Starting phenix.real_space_refine on Tue Apr 29 10:07:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcn_38248/04_2025/8xcn_38248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcn_38248/04_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_38248/04_2025/8xcn_38248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcn_38248/04_2025/8xcn_38248.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcn_38248/04_2025/8xcn_38248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcn_38248/04_2025/8xcn_38248.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.58, per 1000 atoms: 0.65 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: 2.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.48 Time building geometry restraints manager: 3.33 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: 11.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.660 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- 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 : 23.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (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 TRP 0.058 0.002 TRP A 173 HIS 0.021 0.001 HIS C 422 PHE 0.018 0.002 PHE B 54 TYR 0.040 0.003 TYR A 182 ARG 0.021 0.001 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.15315 ( 315) hydrogen bonds : angle 7.26087 ( 900) metal coordination : bond 0.00274 ( 3) metal coordination : angle 12.80312 ( 9) covalent geometry : bond 0.02988 ( 8835) covalent geometry : angle 1.66253 (12078) 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 : 1.000 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: 0.2386 time to fit residues: 99.2055 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 : 0.906 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 476 ASN A 539 ASN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.123869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105774 restraints weight = 16909.143| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.44 r_work: 0.3382 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.214 8849 Z= 0.236 Angle : 1.500 77.889 12087 Z= 0.529 Chirality : 0.051 0.601 1277 Planarity : 0.007 0.076 1568 Dihedral : 9.927 78.204 1299 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 6.10 % Allowed : 23.50 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1083 helix: 0.85 (0.27), residues: 391 sheet: -1.08 (0.52), residues: 87 loop : -0.78 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 188 HIS 0.009 0.001 HIS A 110 PHE 0.019 0.002 PHE C 158 TYR 0.017 0.002 TYR C 135 ARG 0.005 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 315) hydrogen bonds : angle 5.32971 ( 900) metal coordination : bond 0.01434 ( 3) metal coordination : angle 24.12246 ( 9) covalent geometry : bond 0.00524 ( 8835) covalent geometry : angle 1.34822 (12078) Misc. bond : bond 0.08842 ( 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 273 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.6063 (mt0) cc_final: 0.5854 (mp10) REVERT: A 211 ASP cc_start: 0.8654 (t0) cc_final: 0.8247 (t0) REVERT: A 268 ILE cc_start: 0.5175 (OUTLIER) cc_final: 0.4594 (pp) REVERT: A 312 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7142 (m-40) REVERT: A 346 MET cc_start: 0.9022 (mtt) cc_final: 0.8775 (mtp) REVERT: A 483 THR cc_start: 0.5566 (m) cc_final: 0.4781 (p) REVERT: A 485 MET cc_start: 0.7667 (mpt) cc_final: 0.6707 (mpt) REVERT: B 53 ASP cc_start: 0.8679 (m-30) cc_final: 0.8177 (t0) REVERT: B 93 LEU cc_start: 0.8640 (mt) cc_final: 0.8308 (tp) REVERT: B 96 HIS cc_start: 0.8580 (m-70) cc_final: 0.8102 (m90) REVERT: B 100 ASN cc_start: 0.9045 (m-40) cc_final: 0.8574 (m-40) REVERT: B 102 TYR cc_start: 0.7356 (m-80) cc_final: 0.7117 (m-10) REVERT: B 140 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7907 (mtpt) REVERT: C 118 MET cc_start: 0.8183 (tpt) cc_final: 0.7740 (tpt) REVERT: C 180 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5444 (t80) REVERT: C 210 PHE cc_start: 0.8777 (t80) cc_final: 0.8201 (t80) REVERT: C 267 MET cc_start: 0.9108 (tpt) cc_final: 0.8250 (tpt) REVERT: C 374 ASN cc_start: 0.8765 (t0) cc_final: 0.8503 (t0) REVERT: C 395 MET cc_start: 0.7700 (ttt) cc_final: 0.7019 (ttt) REVERT: C 410 GLU cc_start: 0.9043 (tp30) cc_final: 0.8803 (tp30) REVERT: C 425 ASN cc_start: 0.7522 (t0) cc_final: 0.7128 (p0) REVERT: C 437 GLN cc_start: 0.7971 (tt0) cc_final: 0.7582 (tp40) outliers start: 54 outliers final: 20 residues processed: 256 average time/residue: 0.1973 time to fit residues: 69.6880 Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE 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 306 ASN 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 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 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 78 ASN A 312 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 476 ASN A 539 ASN B 118 HIS C 216 GLN C 321 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102452 restraints weight = 17144.047| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.48 r_work: 0.3326 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 8849 Z= 0.204 Angle : 1.337 68.308 12087 Z= 0.438 Chirality : 0.081 2.406 1277 Planarity : 0.005 0.064 1568 Dihedral : 9.490 77.500 1293 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.75 % Allowed : 22.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1083 helix: 1.25 (0.28), residues: 387 sheet: -0.01 (0.58), residues: 68 loop : -0.78 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 173 HIS 0.005 0.001 HIS A 503 PHE 0.026 0.002 PHE C 156 TYR 0.023 0.002 TYR B 142 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 315) hydrogen bonds : angle 4.99362 ( 900) metal coordination : bond 0.02204 ( 3) metal coordination : angle 28.50950 ( 9) covalent geometry : bond 0.00451 ( 8835) covalent geometry : angle 1.08829 (12078) Misc. bond : bond 0.05848 ( 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 222 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.907 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 61 GLN cc_start: 0.7635 (mp10) cc_final: 0.7377 (mp10) REVERT: A 211 ASP cc_start: 0.8586 (t0) cc_final: 0.7844 (t0) REVERT: A 312 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7518 (m-40) REVERT: A 321 MET cc_start: 0.6210 (tpt) cc_final: 0.5975 (tpt) REVERT: A 360 GLU cc_start: 0.7969 (pm20) cc_final: 0.7736 (pm20) REVERT: A 438 TYR cc_start: 0.5359 (t80) cc_final: 0.4263 (t80) REVERT: A 483 THR cc_start: 0.6220 (m) cc_final: 0.5401 (p) REVERT: B 53 ASP cc_start: 0.8597 (m-30) cc_final: 0.8205 (t0) REVERT: B 93 LEU cc_start: 0.8741 (mt) cc_final: 0.8477 (mt) REVERT: B 96 HIS cc_start: 0.8519 (m-70) cc_final: 0.8197 (m90) REVERT: B 117 LEU cc_start: 0.8402 (mm) cc_final: 0.8067 (mt) REVERT: C 159 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8105 (m) REVERT: C 180 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.5326 (t80) REVERT: C 210 PHE cc_start: 0.8858 (t80) cc_final: 0.8447 (t80) REVERT: C 374 ASN cc_start: 0.8901 (t0) cc_final: 0.8694 (t0) REVERT: C 395 MET cc_start: 0.7812 (ttt) cc_final: 0.7609 (ttt) REVERT: C 410 GLU cc_start: 0.9103 (tp30) cc_final: 0.8819 (tp30) REVERT: C 425 ASN cc_start: 0.7807 (t0) cc_final: 0.7399 (p0) outliers start: 42 outliers final: 23 residues processed: 210 average time/residue: 0.1784 time to fit residues: 53.1170 Evaluate side-chains 178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR 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 312 ASN 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 493 VAL 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 75 MET Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 159 SER 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 316 SER Chi-restraints excluded: chain C residue 343 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS A 539 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.114547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095815 restraints weight = 17053.129| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.40 r_work: 0.3234 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 8849 Z= 0.159 Angle : 1.401 85.857 12087 Z= 0.436 Chirality : 0.057 1.272 1277 Planarity : 0.006 0.072 1568 Dihedral : 9.112 78.363 1293 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.41 % Allowed : 22.71 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1083 helix: 1.26 (0.28), residues: 392 sheet: -0.46 (0.57), residues: 76 loop : -0.69 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 173 HIS 0.004 0.001 HIS C 44 PHE 0.024 0.002 PHE C 156 TYR 0.014 0.001 TYR B 142 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 315) hydrogen bonds : angle 4.82885 ( 900) metal coordination : bond 0.00610 ( 3) metal coordination : angle 31.82808 ( 9) covalent geometry : bond 0.00365 ( 8835) covalent geometry : angle 1.09931 (12078) Misc. bond : bond 0.05029 ( 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 215 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7554 (mp10) cc_final: 0.7193 (mp10) REVERT: A 211 ASP cc_start: 0.8644 (t0) cc_final: 0.7920 (t0) REVERT: A 223 MET cc_start: 0.8035 (mmm) cc_final: 0.7489 (mtp) REVERT: A 259 THR cc_start: 0.5994 (p) cc_final: 0.5587 (t) REVERT: A 293 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6629 (mm-30) REVERT: A 312 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7253 (m110) REVERT: A 327 ILE cc_start: 0.8931 (mt) cc_final: 0.8641 (mp) REVERT: A 360 GLU cc_start: 0.8054 (pm20) cc_final: 0.7776 (pm20) REVERT: A 375 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8329 (m) REVERT: A 483 THR cc_start: 0.6262 (m) cc_final: 0.5361 (p) REVERT: A 485 MET cc_start: 0.7766 (mmm) cc_final: 0.7557 (mtt) REVERT: B 53 ASP cc_start: 0.8651 (m-30) cc_final: 0.8123 (t0) REVERT: B 93 LEU cc_start: 0.8876 (mt) cc_final: 0.8628 (mt) REVERT: B 96 HIS cc_start: 0.8473 (m-70) cc_final: 0.8261 (m90) REVERT: B 104 ASP cc_start: 0.7653 (t0) cc_final: 0.7390 (t0) REVERT: B 106 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: B 117 LEU cc_start: 0.8425 (mm) cc_final: 0.8107 (mt) REVERT: B 129 TYR cc_start: 0.8404 (m-80) cc_final: 0.7941 (m-80) REVERT: B 136 GLU cc_start: 0.8325 (pt0) cc_final: 0.8010 (pm20) REVERT: C 97 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8523 (mp0) REVERT: C 115 TYR cc_start: 0.7522 (m-80) cc_final: 0.7314 (m-80) REVERT: C 118 MET cc_start: 0.8259 (tpt) cc_final: 0.7754 (tpt) REVERT: C 159 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8084 (m) REVERT: C 180 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5424 (t80) REVERT: C 210 PHE cc_start: 0.8895 (t80) cc_final: 0.8471 (t80) REVERT: C 354 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8412 (t) REVERT: C 374 ASN cc_start: 0.8928 (t0) cc_final: 0.8726 (t0) REVERT: C 395 MET cc_start: 0.8369 (ttt) cc_final: 0.8096 (ttt) REVERT: C 410 GLU cc_start: 0.9139 (tp30) cc_final: 0.8875 (tp30) outliers start: 39 outliers final: 22 residues processed: 207 average time/residue: 0.2067 time to fit residues: 60.9406 Evaluate side-chains 171 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL 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 312 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 493 VAL Chi-restraints excluded: chain B residue 106 GLU 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 183 PHE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 0.0040 chunk 77 optimal weight: 9.9990 chunk 97 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 219 ASN A 539 ASN B 118 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.113075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095248 restraints weight = 16904.712| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.33 r_work: 0.3204 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8849 Z= 0.146 Angle : 1.223 83.755 12087 Z= 0.419 Chirality : 0.060 1.450 1277 Planarity : 0.005 0.057 1568 Dihedral : 9.002 78.753 1292 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.18 % Allowed : 23.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1083 helix: 1.28 (0.28), residues: 391 sheet: -0.43 (0.57), residues: 77 loop : -0.64 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 173 HIS 0.005 0.001 HIS A 110 PHE 0.024 0.001 PHE C 156 TYR 0.016 0.001 TYR A 438 ARG 0.006 0.000 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 315) hydrogen bonds : angle 4.76488 ( 900) metal coordination : bond 0.00275 ( 3) metal coordination : angle 21.83314 ( 9) covalent geometry : bond 0.00331 ( 8835) covalent geometry : angle 1.06800 (12078) Misc. bond : bond 0.03620 ( 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 197 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7500 (p0) cc_final: 0.6957 (p0) REVERT: A 61 GLN cc_start: 0.7512 (mp10) cc_final: 0.7101 (mp10) REVERT: A 211 ASP cc_start: 0.8646 (t0) cc_final: 0.7913 (t0) REVERT: A 259 THR cc_start: 0.6158 (p) cc_final: 0.5707 (t) REVERT: A 327 ILE cc_start: 0.8923 (mt) cc_final: 0.8655 (mp) REVERT: A 360 GLU cc_start: 0.8096 (pm20) cc_final: 0.7855 (pm20) REVERT: A 375 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8137 (m) REVERT: A 483 THR cc_start: 0.6182 (m) cc_final: 0.5273 (p) REVERT: A 490 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7852 (mmm160) REVERT: B 106 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 112 MET cc_start: 0.8358 (mtp) cc_final: 0.7971 (ttp) REVERT: B 129 TYR cc_start: 0.8427 (m-80) cc_final: 0.7934 (m-80) REVERT: B 136 GLU cc_start: 0.8294 (pt0) cc_final: 0.7945 (pm20) REVERT: C 97 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8606 (mp0) REVERT: C 118 MET cc_start: 0.8285 (tpt) cc_final: 0.7665 (tpt) REVERT: C 159 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8122 (m) REVERT: C 161 ARG cc_start: 0.8136 (ptp-170) cc_final: 0.7729 (ptp-110) REVERT: C 180 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5524 (t80) REVERT: C 210 PHE cc_start: 0.8900 (t80) cc_final: 0.8458 (t80) REVERT: C 354 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8436 (t) REVERT: C 395 MET cc_start: 0.8366 (ttt) cc_final: 0.8163 (ttt) REVERT: C 410 GLU cc_start: 0.9131 (tp30) cc_final: 0.8860 (tp30) outliers start: 37 outliers final: 22 residues processed: 188 average time/residue: 0.1967 time to fit residues: 53.3514 Evaluate side-chains 174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR 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 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 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 120 THR 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 159 SER 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 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 539 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS ** C 321 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 = 0.3519 r_free = 0.3519 target = 0.105766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087519 restraints weight = 16845.049| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.28 r_work: 0.3099 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 8849 Z= 0.166 Angle : 1.238 82.856 12087 Z= 0.421 Chirality : 0.062 1.497 1277 Planarity : 0.005 0.056 1568 Dihedral : 9.048 80.168 1291 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.08 % Allowed : 23.05 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1083 helix: 1.33 (0.28), residues: 398 sheet: -0.45 (0.58), residues: 77 loop : -0.63 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 173 HIS 0.004 0.001 HIS A 487 PHE 0.018 0.001 PHE C 156 TYR 0.016 0.002 TYR B 162 ARG 0.005 0.001 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 315) hydrogen bonds : angle 4.77732 ( 900) metal coordination : bond 0.00103 ( 3) metal coordination : angle 22.76631 ( 9) covalent geometry : bond 0.00387 ( 8835) covalent geometry : angle 1.07169 (12078) Misc. bond : bond 0.04637 ( 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 197 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7898 (p0) cc_final: 0.7330 (p0) REVERT: A 211 ASP cc_start: 0.8704 (t0) cc_final: 0.7995 (t0) REVERT: A 259 THR cc_start: 0.6705 (p) cc_final: 0.6145 (t) REVERT: A 322 MET cc_start: 0.5556 (mmt) cc_final: 0.5056 (mmt) REVERT: A 327 ILE cc_start: 0.8906 (mt) cc_final: 0.8652 (mp) REVERT: A 356 ASP cc_start: 0.8223 (m-30) cc_final: 0.7841 (m-30) REVERT: A 360 GLU cc_start: 0.8151 (pm20) cc_final: 0.7870 (pm20) REVERT: A 483 THR cc_start: 0.6483 (m) cc_final: 0.5483 (p) REVERT: A 490 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7891 (mmm160) REVERT: B 106 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: B 112 MET cc_start: 0.8545 (mtp) cc_final: 0.8015 (ttp) REVERT: C 97 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8639 (mp0) REVERT: C 118 MET cc_start: 0.8463 (tpt) cc_final: 0.7685 (tpt) REVERT: C 180 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5687 (t80) REVERT: C 210 PHE cc_start: 0.8970 (t80) cc_final: 0.8557 (t80) REVERT: C 354 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8592 (t) REVERT: C 395 MET cc_start: 0.8709 (ttt) cc_final: 0.8419 (ttt) REVERT: C 410 GLU cc_start: 0.9133 (tp30) cc_final: 0.8860 (tp30) outliers start: 45 outliers final: 28 residues processed: 187 average time/residue: 0.2014 time to fit residues: 53.0728 Evaluate side-chains 168 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 33 VAL 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 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE 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 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 166 ILE 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 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 431 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 72 optimal weight: 0.0370 chunk 88 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084592 restraints weight = 17135.222| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.28 r_work: 0.3060 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8849 Z= 0.158 Angle : 1.220 82.957 12087 Z= 0.420 Chirality : 0.062 1.496 1277 Planarity : 0.005 0.055 1568 Dihedral : 9.092 80.731 1291 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.52 % Allowed : 24.63 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1083 helix: 1.47 (0.28), residues: 391 sheet: 0.36 (0.65), residues: 61 loop : -0.62 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 173 HIS 0.006 0.001 HIS A 110 PHE 0.015 0.001 PHE C 158 TYR 0.016 0.001 TYR A 79 ARG 0.004 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 315) hydrogen bonds : angle 4.79023 ( 900) metal coordination : bond 0.00108 ( 3) metal coordination : angle 21.57785 ( 9) covalent geometry : bond 0.00369 ( 8835) covalent geometry : angle 1.06919 (12078) Misc. bond : bond 0.02836 ( 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 193 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8044 (p0) cc_final: 0.7426 (p0) REVERT: A 61 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7611 (mm-40) REVERT: A 211 ASP cc_start: 0.8708 (t0) cc_final: 0.7990 (t0) REVERT: A 356 ASP cc_start: 0.8276 (m-30) cc_final: 0.7955 (m-30) REVERT: A 360 GLU cc_start: 0.8227 (pm20) cc_final: 0.7995 (pm20) REVERT: A 375 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8145 (m) REVERT: A 477 ASN cc_start: 0.7779 (m-40) cc_final: 0.7278 (m-40) REVERT: A 479 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7982 (mt) REVERT: A 483 THR cc_start: 0.6269 (m) cc_final: 0.5288 (p) REVERT: A 490 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7879 (mmm160) REVERT: B 89 GLN cc_start: 0.8656 (mt0) cc_final: 0.7948 (mp10) REVERT: B 94 ARG cc_start: 0.9247 (mmm-85) cc_final: 0.8970 (mmm-85) REVERT: B 106 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: B 112 MET cc_start: 0.8643 (mtp) cc_final: 0.8175 (ttp) REVERT: B 115 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.6555 (p0) REVERT: B 136 GLU cc_start: 0.8309 (pt0) cc_final: 0.7911 (pm20) REVERT: C 97 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8649 (mp0) REVERT: C 118 MET cc_start: 0.8505 (tpt) cc_final: 0.7615 (tpt) REVERT: C 180 PHE cc_start: 0.6588 (OUTLIER) cc_final: 0.5629 (t80) REVERT: C 210 PHE cc_start: 0.8988 (t80) cc_final: 0.8569 (t80) REVERT: C 354 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8549 (t) REVERT: C 395 MET cc_start: 0.8630 (ttt) cc_final: 0.8334 (ttt) REVERT: C 410 GLU cc_start: 0.9105 (tp30) cc_final: 0.8834 (tp30) outliers start: 40 outliers final: 29 residues processed: 184 average time/residue: 0.2056 time to fit residues: 54.5504 Evaluate side-chains 178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 33 VAL 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 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 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 479 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR 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 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 431 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 90 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075212 restraints weight = 17579.361| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.19 r_work: 0.2897 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.8171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 8849 Z= 0.198 Angle : 1.267 82.674 12087 Z= 0.439 Chirality : 0.062 1.502 1277 Planarity : 0.005 0.059 1568 Dihedral : 9.334 83.368 1289 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.86 % Allowed : 24.97 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1083 helix: 1.31 (0.28), residues: 397 sheet: 0.12 (0.66), residues: 71 loop : -0.47 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 173 HIS 0.006 0.001 HIS A 110 PHE 0.014 0.002 PHE A 80 TYR 0.018 0.002 TYR A 79 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 315) hydrogen bonds : angle 4.98251 ( 900) metal coordination : bond 0.00107 ( 3) metal coordination : angle 22.60967 ( 9) covalent geometry : bond 0.00477 ( 8835) covalent geometry : angle 1.10672 (12078) Misc. bond : bond 0.06295 ( 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 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.934 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: 0.8256 (p0) cc_final: 0.7723 (p0) REVERT: A 68 TYR cc_start: 0.8941 (m-80) cc_final: 0.8724 (m-80) REVERT: A 211 ASP cc_start: 0.8717 (t0) cc_final: 0.8332 (t0) REVERT: A 293 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 322 MET cc_start: 0.6145 (mmt) cc_final: 0.5845 (mmt) REVERT: A 356 ASP cc_start: 0.8439 (m-30) cc_final: 0.8002 (m-30) REVERT: A 360 GLU cc_start: 0.8378 (pm20) cc_final: 0.8074 (mp0) REVERT: A 375 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8143 (m) REVERT: A 425 TYR cc_start: 0.8723 (m-80) cc_final: 0.8484 (m-80) REVERT: A 476 ASN cc_start: 0.8180 (m-40) cc_final: 0.7861 (m-40) REVERT: A 479 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 56 GLN cc_start: 0.8911 (tt0) cc_final: 0.8675 (tt0) REVERT: B 112 MET cc_start: 0.8730 (mtp) cc_final: 0.8197 (ttp) REVERT: B 115 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.6625 (p0) REVERT: C 97 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8686 (mp0) REVERT: C 118 MET cc_start: 0.8593 (tpt) cc_final: 0.7907 (tpt) REVERT: C 180 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.5921 (t80) REVERT: C 210 PHE cc_start: 0.9104 (t80) cc_final: 0.8586 (t80) REVERT: C 354 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8669 (t) REVERT: C 410 GLU cc_start: 0.9132 (tp30) cc_final: 0.8858 (tp30) outliers start: 43 outliers final: 26 residues processed: 184 average time/residue: 0.1916 time to fit residues: 49.7479 Evaluate side-chains 166 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 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 479 ILE 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 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 166 ILE 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 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 431 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS B 118 HIS ** 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 = 0.3378 r_free = 0.3378 target = 0.096421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078345 restraints weight = 17314.701| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.10 r_work: 0.2948 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.8277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8849 Z= 0.159 Angle : 1.263 82.940 12087 Z= 0.437 Chirality : 0.063 1.498 1277 Planarity : 0.005 0.067 1568 Dihedral : 9.343 82.207 1289 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.62 % Allowed : 25.31 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1083 helix: 1.45 (0.28), residues: 396 sheet: 0.03 (0.66), residues: 61 loop : -0.50 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 PHE 0.019 0.001 PHE C 158 TYR 0.024 0.002 TYR A 255 ARG 0.005 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 315) hydrogen bonds : angle 4.86614 ( 900) metal coordination : bond 0.00096 ( 3) metal coordination : angle 22.50240 ( 9) covalent geometry : bond 0.00371 ( 8835) covalent geometry : angle 1.10378 (12078) Misc. bond : bond 0.04130 ( 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 182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 1.069 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: 0.8296 (p0) cc_final: 0.7742 (p0) REVERT: A 68 TYR cc_start: 0.8965 (m-80) cc_final: 0.8727 (m-80) REVERT: A 211 ASP cc_start: 0.8716 (t0) cc_final: 0.8052 (t0) REVERT: A 293 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 321 MET cc_start: 0.7804 (tpt) cc_final: 0.7499 (tpt) REVERT: A 356 ASP cc_start: 0.8448 (m-30) cc_final: 0.8032 (m-30) REVERT: A 360 GLU cc_start: 0.8399 (pm20) cc_final: 0.8117 (mp0) REVERT: A 375 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8223 (m) REVERT: A 425 TYR cc_start: 0.8739 (m-80) cc_final: 0.8522 (m-80) REVERT: A 476 ASN cc_start: 0.8293 (m-40) cc_final: 0.7956 (m-40) REVERT: A 479 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 94 ARG cc_start: 0.9280 (mmm-85) cc_final: 0.9070 (mmm-85) REVERT: B 112 MET cc_start: 0.8703 (mtp) cc_final: 0.8335 (ttp) REVERT: B 115 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.6523 (p0) REVERT: B 136 GLU cc_start: 0.8535 (pt0) cc_final: 0.8055 (pm20) REVERT: C 97 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8689 (mp0) REVERT: C 118 MET cc_start: 0.8577 (tpt) cc_final: 0.7827 (tpt) REVERT: C 180 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.5862 (t80) REVERT: C 210 PHE cc_start: 0.9078 (t80) cc_final: 0.8600 (t80) REVERT: C 354 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8710 (t) REVERT: C 395 MET cc_start: 0.8658 (ttt) cc_final: 0.8380 (ttt) REVERT: C 408 THR cc_start: 0.8156 (t) cc_final: 0.7951 (p) REVERT: C 410 GLU cc_start: 0.9145 (tp30) cc_final: 0.8877 (tp30) outliers start: 32 outliers final: 20 residues processed: 175 average time/residue: 0.1936 time to fit residues: 48.1465 Evaluate side-chains 167 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL 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 253 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 479 ILE 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 B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 166 ILE 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 354 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.0050 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS B 118 HIS ** 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 = 0.3413 r_free = 0.3413 target = 0.098587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.080540 restraints weight = 17047.731| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.13 r_work: 0.3002 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.8349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 8849 Z= 0.148 Angle : 1.244 82.935 12087 Z= 0.430 Chirality : 0.062 1.504 1277 Planarity : 0.005 0.063 1568 Dihedral : 9.295 82.245 1289 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 3.28 % Allowed : 25.65 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1083 helix: 1.54 (0.28), residues: 394 sheet: -0.14 (0.65), residues: 61 loop : -0.55 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 173 HIS 0.006 0.001 HIS A 110 PHE 0.015 0.001 PHE C 158 TYR 0.032 0.001 TYR A 255 ARG 0.007 0.000 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.02918 ( 315) hydrogen bonds : angle 4.81873 ( 900) metal coordination : bond 0.00068 ( 3) metal coordination : angle 21.39366 ( 9) covalent geometry : bond 0.00338 ( 8835) covalent geometry : angle 1.09882 (12078) Misc. bond : bond 0.02035 ( 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 182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.017 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 37 ASP cc_start: 0.8268 (p0) cc_final: 0.7736 (p0) REVERT: A 68 TYR cc_start: 0.8976 (m-80) cc_final: 0.8765 (m-80) REVERT: A 211 ASP cc_start: 0.8718 (t0) cc_final: 0.8056 (t0) REVERT: A 271 TYR cc_start: 0.8226 (m-80) cc_final: 0.7574 (m-80) REVERT: A 293 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 356 ASP cc_start: 0.8467 (m-30) cc_final: 0.8097 (m-30) REVERT: A 360 GLU cc_start: 0.8304 (pm20) cc_final: 0.8081 (mp0) REVERT: A 476 ASN cc_start: 0.8243 (m-40) cc_final: 0.7881 (m-40) REVERT: B 56 GLN cc_start: 0.8896 (tt0) cc_final: 0.8683 (tt0) REVERT: B 94 ARG cc_start: 0.9283 (mmm-85) cc_final: 0.8985 (mmm-85) REVERT: B 112 MET cc_start: 0.8709 (mtp) cc_final: 0.8421 (ttp) REVERT: B 115 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.6671 (p0) REVERT: C 97 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8653 (mp0) REVERT: C 180 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.5847 (t80) REVERT: C 210 PHE cc_start: 0.9060 (t80) cc_final: 0.8549 (t80) REVERT: C 354 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8722 (t) REVERT: C 395 MET cc_start: 0.8447 (ttt) cc_final: 0.8117 (ttt) REVERT: C 408 THR cc_start: 0.8213 (t) cc_final: 0.7997 (p) REVERT: C 410 GLU cc_start: 0.9151 (tp30) cc_final: 0.8879 (tp30) outliers start: 29 outliers final: 23 residues processed: 176 average time/residue: 0.1888 time to fit residues: 47.2934 Evaluate side-chains 173 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 86 LEU 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 253 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 479 ILE 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 B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 166 ILE 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 354 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 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 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS B 118 HIS ** 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 = 0.3388 r_free = 0.3388 target = 0.097067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078818 restraints weight = 17403.721| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.15 r_work: 0.2964 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.8491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8849 Z= 0.162 Angle : 1.252 82.879 12087 Z= 0.435 Chirality : 0.062 1.502 1277 Planarity : 0.005 0.063 1568 Dihedral : 9.259 82.744 1289 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.05 % Allowed : 25.99 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1083 helix: 1.59 (0.28), residues: 395 sheet: -0.06 (0.67), residues: 61 loop : -0.53 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 173 HIS 0.009 0.001 HIS A 110 PHE 0.017 0.001 PHE C 158 TYR 0.049 0.002 TYR A 255 ARG 0.006 0.000 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 315) hydrogen bonds : angle 4.79122 ( 900) metal coordination : bond 0.00096 ( 3) metal coordination : angle 21.46139 ( 9) covalent geometry : bond 0.00383 ( 8835) covalent geometry : angle 1.10669 (12078) Misc. bond : bond 0.02665 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4421.73 seconds wall clock time: 77 minutes 38.49 seconds (4658.49 seconds total)