Starting phenix.real_space_refine on Mon May 12 00:45:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcn_38248/05_2025/8xcn_38248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcn_38248/05_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_38248/05_2025/8xcn_38248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcn_38248/05_2025/8xcn_38248.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcn_38248/05_2025/8xcn_38248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcn_38248/05_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-5687/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: 5.43, per 1000 atoms: 0.63 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: 2.41 Conformation dependent library (CDL) restraints added in 950.2 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: 2.35 Time building geometry restraints manager: 2.79 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: 1.050 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: 0.090 Process input model: 23.870 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.606 8849 Z= 1.550 Angle : 1.698 73.755 12087 Z= 0.723 Chirality : 0.485 17.245 1277 Planarity : 0.011 0.158 1568 Dihedral : 18.742 96.866 3212 Min Nonbonded Distance : 1.241 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.15 % Allowed : 32.66 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1083 helix: 0.00 (0.26), residues: 399 sheet: -1.14 (0.51), residues: 91 loop : -0.97 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 173 HIS 0.021 0.001 HIS C 422 PHE 0.018 0.002 PHE B 54 TYR 0.040 0.003 TYR A 182 ARG 0.021 0.001 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.15315 ( 315) hydrogen bonds : angle 7.26087 ( 900) metal coordination : bond 0.00274 ( 3) metal coordination : angle 12.80312 ( 9) covalent geometry : bond 0.02988 ( 8835) covalent geometry : angle 1.66253 (12078) Misc. bond : bond 0.19108 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.969 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: 0.2309 time to fit residues: 96.0252 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 : 0.929 ------------------------------------------------------------------------------- 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 : 0.007 0.240 8849 Z= 0.259 Angle : 1.486 69.984 12087 Z= 0.522 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 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 315) hydrogen bonds : angle 5.37413 ( 900) metal coordination : bond 0.03020 ( 3) metal coordination : angle 25.87971 ( 9) covalent geometry : bond 0.00587 ( 8835) covalent geometry : angle 1.30819 (12078) Misc. bond : bond 0.09961 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.945 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: 0.2020 time to fit residues: 69.8970 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 : 0.948 ------------------------------------------------------------------------------- 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 0.185 8849 Z= 0.157 Angle : 1.440 89.553 12087 Z= 0.452 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 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 315) hydrogen bonds : angle 5.04215 ( 900) metal coordination : bond 0.01058 ( 3) metal coordination : angle 32.39693 ( 9) covalent geometry : bond 0.00372 ( 8835) covalent geometry : angle 1.13713 (12078) Misc. bond : bond 0.06716 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.891 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: 0.1857 time to fit residues: 55.1557 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 : 0.988 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 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: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.107313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088700 restraints weight = 17030.857| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.29 r_work: 0.3134 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 8849 Z= 0.173 Angle : 1.426 84.937 12087 Z= 0.444 Chirality : 0.059 1.337 1277 Planarity : 0.005 0.058 1568 Dihedral : 9.190 80.082 1292 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.31 % Allowed : 21.24 % Favored : 73.45 % 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: 0.08 (0.26), residues: 1083 helix: 1.24 (0.27), residues: 392 sheet: -0.65 (0.56), residues: 76 loop : -0.61 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 173 HIS 0.005 0.001 HIS A 110 PHE 0.029 0.002 PHE C 156 TYR 0.016 0.002 TYR C 359 ARG 0.006 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 315) hydrogen bonds : angle 4.90077 ( 900) metal coordination : bond 0.00354 ( 3) metal coordination : angle 32.84878 ( 9) covalent geometry : bond 0.00407 ( 8835) covalent geometry : angle 1.10886 (12078) Misc. bond : bond 0.06387 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.9004 (m-80) cc_final: 0.8787 (m-80) REVERT: A 211 ASP cc_start: 0.8713 (t0) cc_final: 0.8003 (t0) REVERT: A 259 THR cc_start: 0.6448 (p) cc_final: 0.5973 (t) REVERT: A 327 ILE cc_start: 0.8988 (mt) cc_final: 0.8694 (mp) REVERT: A 356 ASP cc_start: 0.8088 (m-30) cc_final: 0.7720 (m-30) REVERT: A 360 GLU cc_start: 0.8045 (pm20) cc_final: 0.7795 (pm20) REVERT: A 480 THR cc_start: 0.7783 (p) cc_final: 0.7575 (p) REVERT: A 483 THR cc_start: 0.6368 (m) cc_final: 0.5464 (p) REVERT: B 53 ASP cc_start: 0.8672 (m-30) cc_final: 0.8060 (t0) REVERT: B 91 LYS cc_start: 0.9387 (mmmt) cc_final: 0.8913 (mmmt) REVERT: B 104 ASP cc_start: 0.7737 (t0) cc_final: 0.7473 (t0) REVERT: B 106 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 136 GLU cc_start: 0.8437 (pt0) cc_final: 0.8071 (pm20) REVERT: C 97 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8530 (mp0) REVERT: C 118 MET cc_start: 0.8444 (tpt) cc_final: 0.7763 (tpt) REVERT: C 180 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5611 (t80) REVERT: C 210 PHE cc_start: 0.8929 (t80) cc_final: 0.8472 (t80) REVERT: C 374 ASN cc_start: 0.8945 (t0) cc_final: 0.8726 (t0) REVERT: C 395 MET cc_start: 0.8758 (ttt) cc_final: 0.8464 (ttt) REVERT: C 410 GLU cc_start: 0.9138 (tp30) cc_final: 0.8873 (tp30) REVERT: C 437 GLN cc_start: 0.8152 (tt0) cc_final: 0.7750 (tp40) outliers start: 47 outliers final: 28 residues processed: 221 average time/residue: 0.1754 time to fit residues: 55.5498 Evaluate side-chains 175 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 179 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: 0.0070 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 overall best weight: 0.5614 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.106357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087639 restraints weight = 16973.652| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.33 r_work: 0.3121 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 8849 Z= 0.151 Angle : 1.223 83.833 12087 Z= 0.419 Chirality : 0.060 1.441 1277 Planarity : 0.005 0.058 1568 Dihedral : 9.195 79.011 1292 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.95 % Allowed : 24.18 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1083 helix: 1.29 (0.28), residues: 392 sheet: -0.19 (0.59), residues: 68 loop : -0.59 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 PHE 0.016 0.001 PHE C 156 TYR 0.014 0.001 TYR C 359 ARG 0.004 0.000 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 315) hydrogen bonds : angle 4.81317 ( 900) metal coordination : bond 0.00193 ( 3) metal coordination : angle 22.09659 ( 9) covalent geometry : bond 0.00351 ( 8835) covalent geometry : angle 1.06463 (12078) Misc. bond : bond 0.03906 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7853 (p0) cc_final: 0.7307 (p0) REVERT: A 61 GLN cc_start: 0.7683 (mp10) cc_final: 0.7322 (mp10) REVERT: A 211 ASP cc_start: 0.8714 (t0) cc_final: 0.8016 (t0) REVERT: A 259 THR cc_start: 0.6584 (p) cc_final: 0.6075 (t) REVERT: A 293 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7345 (mm-30) REVERT: A 327 ILE cc_start: 0.8959 (mt) cc_final: 0.8692 (mp) REVERT: A 356 ASP cc_start: 0.8168 (m-30) cc_final: 0.7780 (m-30) REVERT: A 360 GLU cc_start: 0.8121 (pm20) cc_final: 0.7838 (pm20) REVERT: A 483 THR cc_start: 0.6456 (m) cc_final: 0.5454 (p) REVERT: A 490 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7935 (mmm160) REVERT: B 49 ASP cc_start: 0.8802 (t0) cc_final: 0.8256 (t0) REVERT: B 91 LYS cc_start: 0.9322 (mmmt) cc_final: 0.9008 (mmmt) REVERT: B 94 ARG cc_start: 0.9308 (mmm-85) cc_final: 0.9024 (mmm-85) REVERT: B 106 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: B 117 LEU cc_start: 0.8539 (mm) cc_final: 0.8141 (mt) REVERT: B 136 GLU cc_start: 0.8401 (pt0) cc_final: 0.8008 (pm20) REVERT: C 97 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8568 (mp0) REVERT: C 108 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6363 (mtt90) REVERT: C 118 MET cc_start: 0.8472 (tpt) cc_final: 0.7689 (tpt) REVERT: C 161 ARG cc_start: 0.7722 (ptp-110) cc_final: 0.7460 (ptp-110) REVERT: C 180 PHE cc_start: 0.6494 (OUTLIER) cc_final: 0.5694 (t80) REVERT: C 210 PHE cc_start: 0.8957 (t80) cc_final: 0.8524 (t80) REVERT: C 374 ASN cc_start: 0.8935 (t0) cc_final: 0.8732 (t0) REVERT: C 410 GLU cc_start: 0.9136 (tp30) cc_final: 0.8870 (tp30) REVERT: C 437 GLN cc_start: 0.8125 (tt0) cc_final: 0.7724 (tp40) outliers start: 35 outliers final: 24 residues processed: 178 average time/residue: 0.1861 time to fit residues: 46.8874 Evaluate side-chains 168 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 253 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 479 ILE Chi-restraints excluded: chain A residue 493 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 77 optimal weight: 0.3980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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** ** 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 = 0.3470 r_free = 0.3470 target = 0.102537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.084267 restraints weight = 16981.400| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.24 r_work: 0.3048 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 8849 Z= 0.158 Angle : 1.237 82.833 12087 Z= 0.418 Chirality : 0.061 1.486 1277 Planarity : 0.005 0.056 1568 Dihedral : 9.189 80.331 1289 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.07 % Allowed : 23.73 % Favored : 72.20 % 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: 0.30 (0.26), residues: 1083 helix: 1.43 (0.28), residues: 390 sheet: -0.23 (0.59), residues: 72 loop : -0.53 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 173 HIS 0.006 0.001 HIS B 118 PHE 0.015 0.001 PHE C 156 TYR 0.014 0.001 TYR A 79 ARG 0.003 0.000 ARG C 125 Details of bonding type rmsd hydrogen bonds : bond 0.02834 ( 315) hydrogen bonds : angle 4.79887 ( 900) metal coordination : bond 0.00193 ( 3) metal coordination : angle 22.68821 ( 9) covalent geometry : bond 0.00368 ( 8835) covalent geometry : angle 1.07133 (12078) Misc. bond : bond 0.05328 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7993 (p0) cc_final: 0.7401 (p0) REVERT: A 211 ASP cc_start: 0.8681 (t0) cc_final: 0.8002 (t0) REVERT: A 356 ASP cc_start: 0.8262 (m-30) cc_final: 0.7949 (m-30) REVERT: A 360 GLU cc_start: 0.8254 (pm20) cc_final: 0.8027 (pm20) REVERT: A 479 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7820 (mt) REVERT: A 483 THR cc_start: 0.6191 (m) cc_final: 0.5184 (p) REVERT: A 490 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7890 (mmm160) REVERT: B 49 ASP cc_start: 0.8753 (t0) cc_final: 0.8261 (t0) REVERT: B 86 PHE cc_start: 0.8212 (t80) cc_final: 0.7505 (t80) REVERT: B 89 GLN cc_start: 0.8658 (mt0) cc_final: 0.7917 (mp10) REVERT: B 91 LYS cc_start: 0.9370 (mmmt) cc_final: 0.9085 (mmmt) REVERT: B 94 ARG cc_start: 0.9297 (mmm-85) cc_final: 0.8982 (mmm-85) REVERT: B 106 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: C 97 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8549 (mp0) REVERT: C 108 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6370 (mtt90) REVERT: C 118 MET cc_start: 0.8587 (tpt) cc_final: 0.7870 (tpt) REVERT: C 180 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.5717 (t80) REVERT: C 210 PHE cc_start: 0.9021 (t80) cc_final: 0.8580 (t80) REVERT: C 282 ASP cc_start: 0.8713 (m-30) cc_final: 0.8445 (m-30) REVERT: C 410 GLU cc_start: 0.9138 (tp30) cc_final: 0.8876 (tp30) REVERT: C 437 GLN cc_start: 0.8125 (tt0) cc_final: 0.7728 (tp40) outliers start: 36 outliers final: 25 residues processed: 187 average time/residue: 0.2038 time to fit residues: 52.9320 Evaluate side-chains 172 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.0770 chunk 72 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083417 restraints weight = 17172.005| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.23 r_work: 0.3038 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 8849 Z= 0.151 Angle : 1.223 82.928 12087 Z= 0.418 Chirality : 0.061 1.494 1277 Planarity : 0.005 0.054 1568 Dihedral : 9.093 80.361 1289 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.18 % Allowed : 23.50 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.26), residues: 1083 helix: 1.49 (0.28), residues: 391 sheet: -0.37 (0.58), residues: 71 loop : -0.43 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 173 HIS 0.007 0.001 HIS A 110 PHE 0.011 0.001 PHE C 64 TYR 0.013 0.001 TYR C 359 ARG 0.003 0.000 ARG C 172 Details of bonding type rmsd hydrogen bonds : bond 0.02775 ( 315) hydrogen bonds : angle 4.84436 ( 900) metal coordination : bond 0.00103 ( 3) metal coordination : angle 21.29055 ( 9) covalent geometry : bond 0.00349 ( 8835) covalent geometry : angle 1.07654 (12078) Misc. bond : bond 0.06649 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8092 (p0) cc_final: 0.7481 (p0) REVERT: A 211 ASP cc_start: 0.8673 (t0) cc_final: 0.7981 (t0) REVERT: A 293 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7824 (mm-30) REVERT: A 356 ASP cc_start: 0.8278 (m-30) cc_final: 0.8011 (m-30) REVERT: A 442 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7394 (tp30) REVERT: A 476 ASN cc_start: 0.8054 (m-40) cc_final: 0.7731 (m-40) REVERT: A 483 THR cc_start: 0.6257 (m) cc_final: 0.5232 (p) REVERT: A 490 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7797 (mmm160) REVERT: B 49 ASP cc_start: 0.8762 (t0) cc_final: 0.8260 (t0) REVERT: B 86 PHE cc_start: 0.8270 (t80) cc_final: 0.7607 (t80) REVERT: B 89 GLN cc_start: 0.8701 (mt0) cc_final: 0.7925 (mp10) REVERT: B 91 LYS cc_start: 0.9365 (mmmt) cc_final: 0.9132 (mmmt) REVERT: B 94 ARG cc_start: 0.9339 (mmm-85) cc_final: 0.9001 (mmm-85) REVERT: B 102 TYR cc_start: 0.7671 (m-80) cc_final: 0.7357 (m-10) REVERT: B 106 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: B 117 LEU cc_start: 0.8574 (mm) cc_final: 0.8271 (mt) REVERT: B 136 GLU cc_start: 0.8358 (pt0) cc_final: 0.7962 (pm20) REVERT: C 97 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8566 (mp0) REVERT: C 108 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6327 (mtt90) REVERT: C 118 MET cc_start: 0.8576 (tpt) cc_final: 0.7825 (tpt) REVERT: C 180 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.5611 (t80) REVERT: C 210 PHE cc_start: 0.9020 (t80) cc_final: 0.8572 (t80) REVERT: C 282 ASP cc_start: 0.8762 (m-30) cc_final: 0.8500 (m-30) REVERT: C 395 MET cc_start: 0.8349 (ttt) cc_final: 0.7182 (ttt) REVERT: C 410 GLU cc_start: 0.9137 (tp30) cc_final: 0.8879 (tp30) REVERT: C 437 GLN cc_start: 0.8130 (tt0) cc_final: 0.7758 (tp40) outliers start: 37 outliers final: 30 residues processed: 186 average time/residue: 0.2141 time to fit residues: 55.7481 Evaluate side-chains 178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 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: 1.9990 chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- 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 ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.093207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074508 restraints weight = 17497.602| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.15 r_work: 0.2892 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.8077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 8849 Z= 0.211 Angle : 1.284 82.523 12087 Z= 0.445 Chirality : 0.063 1.502 1277 Planarity : 0.005 0.060 1568 Dihedral : 9.301 81.907 1288 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 4.29 % Allowed : 24.18 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1083 helix: 1.47 (0.28), residues: 391 sheet: -0.43 (0.57), residues: 71 loop : -0.37 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 173 HIS 0.009 0.001 HIS A 110 PHE 0.020 0.002 PHE A 80 TYR 0.045 0.002 TYR A 271 ARG 0.003 0.001 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 315) hydrogen bonds : angle 4.97170 ( 900) metal coordination : bond 0.00085 ( 3) metal coordination : angle 22.96166 ( 9) covalent geometry : bond 0.00502 ( 8835) covalent geometry : angle 1.12122 (12078) Misc. bond : bond 0.08283 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8306 (p0) cc_final: 0.7725 (p0) REVERT: A 68 TYR cc_start: 0.8988 (m-80) cc_final: 0.8493 (m-80) REVERT: A 79 TYR cc_start: 0.8026 (m-80) cc_final: 0.7718 (m-10) REVERT: A 98 GLN cc_start: 0.7947 (mp10) cc_final: 0.7688 (mp10) REVERT: A 211 ASP cc_start: 0.8732 (t0) cc_final: 0.8021 (t0) REVERT: A 356 ASP cc_start: 0.8375 (m-30) cc_final: 0.8042 (m-30) REVERT: A 360 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 476 ASN cc_start: 0.8088 (m-40) cc_final: 0.7635 (m110) REVERT: B 93 LEU cc_start: 0.9185 (mt) cc_final: 0.8907 (mp) REVERT: B 94 ARG cc_start: 0.9348 (mmm-85) cc_final: 0.9038 (mmm-85) REVERT: B 106 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: B 117 LEU cc_start: 0.8678 (mm) cc_final: 0.8329 (mt) REVERT: B 118 HIS cc_start: 0.7522 (t70) cc_final: 0.7263 (t70) REVERT: C 97 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8611 (mp0) REVERT: C 108 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6075 (mtm110) REVERT: C 118 MET cc_start: 0.8646 (tpt) cc_final: 0.7908 (tpt) REVERT: C 180 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.5751 (t80) REVERT: C 210 PHE cc_start: 0.9108 (t80) cc_final: 0.8578 (t80) REVERT: C 395 MET cc_start: 0.8751 (ttt) cc_final: 0.7982 (ttt) REVERT: C 410 GLU cc_start: 0.9152 (tp30) cc_final: 0.8889 (tp30) REVERT: C 437 GLN cc_start: 0.8155 (tt0) cc_final: 0.7780 (tp40) outliers start: 38 outliers final: 28 residues processed: 177 average time/residue: 0.1821 time to fit residues: 45.5066 Evaluate side-chains 161 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 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 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 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: 0.6980 chunk 67 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** 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 = 0.3356 r_free = 0.3356 target = 0.095097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076634 restraints weight = 17174.172| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.11 r_work: 0.2928 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.8260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 8849 Z= 0.167 Angle : 1.261 82.720 12087 Z= 0.433 Chirality : 0.062 1.512 1277 Planarity : 0.005 0.054 1568 Dihedral : 9.267 81.226 1288 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.29 % Allowed : 24.63 % Favored : 71.07 % 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: 1.48 (0.28), residues: 391 sheet: -0.43 (0.60), residues: 71 loop : -0.38 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 173 HIS 0.007 0.001 HIS A 110 PHE 0.013 0.001 PHE A 270 TYR 0.034 0.002 TYR A 255 ARG 0.002 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 315) hydrogen bonds : angle 4.95017 ( 900) metal coordination : bond 0.00041 ( 3) metal coordination : angle 22.54427 ( 9) covalent geometry : bond 0.00396 ( 8835) covalent geometry : angle 1.10169 (12078) Misc. bond : bond 0.06112 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8383 (p0) cc_final: 0.7798 (p0) REVERT: A 79 TYR cc_start: 0.8055 (m-80) cc_final: 0.7580 (m-10) REVERT: A 98 GLN cc_start: 0.7994 (mp10) cc_final: 0.7599 (mp10) REVERT: A 211 ASP cc_start: 0.8720 (t0) cc_final: 0.8152 (t0) REVERT: A 356 ASP cc_start: 0.8417 (m-30) cc_final: 0.8080 (m-30) REVERT: A 476 ASN cc_start: 0.8006 (m-40) cc_final: 0.7711 (m-40) REVERT: B 91 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8990 (mmmm) REVERT: B 94 ARG cc_start: 0.9331 (mmm-85) cc_final: 0.9022 (mmm-85) REVERT: B 102 TYR cc_start: 0.7709 (m-80) cc_final: 0.7349 (m-10) REVERT: B 106 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: C 97 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8599 (mp0) REVERT: C 108 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6048 (mtm110) REVERT: C 118 MET cc_start: 0.8607 (tpt) cc_final: 0.7869 (tpt) REVERT: C 180 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.5871 (t80) REVERT: C 210 PHE cc_start: 0.9081 (t80) cc_final: 0.8621 (t80) REVERT: C 395 MET cc_start: 0.8542 (ttt) cc_final: 0.7609 (ttt) REVERT: C 408 THR cc_start: 0.8150 (t) cc_final: 0.7937 (p) REVERT: C 410 GLU cc_start: 0.9176 (tp30) cc_final: 0.8922 (tp30) REVERT: C 437 GLN cc_start: 0.8160 (tt0) cc_final: 0.7796 (tp40) outliers start: 38 outliers final: 30 residues processed: 173 average time/residue: 0.1888 time to fit residues: 45.8212 Evaluate side-chains 170 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 36 LEU 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 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 477 ASN 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 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: 0.0970 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.077002 restraints weight = 17054.128| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.10 r_work: 0.2938 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.8278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 8849 Z= 0.161 Angle : 1.266 82.934 12087 Z= 0.441 Chirality : 0.063 1.491 1277 Planarity : 0.005 0.054 1568 Dihedral : 9.248 81.202 1288 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.84 % Rotamer: Outliers : 3.73 % Allowed : 25.20 % Favored : 71.07 % 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: 0.35 (0.26), residues: 1083 helix: 1.46 (0.28), residues: 392 sheet: -0.16 (0.68), residues: 51 loop : -0.51 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 173 HIS 0.008 0.001 HIS A 478 PHE 0.012 0.001 PHE A 270 TYR 0.034 0.002 TYR A 255 ARG 0.002 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 315) hydrogen bonds : angle 4.96676 ( 900) metal coordination : bond 0.00125 ( 3) metal coordination : angle 22.27706 ( 9) covalent geometry : bond 0.00378 ( 8835) covalent geometry : angle 1.11065 (12078) Misc. bond : bond 0.05482 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8357 (p0) cc_final: 0.7777 (p0) REVERT: A 79 TYR cc_start: 0.8030 (m-80) cc_final: 0.7539 (m-10) REVERT: A 98 GLN cc_start: 0.7977 (mp10) cc_final: 0.7463 (mp10) REVERT: A 211 ASP cc_start: 0.8720 (t0) cc_final: 0.8036 (t0) REVERT: A 272 ASP cc_start: 0.7572 (t0) cc_final: 0.7245 (t0) REVERT: A 356 ASP cc_start: 0.8325 (m-30) cc_final: 0.8124 (m-30) REVERT: B 94 ARG cc_start: 0.9316 (mmm-85) cc_final: 0.9008 (mmm-85) REVERT: B 102 TYR cc_start: 0.7744 (m-80) cc_final: 0.7384 (m-10) REVERT: B 106 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: C 97 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8597 (mp0) REVERT: C 108 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6031 (mtm110) REVERT: C 118 MET cc_start: 0.8588 (tpt) cc_final: 0.7852 (tpt) REVERT: C 180 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.5878 (t80) REVERT: C 210 PHE cc_start: 0.9084 (t80) cc_final: 0.8616 (t80) REVERT: C 395 MET cc_start: 0.8504 (ttt) cc_final: 0.7518 (ttt) REVERT: C 408 THR cc_start: 0.8150 (t) cc_final: 0.7937 (p) REVERT: C 410 GLU cc_start: 0.9156 (tp30) cc_final: 0.8912 (tp30) REVERT: C 437 GLN cc_start: 0.8161 (tt0) cc_final: 0.7801 (tp40) outliers start: 33 outliers final: 27 residues processed: 160 average time/residue: 0.1879 time to fit residues: 42.2483 Evaluate side-chains 160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 36 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.0918 > 50: distance: 58 - 150: 27.746 distance: 61 - 147: 31.177 distance: 73 - 134: 21.724 distance: 76 - 131: 17.177 distance: 89 - 115: 26.525 distance: 91 - 96: 7.431 distance: 92 - 112: 23.133 distance: 96 - 97: 3.775 distance: 97 - 98: 3.608 distance: 97 - 100: 12.512 distance: 98 - 99: 22.330 distance: 98 - 104: 21.420 distance: 100 - 101: 12.318 distance: 101 - 102: 18.732 distance: 101 - 103: 15.819 distance: 104 - 105: 14.558 distance: 105 - 106: 27.046 distance: 105 - 108: 13.853 distance: 106 - 107: 18.230 distance: 106 - 112: 15.400 distance: 108 - 109: 15.386 distance: 109 - 110: 12.032 distance: 109 - 111: 18.361 distance: 112 - 113: 12.648 distance: 113 - 114: 13.611 distance: 113 - 116: 36.007 distance: 114 - 115: 33.670 distance: 114 - 122: 23.289 distance: 116 - 117: 11.649 distance: 117 - 118: 30.403 distance: 117 - 119: 17.178 distance: 118 - 120: 19.945 distance: 119 - 121: 20.878 distance: 120 - 121: 28.418 distance: 122 - 123: 17.462 distance: 123 - 124: 32.644 distance: 123 - 126: 29.029 distance: 124 - 125: 30.339 distance: 124 - 131: 22.891 distance: 126 - 127: 43.638 distance: 127 - 128: 11.772 distance: 128 - 129: 16.404 distance: 128 - 130: 16.285 distance: 131 - 132: 6.448 distance: 132 - 133: 30.495 distance: 132 - 135: 22.648 distance: 133 - 134: 16.690 distance: 133 - 139: 19.737 distance: 135 - 136: 15.921 distance: 135 - 137: 39.984 distance: 136 - 138: 26.980 distance: 136 - 242: 22.643 distance: 139 - 140: 18.424 distance: 140 - 141: 27.301 distance: 140 - 143: 21.875 distance: 141 - 142: 33.987 distance: 141 - 147: 28.952 distance: 143 - 144: 12.767 distance: 144 - 145: 27.025 distance: 144 - 146: 33.351 distance: 147 - 148: 44.485 distance: 148 - 149: 25.516 distance: 148 - 151: 11.965 distance: 149 - 150: 16.192 distance: 149 - 155: 16.936 distance: 151 - 152: 31.924 distance: 152 - 153: 21.040 distance: 153 - 154: 33.382 distance: 155 - 156: 6.559 distance: 155 - 161: 21.683 distance: 156 - 157: 14.448 distance: 156 - 159: 10.919 distance: 157 - 158: 19.815 distance: 157 - 162: 20.001 distance: 159 - 160: 15.923 distance: 160 - 161: 13.293 distance: 162 - 163: 45.310 distance: 163 - 164: 25.594 distance: 163 - 166: 12.864 distance: 164 - 165: 23.826 distance: 164 - 167: 28.561 distance: 167 - 168: 15.453 distance: 168 - 169: 15.515 distance: 168 - 171: 22.542 distance: 169 - 170: 13.456 distance: 169 - 178: 17.824 distance: 171 - 172: 12.573 distance: 172 - 173: 10.614 distance: 172 - 174: 8.895 distance: 173 - 175: 15.307 distance: 174 - 176: 9.459 distance: 175 - 177: 14.576 distance: 176 - 177: 18.739