MG MG B 402 " model vdw 2.048 2.170 nonbonded pdb=" OD2 ASP A 96 " pdb="MG MG A1002 " model vdw 2.113 2.170 nonbonded pdb=" O PRO B 78 " pdb=" OG1 THR B 81 " model vdw 2.138 3.040 ... (remaining 52210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 388 or resid 1002 or resid 1004 through 1005)) selection = (chain 'B' and (resid 1 through 388 or resid 402 or resid 404 through 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.100 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 0.095 6818 Z= 0.406 Angle : 1.441 25.171 9238 Z= 0.529 Chirality : 0.041 0.221 998 Planarity : 0.004 0.057 1102 Dihedral : 21.441 156.245 2494 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.90 % Allowed : 19.59 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.31), residues: 770 helix: 2.48 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.29 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 160 HIS 0.002 0.001 HIS A 164 PHE 0.014 0.001 PHE B 206 TYR 0.022 0.001 TYR A 169 ARG 0.001 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.13049 ( 442) hydrogen bonds : angle 4.74858 ( 1293) covalent geometry : bond 0.00811 ( 6818) covalent geometry : angle 1.44070 ( 9238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.611 Fit side-chains REVERT: A 128 SER cc_start: 0.8486 (t) cc_final: 0.8104 (p) REVERT: A 326 LEU cc_start: 0.7443 (mt) cc_final: 0.7204 (mt) REVERT: B 41 ILE cc_start: 0.7719 (tt) cc_final: 0.7284 (mm) REVERT: B 127 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6346 (mp) REVERT: B 128 SER cc_start: 0.8467 (t) cc_final: 0.8047 (p) REVERT: B 168 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6178 (mp) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.1298 time to fit residues: 15.8639 Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 290 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.0040 chunk 19 optimal weight: 0.0770 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.138207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.101020 restraints weight = 67883.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.102857 restraints weight = 44360.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.102068 restraints weight = 35981.008| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6818 Z= 0.107 Angle : 0.492 6.421 9238 Z= 0.237 Chirality : 0.037 0.120 998 Planarity : 0.004 0.055 1102 Dihedral : 20.061 137.841 1145 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.05 % Allowed : 18.13 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.31), residues: 770 helix: 2.80 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.31 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 160 HIS 0.003 0.001 HIS B 164 PHE 0.011 0.001 PHE B 206 TYR 0.009 0.001 TYR B 274 ARG 0.001 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 442) hydrogen bonds : angle 3.82734 ( 1293) covalent geometry : bond 0.00209 ( 6818) covalent geometry : angle 0.49206 ( 9238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.722 Fit side-chains REVERT: A 99 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6836 (p0) REVERT: A 193 TYR cc_start: 0.8691 (m-80) cc_final: 0.8422 (m-80) REVERT: B 7 GLN cc_start: 0.7146 (tp40) cc_final: 0.6542 (pt0) REVERT: B 41 ILE cc_start: 0.8113 (tt) cc_final: 0.7588 (mm) REVERT: B 388 LYS cc_start: 0.6285 (OUTLIER) cc_final: 0.4712 (tptt) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.1341 time to fit residues: 17.3625 Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 388 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.133903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.095468 restraints weight = 67863.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.097992 restraints weight = 45022.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.096743 restraints weight = 36077.277| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6818 Z= 0.139 Angle : 0.511 6.272 9238 Z= 0.250 Chirality : 0.039 0.120 998 Planarity : 0.004 0.050 1102 Dihedral : 18.344 133.409 1136 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.63 % Allowed : 17.84 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.31), residues: 770 helix: 2.71 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.28 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 160 HIS 0.004 0.001 HIS A 164 PHE 0.012 0.001 PHE A 275 TYR 0.016 0.001 TYR A 169 ARG 0.001 0.000 ARG B 307 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 442) hydrogen bonds : angle 3.89570 ( 1293) covalent geometry : bond 0.00319 ( 6818) covalent geometry : angle 0.51116 ( 9238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.731 Fit side-chains REVERT: A 99 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6907 (p0) REVERT: A 193 TYR cc_start: 0.8742 (m-80) cc_final: 0.8510 (m-80) REVERT: B 7 GLN cc_start: 0.7182 (tp40) cc_final: 0.6597 (pt0) REVERT: B 41 ILE cc_start: 0.8021 (tt) cc_final: 0.7501 (mm) REVERT: B 104 ARG cc_start: 0.6498 (mmt90) cc_final: 0.6183 (ttm110) REVERT: B 127 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7035 (mp) REVERT: B 157 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8193 (mp) REVERT: B 388 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.4651 (tptt) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 0.1658 time to fit residues: 20.0529 Evaluate side-chains 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 388 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.141265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.099526 restraints weight = 67120.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.100523 restraints weight = 38426.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.101003 restraints weight = 31598.110| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6818 Z= 0.124 Angle : 0.492 6.077 9238 Z= 0.240 Chirality : 0.038 0.118 998 Planarity : 0.004 0.047 1102 Dihedral : 16.563 125.376 1135 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.07 % Allowed : 17.25 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.31), residues: 770 helix: 2.75 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.26 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 160 HIS 0.003 0.001 HIS B 164 PHE 0.012 0.001 PHE A 275 TYR 0.015 0.001 TYR A 169 ARG 0.001 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 442) hydrogen bonds : angle 3.83106 ( 1293) covalent geometry : bond 0.00277 ( 6818) covalent geometry : angle 0.49156 ( 9238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.611 Fit side-chains REVERT: A 79 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7371 (mtt180) REVERT: A 99 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6739 (p0) REVERT: A 193 TYR cc_start: 0.8734 (m-80) cc_final: 0.8507 (m-80) REVERT: B 7 GLN cc_start: 0.7176 (tp40) cc_final: 0.6601 (pt0) REVERT: B 41 ILE cc_start: 0.7996 (tt) cc_final: 0.7484 (mm) REVERT: B 104 ARG cc_start: 0.6416 (mmt90) cc_final: 0.5992 (mtm110) REVERT: B 127 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6933 (mp) REVERT: B 383 TYR cc_start: 0.8191 (m-80) cc_final: 0.7945 (m-80) REVERT: B 388 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.4910 (ttpp) outliers start: 21 outliers final: 14 residues processed: 90 average time/residue: 0.1644 time to fit residues: 20.5066 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 388 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.134485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.095146 restraints weight = 66816.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.097636 restraints weight = 46253.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.096376 restraints weight = 36577.936| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6818 Z= 0.132 Angle : 0.504 6.062 9238 Z= 0.246 Chirality : 0.039 0.152 998 Planarity : 0.004 0.046 1102 Dihedral : 15.460 120.793 1135 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.78 % Allowed : 17.25 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.31), residues: 770 helix: 2.71 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.27 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 160 HIS 0.003 0.001 HIS A 164 PHE 0.012 0.001 PHE A 275 TYR 0.014 0.001 TYR A 169 ARG 0.001 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 442) hydrogen bonds : angle 3.85457 ( 1293) covalent geometry : bond 0.00301 ( 6818) covalent geometry : angle 0.50357 ( 9238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.570 Fit side-chains REVERT: A 79 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7380 (mtt180) REVERT: A 99 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6757 (p0) REVERT: A 193 TYR cc_start: 0.8745 (m-80) cc_final: 0.8527 (m-80) REVERT: B 7 GLN cc_start: 0.7169 (tp40) cc_final: 0.6591 (pt0) REVERT: B 41 ILE cc_start: 0.8064 (tt) cc_final: 0.7538 (mm) REVERT: B 104 ARG cc_start: 0.6304 (mmt90) cc_final: 0.5896 (mtm110) REVERT: B 127 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7086 (mp) REVERT: B 383 TYR cc_start: 0.8319 (m-80) cc_final: 0.8047 (m-80) outliers start: 19 outliers final: 15 residues processed: 87 average time/residue: 0.1742 time to fit residues: 22.2809 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 378 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.135534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.096364 restraints weight = 67105.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.098432 restraints weight = 44350.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.097525 restraints weight = 36396.057| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6818 Z= 0.118 Angle : 0.488 6.971 9238 Z= 0.236 Chirality : 0.038 0.133 998 Planarity : 0.004 0.045 1102 Dihedral : 14.606 115.834 1135 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.92 % Allowed : 17.54 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.31), residues: 770 helix: 2.84 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.27 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 160 HIS 0.002 0.001 HIS B 164 PHE 0.011 0.001 PHE A 275 TYR 0.014 0.001 TYR A 169 ARG 0.000 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 442) hydrogen bonds : angle 3.78399 ( 1293) covalent geometry : bond 0.00257 ( 6818) covalent geometry : angle 0.48760 ( 9238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 1.008 Fit side-chains REVERT: A 7 GLN cc_start: 0.7217 (tp40) cc_final: 0.6533 (tp40) REVERT: A 79 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7392 (mtt180) REVERT: A 99 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6787 (p0) REVERT: A 193 TYR cc_start: 0.8641 (m-80) cc_final: 0.8437 (m-80) REVERT: A 349 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 7 GLN cc_start: 0.7109 (tp40) cc_final: 0.6378 (pt0) REVERT: B 41 ILE cc_start: 0.8024 (tt) cc_final: 0.7512 (mm) REVERT: B 383 TYR cc_start: 0.8243 (m-80) cc_final: 0.7900 (m-80) outliers start: 20 outliers final: 14 residues processed: 87 average time/residue: 0.1911 time to fit residues: 24.1750 Evaluate side-chains 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 378 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 44 optimal weight: 0.0370 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.136897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.097921 restraints weight = 67731.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.100330 restraints weight = 42066.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.099245 restraints weight = 34375.050| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6818 Z= 0.109 Angle : 0.478 6.479 9238 Z= 0.231 Chirality : 0.038 0.125 998 Planarity : 0.003 0.044 1102 Dihedral : 13.956 110.733 1135 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.34 % Allowed : 18.42 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.31), residues: 770 helix: 2.92 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.22 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 160 HIS 0.002 0.001 HIS A 118 PHE 0.010 0.001 PHE B 206 TYR 0.013 0.001 TYR A 169 ARG 0.001 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 442) hydrogen bonds : angle 3.74194 ( 1293) covalent geometry : bond 0.00230 ( 6818) covalent geometry : angle 0.47765 ( 9238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.276 Fit side-chains REVERT: A 7 GLN cc_start: 0.7068 (tp40) cc_final: 0.6394 (tp40) REVERT: A 79 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7297 (mtt180) REVERT: A 99 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6908 (p0) REVERT: A 193 TYR cc_start: 0.8615 (m-80) cc_final: 0.8406 (m-80) REVERT: A 349 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8365 (mm) REVERT: B 7 GLN cc_start: 0.6993 (tp40) cc_final: 0.6282 (pt0) REVERT: B 41 ILE cc_start: 0.8000 (tt) cc_final: 0.7496 (mm) REVERT: B 383 TYR cc_start: 0.8172 (m-80) cc_final: 0.7847 (m-80) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.2036 time to fit residues: 25.4456 Evaluate side-chains 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.135902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.096344 restraints weight = 67985.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.098164 restraints weight = 44710.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.097395 restraints weight = 37209.284| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6818 Z= 0.122 Angle : 0.493 6.847 9238 Z= 0.239 Chirality : 0.038 0.131 998 Planarity : 0.004 0.043 1102 Dihedral : 13.676 106.643 1133 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.78 % Allowed : 17.84 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.31), residues: 770 helix: 2.87 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.21 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 160 HIS 0.003 0.001 HIS A 164 PHE 0.012 0.001 PHE A 275 TYR 0.012 0.001 TYR A 169 ARG 0.001 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 442) hydrogen bonds : angle 3.77936 ( 1293) covalent geometry : bond 0.00271 ( 6818) covalent geometry : angle 0.49346 ( 9238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 1.245 Fit side-chains REVERT: A 7 GLN cc_start: 0.7115 (tp40) cc_final: 0.6457 (tp40) REVERT: A 79 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7372 (mtt180) REVERT: A 99 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6932 (p0) REVERT: A 193 TYR cc_start: 0.8630 (m-80) cc_final: 0.8415 (m-80) REVERT: A 349 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8514 (mm) REVERT: B 7 GLN cc_start: 0.6942 (tp40) cc_final: 0.6238 (pt0) REVERT: B 41 ILE cc_start: 0.8033 (tt) cc_final: 0.7520 (mm) REVERT: B 383 TYR cc_start: 0.8188 (m-10) cc_final: 0.7835 (m-80) outliers start: 19 outliers final: 14 residues processed: 87 average time/residue: 0.2157 time to fit residues: 27.1362 Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 0.0270 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.144687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.102762 restraints weight = 64648.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.104263 restraints weight = 39125.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.104494 restraints weight = 32669.986| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6818 Z= 0.111 Angle : 0.482 6.863 9238 Z= 0.234 Chirality : 0.038 0.122 998 Planarity : 0.004 0.043 1102 Dihedral : 13.221 101.801 1133 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.34 % Allowed : 18.42 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.31), residues: 770 helix: 2.94 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.17 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 160 HIS 0.002 0.001 HIS B 164 PHE 0.022 0.001 PHE B 34 TYR 0.012 0.001 TYR A 169 ARG 0.000 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 442) hydrogen bonds : angle 3.73036 ( 1293) covalent geometry : bond 0.00237 ( 6818) covalent geometry : angle 0.48159 ( 9238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.801 Fit side-chains REVERT: A 7 GLN cc_start: 0.7109 (tp40) cc_final: 0.6459 (tp40) REVERT: A 79 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7274 (mtt180) REVERT: A 99 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6948 (p0) REVERT: A 193 TYR cc_start: 0.8641 (m-80) cc_final: 0.8419 (m-80) REVERT: A 349 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8469 (mm) REVERT: B 7 GLN cc_start: 0.6930 (tp40) cc_final: 0.6239 (pt0) REVERT: B 41 ILE cc_start: 0.7951 (tt) cc_final: 0.7436 (mm) REVERT: B 383 TYR cc_start: 0.8193 (m-10) cc_final: 0.7837 (m-80) outliers start: 16 outliers final: 13 residues processed: 83 average time/residue: 0.1505 time to fit residues: 18.2892 Evaluate side-chains 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.132277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.093270 restraints weight = 68040.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.094946 restraints weight = 47089.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.094268 restraints weight = 39497.338| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6818 Z= 0.164 Angle : 0.540 6.975 9238 Z= 0.266 Chirality : 0.040 0.129 998 Planarity : 0.004 0.042 1102 Dihedral : 13.486 98.560 1133 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.19 % Allowed : 18.86 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.31), residues: 770 helix: 2.67 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.18 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 160 HIS 0.004 0.001 HIS A 164 PHE 0.018 0.001 PHE B 34 TYR 0.016 0.001 TYR B 274 ARG 0.001 0.000 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 442) hydrogen bonds : angle 3.89188 ( 1293) covalent geometry : bond 0.00401 ( 6818) covalent geometry : angle 0.54040 ( 9238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.330 Fit side-chains REVERT: A 7 GLN cc_start: 0.7115 (tp40) cc_final: 0.6451 (tp40) REVERT: A 99 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6763 (p0) REVERT: A 109 GLN cc_start: 0.7275 (mt0) cc_final: 0.6836 (mp10) REVERT: A 349 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8608 (mm) REVERT: B 7 GLN cc_start: 0.7214 (tp40) cc_final: 0.6460 (pt0) REVERT: B 41 ILE cc_start: 0.8028 (tt) cc_final: 0.7473 (mm) REVERT: B 70 ASP cc_start: 0.9040 (t0) cc_final: 0.8676 (t0) REVERT: B 104 ARG cc_start: 0.6338 (mmt90) cc_final: 0.5869 (mtm110) REVERT: B 371 ASP cc_start: 0.7092 (t0) cc_final: 0.6765 (m-30) REVERT: B 383 TYR cc_start: 0.8190 (m-10) cc_final: 0.7876 (m-80) outliers start: 15 outliers final: 12 residues processed: 87 average time/residue: 0.3835 time to fit residues: 50.9770 Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 351 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.142915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.101322 restraints weight = 64653.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.103708 restraints weight = 39198.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.103131 restraints weight = 32148.961| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6818 Z= 0.112 Angle : 0.491 6.951 9238 Z= 0.239 Chirality : 0.038 0.137 998 Planarity : 0.004 0.042 1102 Dihedral : 12.804 95.157 1133 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.90 % Allowed : 19.30 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.31), residues: 770 helix: 2.86 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.19 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 160 HIS 0.002 0.001 HIS B 164 PHE 0.018 0.001 PHE B 34 TYR 0.012 0.001 TYR A 169 ARG 0.001 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 442) hydrogen bonds : angle 3.75991 ( 1293) covalent geometry : bond 0.00234 ( 6818) covalent geometry : angle 0.49081 ( 9238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.66 seconds wall clock time: 44 minutes 12.14 seconds (2652.14 seconds total)