Starting phenix.real_space_refine on Wed Jan 15 16:20:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcn_38248/01_2025/8xcn_38248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcn_38248/01_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_38248/01_2025/8xcn_38248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcn_38248/01_2025/8xcn_38248.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcn_38248/01_2025/8xcn_38248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcn_38248/01_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-5571/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: 5.65, per 1000 atoms: 0.66 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: 2.74 Conformation dependent library (CDL) restraints added in 990.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 41.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 2.43 Time building geometry restraints manager: 3.01 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: 1.260 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.070 ------------------------------------------------------------------------------- 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 : 0.030 1.606 8835 Z= 1.907 Angle : 1.663 73.755 12078 Z= 0.722 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.918 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: 0.2447 time to fit residues: 101.6071 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 : 0.952 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.120492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102144 restraints weight = 16875.629| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.39 r_work: 0.3332 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.171 8835 Z= 0.390 Angle : 1.308 69.984 12078 Z= 0.519 Chirality : 0.063 1.418 1277 Planarity : 0.007 0.075 1568 Dihedral : 9.954 77.647 1299 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 6.33 % Allowed : 22.37 % Favored : 71.30 % 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: -0.31 (0.25), residues: 1083 helix: 0.86 (0.27), residues: 391 sheet: -1.17 (0.51), residues: 87 loop : -0.74 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 173 HIS 0.009 0.001 HIS A 110 PHE 0.018 0.002 PHE C 250 TYR 0.019 0.002 TYR C 135 ARG 0.005 0.001 ARG C 190 *********************** 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 266 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.6096 (mt0) cc_final: 0.5893 (mp10) REVERT: A 211 ASP cc_start: 0.8711 (t0) cc_final: 0.8037 (t0) REVERT: A 312 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7169 (m-40) REVERT: A 346 MET cc_start: 0.9045 (mtt) cc_final: 0.8789 (mtp) REVERT: A 483 THR cc_start: 0.5722 (m) cc_final: 0.4894 (p) REVERT: A 485 MET cc_start: 0.7742 (mpt) cc_final: 0.7058 (mpt) REVERT: B 53 ASP cc_start: 0.8690 (m-30) cc_final: 0.8202 (t0) REVERT: B 93 LEU cc_start: 0.8674 (mt) cc_final: 0.8342 (tp) REVERT: B 96 HIS cc_start: 0.8550 (m-70) cc_final: 0.8025 (m90) REVERT: B 100 ASN cc_start: 0.9043 (m-40) cc_final: 0.8555 (m-40) REVERT: B 102 TYR cc_start: 0.7410 (m-80) cc_final: 0.7198 (m-80) REVERT: C 118 MET cc_start: 0.8246 (tpt) cc_final: 0.7807 (tpt) REVERT: C 180 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5532 (t80) REVERT: C 210 PHE cc_start: 0.8820 (t80) cc_final: 0.8274 (t80) REVERT: C 374 ASN cc_start: 0.8859 (t0) cc_final: 0.8604 (t0) REVERT: C 395 MET cc_start: 0.7990 (ttt) cc_final: 0.7472 (ttt) REVERT: C 410 GLU cc_start: 0.9063 (tp30) cc_final: 0.8828 (tp30) REVERT: C 437 GLN cc_start: 0.8021 (tt0) cc_final: 0.7656 (tp40) outliers start: 56 outliers final: 19 residues processed: 251 average time/residue: 0.2028 time to fit residues: 70.6277 Evaluate side-chains 178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 306 ASN 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 479 ILE 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: 1.9990 chunk 84 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.0020 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.4726 ------------------------------------------------------------------------------- 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 476 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN B 118 HIS C 216 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.118132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099035 restraints weight = 17122.993| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.46 r_work: 0.3275 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 8835 Z= 0.258 Angle : 1.137 89.553 12078 Z= 0.446 Chirality : 0.053 1.005 1277 Planarity : 0.005 0.066 1568 Dihedral : 9.541 77.486 1292 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.29 % Allowed : 21.58 % Favored : 74.12 % 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: 0.01 (0.25), residues: 1083 helix: 1.23 (0.27), residues: 387 sheet: 0.02 (0.59), residues: 68 loop : -0.79 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 173 HIS 0.006 0.001 HIS A 110 PHE 0.027 0.002 PHE C 156 TYR 0.016 0.002 TYR C 359 ARG 0.004 0.000 ARG C 190 *********************** 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 217 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.7675 (mp10) cc_final: 0.7445 (mp10) REVERT: A 211 ASP cc_start: 0.8617 (t0) cc_final: 0.7837 (t0) REVERT: A 312 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7252 (m110) REVERT: A 360 GLU cc_start: 0.7896 (pm20) cc_final: 0.7636 (pm20) REVERT: A 438 TYR cc_start: 0.5403 (t80) cc_final: 0.4310 (t80) REVERT: A 483 THR cc_start: 0.6110 (m) cc_final: 0.5260 (p) REVERT: B 53 ASP cc_start: 0.8652 (m-30) cc_final: 0.7985 (t0) REVERT: B 56 GLN cc_start: 0.8798 (tt0) cc_final: 0.8463 (tt0) REVERT: B 91 LYS cc_start: 0.9366 (mmmt) cc_final: 0.8969 (mmmt) REVERT: B 96 HIS cc_start: 0.8540 (m-70) cc_final: 0.8190 (m170) REVERT: B 117 LEU cc_start: 0.8485 (mm) cc_final: 0.8159 (mt) REVERT: C 161 ARG cc_start: 0.7927 (ptp-110) cc_final: 0.7601 (ptp-110) REVERT: C 180 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.5386 (t80) REVERT: C 210 PHE cc_start: 0.8893 (t80) cc_final: 0.8445 (t80) REVERT: C 374 ASN cc_start: 0.8890 (t0) cc_final: 0.8658 (t0) REVERT: C 395 MET cc_start: 0.7985 (ttt) cc_final: 0.7567 (ttt) REVERT: C 410 GLU cc_start: 0.9098 (tp30) cc_final: 0.8830 (tp30) REVERT: C 437 GLN cc_start: 0.8042 (tt0) cc_final: 0.7639 (tp40) outliers start: 38 outliers final: 21 residues processed: 209 average time/residue: 0.1936 time to fit residues: 57.3264 Evaluate side-chains 181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 306 ASN Chi-restraints excluded: chain A residue 312 ASN 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 95 THR Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 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: 4.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 320 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 = 0.3585 r_free = 0.3585 target = 0.109834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091313 restraints weight = 16993.267| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.34 r_work: 0.3156 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 8835 Z= 0.256 Angle : 1.097 85.127 12078 Z= 0.431 Chirality : 0.059 1.327 1277 Planarity : 0.005 0.057 1568 Dihedral : 9.136 79.412 1292 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.20 % Allowed : 21.24 % Favored : 73.56 % 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: 0.09 (0.26), residues: 1083 helix: 1.25 (0.27), residues: 392 sheet: -0.64 (0.56), residues: 76 loop : -0.62 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 173 HIS 0.005 0.001 HIS A 110 PHE 0.029 0.002 PHE C 156 TYR 0.015 0.001 TYR C 359 ARG 0.004 0.000 ARG A 490 *********************** 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 228 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8696 (t0) cc_final: 0.7971 (t0) REVERT: A 259 THR cc_start: 0.6232 (p) cc_final: 0.5794 (t) REVERT: A 327 ILE cc_start: 0.8980 (mt) cc_final: 0.8688 (mp) REVERT: A 360 GLU cc_start: 0.8002 (pm20) cc_final: 0.7753 (pm20) REVERT: A 483 THR cc_start: 0.6270 (m) cc_final: 0.5361 (p) REVERT: B 53 ASP cc_start: 0.8643 (m-30) cc_final: 0.8023 (t0) REVERT: B 91 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9113 (mmmt) REVERT: B 104 ASP cc_start: 0.7657 (t0) cc_final: 0.7397 (t0) REVERT: B 106 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: B 129 TYR cc_start: 0.8413 (m-80) cc_final: 0.7950 (m-80) REVERT: B 136 GLU cc_start: 0.8399 (pt0) cc_final: 0.8046 (pm20) REVERT: C 118 MET cc_start: 0.8398 (tpt) cc_final: 0.7782 (tpt) REVERT: C 180 PHE cc_start: 0.6285 (OUTLIER) cc_final: 0.5565 (t80) REVERT: C 210 PHE cc_start: 0.8918 (t80) cc_final: 0.8480 (t80) REVERT: C 374 ASN cc_start: 0.8923 (t0) cc_final: 0.8698 (t0) REVERT: C 410 GLU cc_start: 0.9142 (tp30) cc_final: 0.8866 (tp30) REVERT: C 437 GLN cc_start: 0.8140 (tt0) cc_final: 0.7744 (tp40) outliers start: 46 outliers final: 28 residues processed: 217 average time/residue: 0.1856 time to fit residues: 57.2279 Evaluate side-chains 170 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 31 LEU 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 274 ASP Chi-restraints excluded: chain A residue 306 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 106 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 THR 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 96 LEU Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 387 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 503 HIS A 539 ASN B 118 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.081672 restraints weight = 16999.392| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.25 r_work: 0.3021 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 8835 Z= 0.291 Angle : 1.093 83.695 12078 Z= 0.432 Chirality : 0.060 1.422 1277 Planarity : 0.005 0.061 1568 Dihedral : 9.336 80.219 1291 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.75 % Allowed : 23.50 % Favored : 71.75 % 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: 0.20 (0.26), residues: 1083 helix: 1.30 (0.28), residues: 390 sheet: 0.27 (0.64), residues: 61 loop : -0.63 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 PHE 0.020 0.002 PHE C 156 TYR 0.015 0.002 TYR C 359 ARG 0.006 0.001 ARG A 52 *********************** 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 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.009 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: 0.8022 (p0) cc_final: 0.7487 (p0) REVERT: A 211 ASP cc_start: 0.8748 (t0) cc_final: 0.8060 (t0) REVERT: A 259 THR cc_start: 0.6697 (p) cc_final: 0.6125 (t) REVERT: A 322 MET cc_start: 0.5940 (mmt) cc_final: 0.5233 (mmt) REVERT: A 356 ASP cc_start: 0.8242 (m-30) cc_final: 0.7875 (m-30) REVERT: A 360 GLU cc_start: 0.8229 (pm20) cc_final: 0.7936 (pm20) REVERT: A 479 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7829 (mt) REVERT: A 490 ARG cc_start: 0.8300 (mmm160) cc_final: 0.8041 (mmm160) REVERT: B 86 PHE cc_start: 0.8202 (t80) cc_final: 0.7479 (t80) REVERT: B 89 GLN cc_start: 0.8709 (mt0) cc_final: 0.7928 (mp10) REVERT: B 94 ARG cc_start: 0.9284 (mmm-85) cc_final: 0.9033 (mmm-85) REVERT: B 100 ASN cc_start: 0.9060 (m-40) cc_final: 0.8832 (m-40) REVERT: B 106 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: B 112 MET cc_start: 0.8485 (mtp) cc_final: 0.8090 (ttp) REVERT: B 117 LEU cc_start: 0.8499 (mm) cc_final: 0.8040 (mt) REVERT: C 97 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8624 (mp0) REVERT: C 108 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6082 (mtm110) REVERT: C 180 PHE cc_start: 0.6568 (OUTLIER) cc_final: 0.5729 (t80) REVERT: C 210 PHE cc_start: 0.9019 (t80) cc_final: 0.8566 (t80) REVERT: C 374 ASN cc_start: 0.8937 (t0) cc_final: 0.8703 (t0) REVERT: C 410 GLU cc_start: 0.9142 (tp30) cc_final: 0.8894 (tp30) REVERT: C 437 GLN cc_start: 0.8146 (tt0) cc_final: 0.7779 (tp40) outliers start: 42 outliers final: 26 residues processed: 185 average time/residue: 0.1961 time to fit residues: 51.6177 Evaluate side-chains 168 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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 A residue 500 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 106 GLU 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 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 387 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 0.0570 chunk 77 optimal weight: 20.0000 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 503 HIS B 118 HIS ** B 123 GLN ** 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 = 0.3402 r_free = 0.3402 target = 0.097794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079375 restraints weight = 16996.320| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.16 r_work: 0.2980 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.7589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8835 Z= 0.279 Angle : 1.078 82.743 12078 Z= 0.421 Chirality : 0.062 1.506 1277 Planarity : 0.005 0.058 1568 Dihedral : 9.259 80.436 1291 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.75 % Allowed : 23.28 % Favored : 71.98 % 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: 0.27 (0.26), residues: 1083 helix: 1.37 (0.28), residues: 391 sheet: -0.53 (0.57), residues: 76 loop : -0.48 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 PHE 0.014 0.001 PHE C 156 TYR 0.014 0.001 TYR A 79 ARG 0.003 0.000 ARG A 418 *********************** 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 189 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8161 (p0) cc_final: 0.7548 (p0) REVERT: A 68 TYR cc_start: 0.8933 (m-80) cc_final: 0.8525 (m-80) REVERT: A 211 ASP cc_start: 0.8707 (t0) cc_final: 0.8005 (t0) REVERT: A 293 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 322 MET cc_start: 0.5982 (mmt) cc_final: 0.5760 (mmt) REVERT: A 356 ASP cc_start: 0.8355 (m-30) cc_final: 0.8069 (m-30) REVERT: A 442 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7525 (tp30) REVERT: A 483 THR cc_start: 0.6586 (m) cc_final: 0.5671 (p) REVERT: A 490 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7967 (mmm160) REVERT: B 89 GLN cc_start: 0.8696 (mt0) cc_final: 0.7933 (mp10) REVERT: B 91 LYS cc_start: 0.9391 (mmtm) cc_final: 0.8958 (mmmt) REVERT: B 94 ARG cc_start: 0.9332 (mmm-85) cc_final: 0.9013 (mmm-85) REVERT: B 112 MET cc_start: 0.8596 (mtp) cc_final: 0.8244 (ttp) REVERT: B 115 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.6488 (p0) REVERT: B 136 GLU cc_start: 0.8319 (pt0) cc_final: 0.7907 (pm20) REVERT: C 97 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8578 (mp0) REVERT: C 108 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6442 (mtt90) REVERT: C 118 MET cc_start: 0.8600 (tpt) cc_final: 0.7895 (tpt) REVERT: C 180 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5821 (t80) REVERT: C 210 PHE cc_start: 0.9052 (t80) cc_final: 0.8606 (t80) REVERT: C 395 MET cc_start: 0.8414 (ttt) cc_final: 0.8033 (ttt) REVERT: C 410 GLU cc_start: 0.9129 (tp30) cc_final: 0.8878 (tp30) REVERT: C 437 GLN cc_start: 0.8145 (tt0) cc_final: 0.7786 (tp40) outliers start: 42 outliers final: 28 residues processed: 181 average time/residue: 0.2022 time to fit residues: 50.8569 Evaluate side-chains 169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 11 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 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 281 VAL Chi-restraints excluded: chain A residue 306 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 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 161 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 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 0.0050 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS B 118 HIS ** B 123 GLN ** 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 = 0.3417 r_free = 0.3417 target = 0.098725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.080201 restraints weight = 17224.992| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.19 r_work: 0.2995 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.7776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8835 Z= 0.242 Angle : 1.071 83.006 12078 Z= 0.418 Chirality : 0.061 1.484 1277 Planarity : 0.005 0.057 1568 Dihedral : 9.187 80.394 1289 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.63 % Allowed : 24.07 % Favored : 71.30 % 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: 0.33 (0.26), residues: 1083 helix: 1.44 (0.28), residues: 389 sheet: -0.43 (0.59), residues: 71 loop : -0.47 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 PHE 0.013 0.001 PHE A 270 TYR 0.044 0.002 TYR A 255 ARG 0.002 0.000 ARG A 418 *********************** 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 195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8274 (p0) cc_final: 0.7700 (p0) REVERT: A 68 TYR cc_start: 0.8978 (m-80) cc_final: 0.8677 (m-80) REVERT: A 79 TYR cc_start: 0.8148 (m-80) cc_final: 0.7781 (m-80) REVERT: A 211 ASP cc_start: 0.8709 (t0) cc_final: 0.8036 (t0) REVERT: A 276 GLN cc_start: 0.6292 (mp10) cc_final: 0.6090 (mp10) REVERT: A 293 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 356 ASP cc_start: 0.8387 (m-30) cc_final: 0.8027 (m-30) REVERT: A 360 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: A 425 TYR cc_start: 0.8746 (m-80) cc_final: 0.8509 (m-80) REVERT: A 453 GLN cc_start: 0.8582 (tp40) cc_final: 0.8377 (tp-100) REVERT: A 483 THR cc_start: 0.6474 (m) cc_final: 0.5511 (p) REVERT: B 89 GLN cc_start: 0.8684 (mt0) cc_final: 0.7983 (mp10) REVERT: B 91 LYS cc_start: 0.9371 (mmtm) cc_final: 0.9071 (mmmt) REVERT: B 94 ARG cc_start: 0.9315 (mmm-85) cc_final: 0.8867 (mmm-85) REVERT: B 112 MET cc_start: 0.8614 (mtp) cc_final: 0.8319 (ttp) REVERT: B 115 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.6478 (p0) REVERT: C 97 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8599 (mp0) REVERT: C 108 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6380 (mtt90) REVERT: C 118 MET cc_start: 0.8583 (tpt) cc_final: 0.7926 (tpt) REVERT: C 161 ARG cc_start: 0.7688 (ptp-110) cc_final: 0.7249 (ptp-110) REVERT: C 180 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.5766 (t80) REVERT: C 210 PHE cc_start: 0.9065 (t80) cc_final: 0.8629 (t80) REVERT: C 282 ASP cc_start: 0.8787 (m-30) cc_final: 0.8544 (m-30) REVERT: C 408 THR cc_start: 0.8154 (t) cc_final: 0.7943 (p) REVERT: C 410 GLU cc_start: 0.9165 (tp30) cc_final: 0.8917 (tp30) REVERT: C 437 GLN cc_start: 0.8139 (tt0) cc_final: 0.7768 (tp40) outliers start: 41 outliers final: 31 residues processed: 185 average time/residue: 0.2045 time to fit residues: 52.9653 Evaluate side-chains 177 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 86 LEU 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 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 281 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS ** B 123 GLN ** 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 = 0.3292 r_free = 0.3292 target = 0.091030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.072310 restraints weight = 17605.909| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.07 r_work: 0.2851 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.8390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 8835 Z= 0.365 Angle : 1.128 82.714 12078 Z= 0.453 Chirality : 0.064 1.494 1277 Planarity : 0.005 0.065 1568 Dihedral : 9.430 83.445 1288 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 4.07 % Allowed : 24.52 % Favored : 71.41 % 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: 0.38 (0.26), residues: 1083 helix: 1.47 (0.28), residues: 390 sheet: -0.41 (0.59), residues: 71 loop : -0.43 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 173 HIS 0.021 0.001 HIS A 503 PHE 0.027 0.002 PHE A 80 TYR 0.039 0.002 TYR A 255 ARG 0.003 0.000 ARG A 418 *********************** 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 172 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8397 (p0) cc_final: 0.7798 (p0) REVERT: A 68 TYR cc_start: 0.9037 (m-80) cc_final: 0.8688 (m-80) REVERT: A 79 TYR cc_start: 0.8082 (m-80) cc_final: 0.7646 (m-80) REVERT: A 211 ASP cc_start: 0.8752 (t0) cc_final: 0.8162 (t0) REVERT: A 271 TYR cc_start: 0.8302 (m-80) cc_final: 0.7918 (m-80) REVERT: A 356 ASP cc_start: 0.8522 (m-30) cc_final: 0.8108 (m-30) REVERT: A 360 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: A 476 ASN cc_start: 0.8081 (m-40) cc_final: 0.7838 (m-40) REVERT: B 91 LYS cc_start: 0.9417 (mmtm) cc_final: 0.9118 (mmmt) REVERT: B 94 ARG cc_start: 0.9356 (mmm-85) cc_final: 0.8988 (mmm-85) REVERT: B 112 MET cc_start: 0.8681 (mtp) cc_final: 0.8409 (ttp) REVERT: B 115 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.6612 (p0) REVERT: C 97 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8615 (mp0) REVERT: C 108 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6193 (mtm110) REVERT: C 118 MET cc_start: 0.8720 (tpt) cc_final: 0.7899 (tpt) REVERT: C 180 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.5996 (t80) REVERT: C 395 MET cc_start: 0.8567 (ttt) cc_final: 0.7988 (ttt) REVERT: C 410 GLU cc_start: 0.9174 (tp30) cc_final: 0.8916 (tp30) REVERT: C 437 GLN cc_start: 0.8303 (tt0) cc_final: 0.7934 (tp40) outliers start: 36 outliers final: 27 residues processed: 165 average time/residue: 0.2137 time to fit residues: 50.1767 Evaluate side-chains 153 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain A residue 131 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 306 ASN Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 HIS 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 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 387 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 106 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 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 290 ASN A 503 HIS B 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075550 restraints weight = 17317.564| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.08 r_work: 0.2911 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.8511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8835 Z= 0.258 Angle : 1.089 83.073 12078 Z= 0.429 Chirality : 0.062 1.491 1277 Planarity : 0.005 0.064 1568 Dihedral : 9.335 81.391 1288 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 3.62 % Allowed : 25.20 % Favored : 71.19 % 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: 0.36 (0.26), residues: 1083 helix: 1.52 (0.28), residues: 390 sheet: -0.23 (0.66), residues: 51 loop : -0.52 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 173 HIS 0.016 0.001 HIS A 503 PHE 0.012 0.001 PHE A 270 TYR 0.031 0.002 TYR A 255 ARG 0.006 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8362 (p0) cc_final: 0.7783 (p0) REVERT: A 54 MET cc_start: 0.8331 (ttp) cc_final: 0.8067 (ttp) REVERT: A 68 TYR cc_start: 0.9036 (m-80) cc_final: 0.8818 (m-80) REVERT: A 79 TYR cc_start: 0.8110 (m-80) cc_final: 0.7597 (m-10) REVERT: A 211 ASP cc_start: 0.8721 (t0) cc_final: 0.8035 (t0) REVERT: A 223 MET cc_start: 0.7666 (mtt) cc_final: 0.7457 (mtt) REVERT: A 271 TYR cc_start: 0.8349 (m-80) cc_final: 0.7904 (m-80) REVERT: A 356 ASP cc_start: 0.8529 (m-30) cc_final: 0.8140 (m-30) REVERT: A 360 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: B 91 LYS cc_start: 0.9419 (mmtm) cc_final: 0.9114 (mmmt) REVERT: B 94 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.9005 (mmm-85) REVERT: B 115 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6544 (p0) REVERT: C 97 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8609 (mp0) REVERT: C 108 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6101 (mtm110) REVERT: C 118 MET cc_start: 0.8592 (tpt) cc_final: 0.7866 (tpt) REVERT: C 180 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6008 (t80) REVERT: C 395 MET cc_start: 0.8346 (ttt) cc_final: 0.7514 (ttt) REVERT: C 408 THR cc_start: 0.8161 (t) cc_final: 0.7956 (p) REVERT: C 410 GLU cc_start: 0.9180 (tp30) cc_final: 0.8913 (tp30) REVERT: C 437 GLN cc_start: 0.8174 (tt0) cc_final: 0.7821 (tp40) outliers start: 32 outliers final: 24 residues processed: 161 average time/residue: 0.1984 time to fit residues: 45.0057 Evaluate side-chains 150 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 306 ASN Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 HIS 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 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 77 optimal weight: 0.0370 chunk 56 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 503 HIS B 101 ASN B 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.093865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075520 restraints weight = 17248.245| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.07 r_work: 0.2911 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.8591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8835 Z= 0.261 Angle : 1.091 83.080 12078 Z= 0.429 Chirality : 0.062 1.485 1277 Planarity : 0.005 0.066 1568 Dihedral : 9.339 82.129 1288 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 3.39 % Allowed : 25.88 % Favored : 70.73 % 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: 0.39 (0.26), residues: 1083 helix: 1.53 (0.28), residues: 391 sheet: -0.17 (0.66), residues: 51 loop : -0.50 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 173 HIS 0.011 0.001 HIS A 503 PHE 0.013 0.001 PHE A 270 TYR 0.027 0.002 TYR A 255 ARG 0.005 0.000 ARG A 499 ********************** 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 157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8328 (p0) cc_final: 0.7773 (p0) REVERT: A 54 MET cc_start: 0.8312 (ttp) cc_final: 0.8102 (ttp) REVERT: A 79 TYR cc_start: 0.8030 (m-80) cc_final: 0.7523 (m-10) REVERT: A 211 ASP cc_start: 0.8733 (t0) cc_final: 0.8060 (t0) REVERT: A 223 MET cc_start: 0.7611 (mtt) cc_final: 0.7379 (mtt) REVERT: A 271 TYR cc_start: 0.8402 (m-80) cc_final: 0.7965 (m-80) REVERT: A 356 ASP cc_start: 0.8535 (m-30) cc_final: 0.8143 (m-30) REVERT: A 360 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: A 476 ASN cc_start: 0.7859 (m-40) cc_final: 0.7518 (m110) REVERT: A 479 ILE cc_start: 0.8658 (mt) cc_final: 0.8434 (tp) REVERT: B 91 LYS cc_start: 0.9409 (mmtm) cc_final: 0.9099 (mmmt) REVERT: B 94 ARG cc_start: 0.9323 (mmm-85) cc_final: 0.8996 (mmm-85) REVERT: C 97 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8612 (mp0) REVERT: C 108 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6105 (mtm110) REVERT: C 118 MET cc_start: 0.8585 (tpt) cc_final: 0.7846 (tpt) REVERT: C 180 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6041 (t80) REVERT: C 395 MET cc_start: 0.8398 (ttt) cc_final: 0.7777 (ttt) REVERT: C 408 THR cc_start: 0.8179 (t) cc_final: 0.7972 (p) REVERT: C 410 GLU cc_start: 0.9183 (tp30) cc_final: 0.8938 (tp30) REVERT: C 437 GLN cc_start: 0.8199 (tt0) cc_final: 0.7839 (tp40) outliers start: 30 outliers final: 24 residues processed: 150 average time/residue: 0.1990 time to fit residues: 42.2559 Evaluate side-chains 150 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 306 ASN Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 HIS 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 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 503 HIS B 118 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 = 0.3338 r_free = 0.3338 target = 0.093983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.075010 restraints weight = 17565.216| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.16 r_work: 0.2900 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.8651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8835 Z= 0.268 Angle : 1.090 83.086 12078 Z= 0.429 Chirality : 0.062 1.485 1277 Planarity : 0.005 0.068 1568 Dihedral : 9.313 82.332 1288 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 3.50 % Allowed : 26.33 % Favored : 70.17 % 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: 0.42 (0.26), residues: 1083 helix: 1.56 (0.28), residues: 391 sheet: -0.14 (0.66), residues: 51 loop : -0.49 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 173 HIS 0.009 0.001 HIS A 503 PHE 0.013 0.001 PHE A 270 TYR 0.026 0.002 TYR A 255 ARG 0.005 0.000 ARG A 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3992.56 seconds wall clock time: 71 minutes 48.96 seconds (4308.96 seconds total)