Starting phenix.real_space_refine on Fri Aug 22 23:32:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcn_38248/08_2025/8xcn_38248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcn_38248/08_2025/8xcn_38248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcn_38248/08_2025/8xcn_38248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcn_38248/08_2025/8xcn_38248.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcn_38248/08_2025/8xcn_38248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcn_38248/08_2025/8xcn_38248.cif" } resolution = 3.02 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= 0.001 sd= 0.015 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 Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5420 2.51 5 N 1489 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s 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: 8601 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4164 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 52.692 62.655 35.511 1.00 87.42 S ATOM 1738 SG CYS A 222 54.833 67.275 31.351 1.00 83.60 S ATOM 1698 SG CYS A 216 52.906 62.684 28.727 1.00 88.54 S Time building chain proxies: 1.89, per 1000 atoms: 0.22 Number of scatterers: 8601 At special positions: 0 Unit cell: (105.78, 107.5, 76.54, 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) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1638 8.00 N 1489 7.00 C 5420 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 364.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 41.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.587A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.591A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.690A pdb=" N TRP A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.607A pdb=" N LEU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.165A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.565A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.041A pdb=" N MET A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.625A pdb=" N ASP A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 463 removed outlier: 4.004A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.798A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.757A pdb=" N MET A 514 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 542 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 100 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.532A pdb=" N TYR B 150 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 151 " --> pdb=" O LEU B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.581A pdb=" N VAL B 171 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.212A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 3.864A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.880A pdb=" N TRP C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.504A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 3.522A pdb=" N LYS A 247 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 3.522A pdb=" N LYS A 247 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.527A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.215A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA6, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA7, first strand: chain 'C' and resid 384 through 388 324 hydrogen bonds defined for protein. 900 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: 0.97 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.57: 8733 1.57 - 2.15: 93 2.15 - 2.74: 6 2.74 - 3.32: 0 3.32 - 3.91: 3 Bond restraints: 8835 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.906 -1.606 2.00e-02 2.50e+03 6.44e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.762 -1.529 2.00e-02 2.50e+03 5.84e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.736 -1.478 2.00e-02 2.50e+03 5.46e+03 bond pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 1.492 0.987 0.505 5.00e-02 4.00e+02 1.02e+02 bond pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 1.503 1.220 0.283 3.40e-02 8.65e+02 6.93e+01 ... (remaining 8830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.75: 12061 14.75 - 29.50: 5 29.50 - 44.25: 10 44.25 - 59.00: 1 59.00 - 73.75: 1 Bond angle restraints: 12078 Sorted by residual: angle pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 106.10 179.85 -73.75 3.20e+00 9.77e-02 5.31e+02 angle pdb=" N PRO A 144 " pdb=" CD PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 103.20 76.60 26.60 1.50e+00 4.44e-01 3.14e+02 angle pdb=" CA PRO A 144 " pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 104.50 71.64 32.86 1.90e+00 2.77e-01 2.99e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 68.36 46.39 3.00e+00 1.11e-01 2.39e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 69.90 42.69 3.00e+00 1.11e-01 2.03e+02 ... (remaining 12073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.37: 4457 19.37 - 38.75: 580 38.75 - 58.12: 146 58.12 - 77.49: 30 77.49 - 96.87: 11 Dihedral angle restraints: 5224 sinusoidal: 2072 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" N PRO A 144 " pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " pdb=" CB PRO A 144 " ideal model delta sinusoidal sigma weight residual 30.00 126.87 -96.87 1 1.50e+01 4.44e-03 4.78e+01 dihedral pdb=" CA TYR A 79 " pdb=" C TYR A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 5221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.449: 1276 3.449 - 6.898: 0 6.898 - 10.347: 0 10.347 - 13.796: 0 13.796 - 17.245: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.48 17.24 2.00e-01 2.50e+01 7.43e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CG LEU A 35 " pdb=" CB LEU A 35 " pdb=" CD1 LEU A 35 " pdb=" CD2 LEU A 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1274 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 502 " 0.019 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" C2C HEC C 502 " -0.191 2.00e-02 2.50e+03 pdb=" C3C HEC C 502 " 0.056 2.00e-02 2.50e+03 pdb=" C4C HEC C 502 " 0.009 2.00e-02 2.50e+03 pdb=" CAC HEC C 502 " 0.020 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " 0.029 2.00e-02 2.50e+03 pdb=" CHD HEC C 502 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC C 502 " 0.059 2.00e-02 2.50e+03 pdb=" NC HEC C 502 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 66 " -0.115 5.00e-02 4.00e+02 1.58e-01 4.02e+01 pdb=" N PRO A 67 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 147 " -0.111 5.00e-02 4.00e+02 1.55e-01 3.83e+01 pdb=" N PRO C 148 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO C 148 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 148 " -0.077 5.00e-02 4.00e+02 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.70: 380 2.70 - 3.44: 13164 3.44 - 4.17: 22493 4.17 - 4.90: 39113 Nonbonded interactions: 75152 Sorted by model distance: nonbonded pdb=" OD2 ASP C 375 " pdb=" O1D HEC C 502 " model vdw 1.241 3.040 nonbonded pdb=" CG ASP C 375 " pdb=" O1D HEC C 502 " model vdw 1.377 3.270 nonbonded pdb=" NE2 GLN A 46 " pdb=" OD1 ASN A 50 " model vdw 1.988 3.120 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.092 3.040 nonbonded pdb=" OG1 THR C 234 " pdb=" O PRO C 294 " model vdw 2.106 3.040 ... (remaining 75147 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.080 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.031 1.606 8849 Z= 1.550 Angle : 1.698 73.755 12087 Z= 0.723 Chirality : 0.485 17.245 1277 Planarity : 0.011 0.158 1568 Dihedral : 18.742 96.866 3212 Min Nonbonded Distance : 1.241 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.15 % Allowed : 32.66 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: -0.97 (0.25), residues: 1083 helix: 0.00 (0.26), residues: 399 sheet: -1.14 (0.51), residues: 91 loop : -0.97 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 133 TYR 0.040 0.003 TYR A 182 PHE 0.018 0.002 PHE B 54 TRP 0.058 0.002 TRP A 173 HIS 0.021 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.02988 ( 8835) covalent geometry : angle 1.66253 (12078) hydrogen bonds : bond 0.15315 ( 315) hydrogen bonds : angle 7.26087 ( 900) metal coordination : bond 0.00274 ( 3) metal coordination : angle 12.80312 ( 9) Misc. bond : bond 0.19108 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.4887 (tpt) cc_final: 0.4682 (tpp) REVERT: A 330 SER cc_start: 0.8253 (m) cc_final: 0.7989 (t) REVERT: A 438 TYR cc_start: 0.4133 (t80) cc_final: 0.3841 (t80) REVERT: A 439 ASP cc_start: 0.7416 (m-30) cc_final: 0.7004 (t0) REVERT: A 453 GLN cc_start: 0.8496 (tp40) cc_final: 0.8005 (mm-40) REVERT: A 514 MET cc_start: 0.6719 (mmp) cc_final: 0.6294 (mpp) REVERT: B 51 ILE cc_start: 0.8267 (mt) cc_final: 0.7989 (tp) REVERT: B 53 ASP cc_start: 0.8567 (m-30) cc_final: 0.8262 (t0) REVERT: B 93 LEU cc_start: 0.8556 (mt) cc_final: 0.8343 (tp) REVERT: B 96 HIS cc_start: 0.8304 (m-70) cc_final: 0.8051 (m90) REVERT: B 100 ASN cc_start: 0.8856 (m-40) cc_final: 0.8420 (m-40) REVERT: B 134 GLU cc_start: 0.7744 (mp0) cc_final: 0.7431 (mt-10) REVERT: C 107 ILE cc_start: 0.8649 (mp) cc_final: 0.8354 (mm) REVERT: C 284 SER cc_start: 0.8052 (t) cc_final: 0.7712 (p) outliers start: 19 outliers final: 10 residues processed: 316 average time/residue: 0.0756 time to fit residues: 31.9213 Evaluate side-chains 182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 312 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.136259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119127 restraints weight = 17192.956| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.50 r_work: 0.3546 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 8849 Z= 0.197 Angle : 1.444 76.034 12087 Z= 0.506 Chirality : 0.051 0.813 1277 Planarity : 0.006 0.074 1568 Dihedral : 9.905 77.007 1299 Min Nonbonded Distance : 1.540 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.65 % Allowed : 24.41 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: -0.29 (0.25), residues: 1083 helix: 0.82 (0.27), residues: 396 sheet: -0.83 (0.54), residues: 81 loop : -0.77 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 190 TYR 0.017 0.002 TYR A 443 PHE 0.017 0.002 PHE C 158 TRP 0.017 0.002 TRP C 188 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8835) covalent geometry : angle 1.29719 (12078) hydrogen bonds : bond 0.03786 ( 315) hydrogen bonds : angle 5.38585 ( 900) metal coordination : bond 0.01453 ( 3) metal coordination : angle 23.31885 ( 9) Misc. bond : bond 0.07408 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8491 (ttp) cc_final: 0.7958 (ptm) REVERT: A 175 MET cc_start: 0.7885 (mtt) cc_final: 0.7636 (mtt) REVERT: A 211 ASP cc_start: 0.8417 (t0) cc_final: 0.7808 (t0) REVERT: A 268 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.4037 (pp) REVERT: A 312 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.6805 (m-40) REVERT: A 346 MET cc_start: 0.9077 (mtt) cc_final: 0.8847 (mtp) REVERT: A 514 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5529 (mpp) REVERT: B 53 ASP cc_start: 0.8648 (m-30) cc_final: 0.8197 (t0) REVERT: B 93 LEU cc_start: 0.8591 (mt) cc_final: 0.8291 (tp) REVERT: B 96 HIS cc_start: 0.8507 (m-70) cc_final: 0.8106 (m90) REVERT: B 100 ASN cc_start: 0.9013 (m-40) cc_final: 0.8566 (m-40) REVERT: B 102 TYR cc_start: 0.7358 (m-80) cc_final: 0.7123 (m-10) REVERT: B 115 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7864 (p0) REVERT: B 140 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7920 (mtpt) REVERT: C 118 MET cc_start: 0.7972 (tpt) cc_final: 0.7704 (tpt) REVERT: C 180 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.5280 (t80) REVERT: C 210 PHE cc_start: 0.8756 (t80) cc_final: 0.8224 (t80) REVERT: C 267 MET cc_start: 0.9034 (tpt) cc_final: 0.8505 (tpt) REVERT: C 284 SER cc_start: 0.8051 (t) cc_final: 0.7735 (p) REVERT: C 410 GLU cc_start: 0.8986 (tp30) cc_final: 0.8765 (tp30) outliers start: 50 outliers final: 20 residues processed: 245 average time/residue: 0.0644 time to fit residues: 22.6013 Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.0020 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 46 GLN A 78 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN A 312 ASN A 320 ASN A 503 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.077664 restraints weight = 17200.017| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.33 r_work: 0.2935 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.344 8849 Z= 0.312 Angle : 1.529 91.182 12087 Z= 0.527 Chirality : 0.060 1.092 1277 Planarity : 0.007 0.076 1568 Dihedral : 10.587 87.762 1295 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 7.34 % Allowed : 20.68 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: -0.20 (0.25), residues: 1083 helix: 1.04 (0.27), residues: 388 sheet: -0.96 (0.54), residues: 80 loop : -0.77 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 499 TYR 0.030 0.003 TYR C 339 PHE 0.024 0.003 PHE C 156 TRP 0.031 0.003 TRP A 173 HIS 0.016 0.002 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00745 ( 8835) covalent geometry : angle 1.25513 (12078) hydrogen bonds : bond 0.04304 ( 315) hydrogen bonds : angle 5.43269 ( 900) metal coordination : bond 0.00714 ( 3) metal coordination : angle 32.04468 ( 9) Misc. bond : bond 0.11577 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 178 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 78 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7496 (t0) REVERT: A 98 GLN cc_start: 0.6334 (mt0) cc_final: 0.5474 (mm-40) REVERT: A 135 TYR cc_start: 0.5315 (t80) cc_final: 0.4679 (t80) REVERT: A 211 ASP cc_start: 0.8704 (t0) cc_final: 0.8030 (t0) REVERT: A 316 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8017 (tt) REVERT: A 322 MET cc_start: 0.5702 (mmt) cc_final: 0.5375 (mmt) REVERT: A 356 ASP cc_start: 0.8312 (m-30) cc_final: 0.7959 (m-30) REVERT: A 360 GLU cc_start: 0.8628 (pm20) cc_final: 0.8413 (pm20) REVERT: A 375 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8181 (m) REVERT: A 438 TYR cc_start: 0.5862 (t80) cc_final: 0.4548 (t80) REVERT: A 476 ASN cc_start: 0.8375 (m-40) cc_final: 0.8146 (m-40) REVERT: A 490 ARG cc_start: 0.8435 (mmm160) cc_final: 0.8168 (mmm160) REVERT: B 53 ASP cc_start: 0.8750 (m-30) cc_final: 0.8334 (t0) REVERT: B 56 GLN cc_start: 0.8927 (tt0) cc_final: 0.8700 (tt0) REVERT: B 68 ASP cc_start: 0.7230 (t0) cc_final: 0.7005 (t0) REVERT: B 96 HIS cc_start: 0.8787 (m-70) cc_final: 0.8412 (m90) REVERT: B 136 GLU cc_start: 0.8464 (pt0) cc_final: 0.8108 (pm20) REVERT: C 97 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8506 (mp0) REVERT: C 118 MET cc_start: 0.8588 (tpt) cc_final: 0.7832 (tpt) REVERT: C 180 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.5893 (t80) REVERT: C 410 GLU cc_start: 0.9167 (tp30) cc_final: 0.8799 (tp30) REVERT: C 437 GLN cc_start: 0.8279 (tt0) cc_final: 0.7909 (tp40) outliers start: 65 outliers final: 25 residues processed: 223 average time/residue: 0.0592 time to fit residues: 19.1204 Evaluate side-chains 151 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 219 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.079511 restraints weight = 17418.153| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.24 r_work: 0.2977 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 8849 Z= 0.168 Angle : 1.407 85.317 12087 Z= 0.449 Chirality : 0.059 1.318 1277 Planarity : 0.006 0.074 1568 Dihedral : 9.981 83.917 1293 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 4.63 % Allowed : 22.15 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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 (0.26), residues: 1083 helix: 1.35 (0.28), residues: 386 sheet: -0.60 (0.55), residues: 77 loop : -0.62 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 418 TYR 0.016 0.002 TYR C 359 PHE 0.015 0.002 PHE B 183 TRP 0.026 0.001 TRP A 173 HIS 0.013 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8835) covalent geometry : angle 1.11321 (12078) hydrogen bonds : bond 0.03358 ( 315) hydrogen bonds : angle 5.12407 ( 900) metal coordination : bond 0.00217 ( 3) metal coordination : angle 31.56190 ( 9) Misc. bond : bond 0.06445 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8857 (m-80) cc_final: 0.8643 (m-80) REVERT: A 79 TYR cc_start: 0.8274 (m-80) cc_final: 0.7851 (m-10) REVERT: A 211 ASP cc_start: 0.8761 (t0) cc_final: 0.8234 (t0) REVERT: A 259 THR cc_start: 0.6485 (p) cc_final: 0.5942 (t) REVERT: A 356 ASP cc_start: 0.8254 (m-30) cc_final: 0.7886 (m-30) REVERT: A 360 GLU cc_start: 0.8558 (pm20) cc_final: 0.8302 (pm20) REVERT: A 375 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 425 TYR cc_start: 0.8688 (m-80) cc_final: 0.8485 (m-80) REVERT: A 490 ARG cc_start: 0.8430 (mmm160) cc_final: 0.7977 (mmm160) REVERT: B 106 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: B 136 GLU cc_start: 0.8351 (pt0) cc_final: 0.7992 (pm20) REVERT: C 97 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8588 (mp0) REVERT: C 118 MET cc_start: 0.8469 (tpt) cc_final: 0.7639 (tpt) REVERT: C 180 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5875 (t80) REVERT: C 210 PHE cc_start: 0.9040 (t80) cc_final: 0.8518 (t80) REVERT: C 410 GLU cc_start: 0.9166 (tp30) cc_final: 0.8826 (tp30) REVERT: C 437 GLN cc_start: 0.8182 (tt0) cc_final: 0.7816 (tp40) outliers start: 41 outliers final: 24 residues processed: 177 average time/residue: 0.0626 time to fit residues: 16.0163 Evaluate side-chains 162 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 84 optimal weight: 0.0050 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081007 restraints weight = 17429.781| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.25 r_work: 0.3007 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 8849 Z= 0.147 Angle : 1.304 84.576 12087 Z= 0.428 Chirality : 0.060 1.401 1277 Planarity : 0.005 0.079 1568 Dihedral : 9.638 80.571 1293 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.52 % Allowed : 22.26 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.27 (0.26), residues: 1083 helix: 1.49 (0.28), residues: 384 sheet: -0.30 (0.56), residues: 76 loop : -0.59 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 94 TYR 0.019 0.001 TYR A 79 PHE 0.015 0.002 PHE B 86 TRP 0.025 0.001 TRP A 173 HIS 0.009 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8835) covalent geometry : angle 1.08649 (12078) hydrogen bonds : bond 0.03028 ( 315) hydrogen bonds : angle 4.94746 ( 900) metal coordination : bond 0.00174 ( 3) metal coordination : angle 26.42946 ( 9) Misc. bond : bond 0.04433 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8065 (p0) cc_final: 0.7546 (p0) REVERT: A 68 TYR cc_start: 0.8960 (m-80) cc_final: 0.8689 (m-80) REVERT: A 79 TYR cc_start: 0.8425 (m-80) cc_final: 0.7895 (m-10) REVERT: A 96 TYR cc_start: 0.7987 (m-10) cc_final: 0.6913 (m-10) REVERT: A 211 ASP cc_start: 0.8780 (t0) cc_final: 0.8039 (t0) REVERT: A 285 PHE cc_start: 0.8588 (m-80) cc_final: 0.8344 (m-80) REVERT: A 316 LEU cc_start: 0.8537 (tp) cc_final: 0.8332 (tt) REVERT: A 321 MET cc_start: 0.7180 (tpt) cc_final: 0.6317 (tpt) REVERT: A 322 MET cc_start: 0.5955 (mmt) cc_final: 0.5612 (mmt) REVERT: A 356 ASP cc_start: 0.8338 (m-30) cc_final: 0.8010 (m-30) REVERT: A 360 GLU cc_start: 0.8497 (pm20) cc_final: 0.8282 (pm20) REVERT: A 375 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.7940 (m) REVERT: A 425 TYR cc_start: 0.8717 (m-80) cc_final: 0.8500 (m-80) REVERT: A 485 MET cc_start: 0.7432 (mpp) cc_final: 0.6758 (mtt) REVERT: A 490 ARG cc_start: 0.8389 (mmm160) cc_final: 0.8035 (mmm160) REVERT: B 86 PHE cc_start: 0.8052 (t80) cc_final: 0.7432 (t80) REVERT: B 89 GLN cc_start: 0.8688 (mt0) cc_final: 0.7866 (mp10) REVERT: B 91 LYS cc_start: 0.9484 (mmtm) cc_final: 0.9026 (mmmt) REVERT: B 96 HIS cc_start: 0.8600 (m90) cc_final: 0.7906 (m90) REVERT: B 102 TYR cc_start: 0.7749 (m-80) cc_final: 0.7440 (m-10) REVERT: B 112 MET cc_start: 0.8045 (mtt) cc_final: 0.7770 (ttp) REVERT: C 97 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8607 (mp0) REVERT: C 118 MET cc_start: 0.8400 (tpt) cc_final: 0.7627 (tpt) REVERT: C 180 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.5925 (t80) REVERT: C 210 PHE cc_start: 0.9019 (t80) cc_final: 0.8533 (t80) REVERT: C 395 MET cc_start: 0.8889 (ttt) cc_final: 0.8495 (ttt) REVERT: C 410 GLU cc_start: 0.9184 (tp30) cc_final: 0.8939 (tp30) REVERT: C 437 GLN cc_start: 0.8154 (tt0) cc_final: 0.7751 (tp40) outliers start: 40 outliers final: 26 residues processed: 176 average time/residue: 0.0624 time to fit residues: 15.5944 Evaluate side-chains 174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.092139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.073062 restraints weight = 17607.064| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.11 r_work: 0.2868 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.193 8849 Z= 0.210 Angle : 1.305 82.980 12087 Z= 0.444 Chirality : 0.062 1.459 1277 Planarity : 0.006 0.073 1568 Dihedral : 9.806 82.405 1292 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.63 % Allowed : 23.16 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.33 (0.26), residues: 1083 helix: 1.50 (0.28), residues: 383 sheet: -0.33 (0.58), residues: 77 loop : -0.51 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 94 TYR 0.036 0.002 TYR A 438 PHE 0.018 0.002 PHE B 86 TRP 0.029 0.002 TRP A 173 HIS 0.007 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8835) covalent geometry : angle 1.12438 (12078) hydrogen bonds : bond 0.03220 ( 315) hydrogen bonds : angle 4.97100 ( 900) metal coordination : bond 0.00333 ( 3) metal coordination : angle 24.30076 ( 9) Misc. bond : bond 0.07846 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8385 (p0) cc_final: 0.7875 (p0) REVERT: A 68 TYR cc_start: 0.8997 (m-80) cc_final: 0.8793 (m-80) REVERT: A 79 TYR cc_start: 0.8426 (m-80) cc_final: 0.8075 (m-10) REVERT: A 271 TYR cc_start: 0.8130 (m-80) cc_final: 0.7797 (m-80) REVERT: A 356 ASP cc_start: 0.8532 (m-30) cc_final: 0.8062 (m-30) REVERT: A 360 GLU cc_start: 0.8668 (pm20) cc_final: 0.8293 (mp0) REVERT: A 375 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8094 (m) REVERT: A 376 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7153 (ttp80) REVERT: A 404 ASP cc_start: 0.7570 (m-30) cc_final: 0.7354 (m-30) REVERT: A 425 TYR cc_start: 0.8748 (m-80) cc_final: 0.8543 (m-80) REVERT: A 476 ASN cc_start: 0.8343 (m-40) cc_final: 0.7901 (m-40) REVERT: A 490 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8098 (mmm160) REVERT: B 86 PHE cc_start: 0.8451 (t80) cc_final: 0.7818 (t80) REVERT: B 89 GLN cc_start: 0.8732 (mt0) cc_final: 0.7877 (mp10) REVERT: B 91 LYS cc_start: 0.9494 (mmtm) cc_final: 0.9050 (mmmt) REVERT: B 94 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.8930 (mmm-85) REVERT: B 96 HIS cc_start: 0.8598 (m90) cc_final: 0.8071 (m90) REVERT: B 112 MET cc_start: 0.8194 (mtt) cc_final: 0.7834 (ttt) REVERT: B 136 GLU cc_start: 0.8262 (pt0) cc_final: 0.7845 (pm20) REVERT: C 97 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8611 (mp0) REVERT: C 108 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6154 (mtm110) REVERT: C 118 MET cc_start: 0.8646 (tpt) cc_final: 0.7915 (tpt) REVERT: C 180 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6168 (t80) REVERT: C 210 PHE cc_start: 0.9084 (t80) cc_final: 0.8545 (t80) REVERT: C 395 MET cc_start: 0.9112 (ttt) cc_final: 0.8821 (ttt) REVERT: C 410 GLU cc_start: 0.9185 (tp30) cc_final: 0.8915 (tp30) REVERT: C 437 GLN cc_start: 0.8231 (tt0) cc_final: 0.7844 (tp40) outliers start: 41 outliers final: 23 residues processed: 180 average time/residue: 0.0784 time to fit residues: 19.9617 Evaluate side-chains 163 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.070579 restraints weight = 17706.002| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.05 r_work: 0.2820 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.8649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 8849 Z= 0.217 Angle : 1.242 83.153 12087 Z= 0.444 Chirality : 0.063 1.479 1277 Planarity : 0.005 0.069 1568 Dihedral : 9.774 82.962 1292 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.62 % Allowed : 23.50 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.41 (0.26), residues: 1083 helix: 1.54 (0.28), residues: 385 sheet: -0.30 (0.58), residues: 77 loop : -0.44 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 94 TYR 0.022 0.002 TYR A 79 PHE 0.019 0.002 PHE C 64 TRP 0.028 0.002 TRP A 173 HIS 0.011 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 8835) covalent geometry : angle 1.12528 (12078) hydrogen bonds : bond 0.03127 ( 315) hydrogen bonds : angle 4.95166 ( 900) metal coordination : bond 0.00229 ( 3) metal coordination : angle 19.30627 ( 9) Misc. bond : bond 0.06488 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8414 (p0) cc_final: 0.7957 (p0) REVERT: A 68 TYR cc_start: 0.9002 (m-80) cc_final: 0.8685 (m-80) REVERT: A 79 TYR cc_start: 0.8578 (m-80) cc_final: 0.8178 (m-10) REVERT: A 211 ASP cc_start: 0.8823 (t0) cc_final: 0.8338 (t0) REVERT: A 271 TYR cc_start: 0.8270 (m-80) cc_final: 0.8024 (m-80) REVERT: A 356 ASP cc_start: 0.8634 (m-30) cc_final: 0.8188 (m-30) REVERT: A 360 GLU cc_start: 0.8663 (pm20) cc_final: 0.8306 (mp0) REVERT: A 514 MET cc_start: 0.9010 (mmm) cc_final: 0.8622 (mtm) REVERT: B 91 LYS cc_start: 0.9496 (mmtm) cc_final: 0.9076 (mmmt) REVERT: B 94 ARG cc_start: 0.9358 (mmm-85) cc_final: 0.9140 (mmm-85) REVERT: B 96 HIS cc_start: 0.8710 (m90) cc_final: 0.8110 (m90) REVERT: B 112 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7917 (ttt) REVERT: C 118 MET cc_start: 0.8681 (tpt) cc_final: 0.7987 (tpt) REVERT: C 210 PHE cc_start: 0.9123 (t80) cc_final: 0.8612 (t80) REVERT: C 395 MET cc_start: 0.9091 (ttt) cc_final: 0.8889 (ttt) REVERT: C 410 GLU cc_start: 0.9193 (tp30) cc_final: 0.8939 (tp30) REVERT: C 437 GLN cc_start: 0.8263 (tt0) cc_final: 0.7934 (tp40) outliers start: 32 outliers final: 21 residues processed: 160 average time/residue: 0.0876 time to fit residues: 19.8429 Evaluate side-chains 147 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 64 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.073158 restraints weight = 17255.258| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.06 r_work: 0.2871 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.8770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8849 Z= 0.160 Angle : 1.205 83.186 12087 Z= 0.427 Chirality : 0.062 1.485 1277 Planarity : 0.005 0.072 1568 Dihedral : 9.596 81.769 1292 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.28 % Allowed : 24.18 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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 (0.26), residues: 1083 helix: 1.59 (0.28), residues: 383 sheet: -0.48 (0.57), residues: 77 loop : -0.42 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 94 TYR 0.020 0.001 TYR A 79 PHE 0.014 0.002 PHE A 285 TRP 0.025 0.001 TRP A 173 HIS 0.009 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8835) covalent geometry : angle 1.09103 (12078) hydrogen bonds : bond 0.02903 ( 315) hydrogen bonds : angle 4.83958 ( 900) metal coordination : bond 0.00165 ( 3) metal coordination : angle 18.75540 ( 9) Misc. bond : bond 0.03648 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8337 (p0) cc_final: 0.7902 (p0) REVERT: A 68 TYR cc_start: 0.9027 (m-80) cc_final: 0.8626 (m-80) REVERT: A 79 TYR cc_start: 0.8571 (m-80) cc_final: 0.8168 (m-10) REVERT: A 211 ASP cc_start: 0.8839 (t0) cc_final: 0.8154 (t0) REVERT: A 271 TYR cc_start: 0.8338 (m-80) cc_final: 0.8072 (m-80) REVERT: A 272 ASP cc_start: 0.7197 (t0) cc_final: 0.6831 (t0) REVERT: A 356 ASP cc_start: 0.8700 (m-30) cc_final: 0.8237 (m-30) REVERT: A 360 GLU cc_start: 0.8640 (pm20) cc_final: 0.8313 (mp0) REVERT: A 375 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8076 (m) REVERT: A 476 ASN cc_start: 0.8402 (m-40) cc_final: 0.7944 (m-40) REVERT: A 514 MET cc_start: 0.9013 (mmm) cc_final: 0.8583 (mtm) REVERT: B 91 LYS cc_start: 0.9469 (mmtm) cc_final: 0.9091 (mmmt) REVERT: B 94 ARG cc_start: 0.9338 (mmm-85) cc_final: 0.9092 (mmm-85) REVERT: B 96 HIS cc_start: 0.8659 (m90) cc_final: 0.8076 (m90) REVERT: B 112 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7895 (ttt) REVERT: B 136 GLU cc_start: 0.8199 (pt0) cc_final: 0.7813 (pm20) REVERT: C 108 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6218 (mtm110) REVERT: C 118 MET cc_start: 0.8602 (tpt) cc_final: 0.7901 (tpt) REVERT: C 210 PHE cc_start: 0.9106 (t80) cc_final: 0.8590 (t80) REVERT: C 395 MET cc_start: 0.8948 (ttt) cc_final: 0.8731 (ttt) REVERT: C 410 GLU cc_start: 0.9196 (tp30) cc_final: 0.8931 (tp30) REVERT: C 437 GLN cc_start: 0.8188 (tt0) cc_final: 0.7838 (tp40) outliers start: 29 outliers final: 23 residues processed: 155 average time/residue: 0.0926 time to fit residues: 20.3613 Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.074079 restraints weight = 17342.251| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.06 r_work: 0.2881 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.8825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8849 Z= 0.154 Angle : 1.180 82.924 12087 Z= 0.423 Chirality : 0.061 1.495 1277 Planarity : 0.005 0.072 1568 Dihedral : 9.534 81.834 1292 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.39 % Allowed : 24.29 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.53 (0.27), residues: 1083 helix: 1.68 (0.28), residues: 385 sheet: -0.05 (0.59), residues: 69 loop : -0.43 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.016 0.001 TYR A 96 PHE 0.020 0.002 PHE B 86 TRP 0.023 0.001 TRP A 173 HIS 0.007 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8835) covalent geometry : angle 1.08591 (12078) hydrogen bonds : bond 0.02804 ( 315) hydrogen bonds : angle 4.78964 ( 900) metal coordination : bond 0.00131 ( 3) metal coordination : angle 16.99401 ( 9) Misc. bond : bond 0.02762 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.8614 (t) cc_final: 0.8372 (p) REVERT: A 37 ASP cc_start: 0.8218 (p0) cc_final: 0.7767 (p0) REVERT: A 68 TYR cc_start: 0.8996 (m-80) cc_final: 0.8637 (m-80) REVERT: A 79 TYR cc_start: 0.8159 (m-80) cc_final: 0.7862 (m-10) REVERT: A 211 ASP cc_start: 0.8808 (t0) cc_final: 0.8144 (t0) REVERT: A 271 TYR cc_start: 0.8341 (m-80) cc_final: 0.8110 (m-80) REVERT: A 272 ASP cc_start: 0.7086 (t0) cc_final: 0.6690 (t0) REVERT: A 356 ASP cc_start: 0.8694 (m-30) cc_final: 0.8225 (m-30) REVERT: A 360 GLU cc_start: 0.8601 (pm20) cc_final: 0.8304 (mp0) REVERT: A 476 ASN cc_start: 0.8324 (m-40) cc_final: 0.7866 (m-40) REVERT: A 514 MET cc_start: 0.8974 (mmm) cc_final: 0.8592 (mtm) REVERT: B 91 LYS cc_start: 0.9457 (mmtm) cc_final: 0.9101 (mmmt) REVERT: B 94 ARG cc_start: 0.9336 (mmm-85) cc_final: 0.8948 (mmm-85) REVERT: C 108 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6217 (mtm110) REVERT: C 118 MET cc_start: 0.8599 (tpt) cc_final: 0.7890 (tpt) REVERT: C 210 PHE cc_start: 0.9101 (t80) cc_final: 0.8609 (t80) REVERT: C 395 MET cc_start: 0.8899 (ttt) cc_final: 0.8675 (ttt) REVERT: C 410 GLU cc_start: 0.9198 (tp30) cc_final: 0.8931 (tp30) REVERT: C 437 GLN cc_start: 0.8216 (tt0) cc_final: 0.7816 (tp40) outliers start: 30 outliers final: 24 residues processed: 162 average time/residue: 0.0886 time to fit residues: 20.1260 Evaluate side-chains 154 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 477 ASN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075839 restraints weight = 17320.669| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.05 r_work: 0.2901 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.8889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8849 Z= 0.157 Angle : 1.171 82.815 12087 Z= 0.426 Chirality : 0.061 1.497 1277 Planarity : 0.005 0.072 1568 Dihedral : 9.533 81.928 1292 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.16 % Allowed : 25.31 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.52 (0.27), residues: 1083 helix: 1.69 (0.28), residues: 385 sheet: -0.50 (0.57), residues: 77 loop : -0.37 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 264 TYR 0.019 0.001 TYR A 96 PHE 0.013 0.001 PHE A 270 TRP 0.023 0.001 TRP A 173 HIS 0.007 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8835) covalent geometry : angle 1.09513 (12078) hydrogen bonds : bond 0.02788 ( 315) hydrogen bonds : angle 4.76688 ( 900) metal coordination : bond 0.00112 ( 3) metal coordination : angle 15.27443 ( 9) Misc. bond : bond 0.03012 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.8591 (t) cc_final: 0.8366 (p) REVERT: A 37 ASP cc_start: 0.8185 (p0) cc_final: 0.7708 (p0) REVERT: A 68 TYR cc_start: 0.8998 (m-80) cc_final: 0.8661 (m-80) REVERT: A 211 ASP cc_start: 0.8801 (t0) cc_final: 0.8121 (t0) REVERT: A 272 ASP cc_start: 0.7026 (t0) cc_final: 0.6621 (t0) REVERT: A 316 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 356 ASP cc_start: 0.8702 (m-30) cc_final: 0.8228 (m-30) REVERT: A 360 GLU cc_start: 0.8581 (pm20) cc_final: 0.8295 (mp0) REVERT: A 476 ASN cc_start: 0.8255 (m-40) cc_final: 0.7750 (m-40) REVERT: A 477 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7739 (m-40) REVERT: A 514 MET cc_start: 0.8948 (mmm) cc_final: 0.8565 (mtm) REVERT: B 91 LYS cc_start: 0.9456 (mmtm) cc_final: 0.9111 (mmmt) REVERT: B 94 ARG cc_start: 0.9315 (mmm-85) cc_final: 0.8938 (mmm-85) REVERT: C 108 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6195 (mtm110) REVERT: C 118 MET cc_start: 0.8591 (tpt) cc_final: 0.7858 (tpt) REVERT: C 210 PHE cc_start: 0.9108 (t80) cc_final: 0.8642 (t80) REVERT: C 395 MET cc_start: 0.8840 (ttt) cc_final: 0.8603 (ttt) REVERT: C 410 GLU cc_start: 0.9149 (tp30) cc_final: 0.8791 (tp30) REVERT: C 437 GLN cc_start: 0.8199 (tt0) cc_final: 0.7789 (tp40) outliers start: 28 outliers final: 22 residues processed: 160 average time/residue: 0.0921 time to fit residues: 20.8878 Evaluate side-chains 153 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN A 477 ASN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075802 restraints weight = 17350.148| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.06 r_work: 0.2898 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.8884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 8849 Z= 0.224 Angle : 1.362 82.813 12087 Z= 0.612 Chirality : 0.063 1.496 1277 Planarity : 0.005 0.072 1568 Dihedral : 9.522 81.929 1291 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.16 % Allowed : 24.52 % Favored : 72.32 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.52 (0.27), residues: 1083 helix: 1.70 (0.28), residues: 385 sheet: -0.50 (0.56), residues: 77 loop : -0.39 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.033 0.001 TYR A 443 PHE 0.021 0.001 PHE A 80 TRP 0.023 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8835) covalent geometry : angle 1.29728 (12078) hydrogen bonds : bond 0.02792 ( 315) hydrogen bonds : angle 4.76516 ( 900) metal coordination : bond 0.00105 ( 3) metal coordination : angle 15.26730 ( 9) Misc. bond : bond 0.03006 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1840.08 seconds wall clock time: 32 minutes 24.08 seconds (1944.08 seconds total)