Starting phenix.real_space_refine on Thu Aug 6 13:17:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30uu_58072/08_2026/30uu_58072_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/30uu_58072/08_2026/30uu_58072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30uu_58072/08_2026/30uu_58072_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30uu_58072/08_2026/30uu_58072_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30uu_58072/08_2026/30uu_58072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30uu_58072/08_2026/30uu_58072.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.042 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 4908 2.51 5 N 1152 2.21 5 O 1218 1.98 5 H 7668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15010 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7491 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 6.05, per 1000 atoms: 0.40 Number of scatterers: 15010 At special positions: 0 Unit cell: (80.025, 108.075, 82.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 O 1218 8.00 N 1152 7.00 C 4908 6.00 H 7668 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 562 " " NAG B 601 " - " ASN B 562 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 372.5 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 Proline residue: A 21 - end of helix removed outlier: 3.569A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.558A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.770A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.782A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 140 through 158 Proline residue: A 150 - end of helix removed outlier: 3.754A pdb=" N GLN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 221 removed outlier: 3.811A pdb=" N LYS A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.519A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 277 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 292 through 308 removed outlier: 3.609A pdb=" N ALA A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.568A pdb=" N ILE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.796A pdb=" N VAL A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 407 through 428 Processing helix chain 'A' and resid 428 through 436 Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.516A pdb=" N LEU A 440 " --> pdb=" O MET A 437 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 443 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 Processing helix chain 'A' and resid 464 through 484 Proline residue: A 474 - end of helix Processing helix chain 'A' and resid 486 through 498 removed outlier: 4.087A pdb=" N ILE A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.692A pdb=" N ALA A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.583A pdb=" N MET A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 removed outlier: 4.010A pdb=" N ILE A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 Proline residue: B 21 - end of helix removed outlier: 3.569A pdb=" N LEU B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 33 through 51 removed outlier: 3.558A pdb=" N ARG B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.771A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.781A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 120 through 137 Processing helix chain 'B' and resid 140 through 158 Proline residue: B 150 - end of helix removed outlier: 3.753A pdb=" N GLN B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 221 removed outlier: 3.811A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.519A pdb=" N VAL B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 277 Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 292 through 308 removed outlier: 3.609A pdb=" N ALA B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 333 removed outlier: 3.567A pdb=" N ILE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.797A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 407 through 428 Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 437 through 443 removed outlier: 3.516A pdb=" N LEU B 440 " --> pdb=" O MET B 437 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 443 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 464 through 484 Proline residue: B 474 - end of helix Processing helix chain 'B' and resid 486 through 498 removed outlier: 4.087A pdb=" N ILE B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.692A pdb=" N ALA B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 547 removed outlier: 3.583A pdb=" N MET B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 4.009A pdb=" N ILE B 551 " --> pdb=" O TRP B 547 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1410 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: 2.83 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7648 1.03 - 1.23: 20 1.23 - 1.42: 2998 1.42 - 1.62: 4428 1.62 - 1.81: 108 Bond restraints: 15202 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.603 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.602 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.402 -0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C7 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.346 1.402 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C5 NAG B 601 " pdb=" C6 NAG B 601 " ideal model delta sigma weight residual 1.513 1.569 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 15197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 27440 7.09 - 14.18: 30 14.18 - 21.27: 12 21.27 - 28.36: 120 28.36 - 35.45: 84 Bond angle restraints: 27686 Sorted by residual: angle pdb=" C SER B 291 " pdb=" CA SER B 291 " pdb=" HA SER B 291 " ideal model delta sigma weight residual 109.00 73.55 35.45 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 109.00 73.58 35.42 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB VAL B 263 " pdb=" CA VAL B 263 " pdb=" HA VAL B 263 " ideal model delta sigma weight residual 109.00 73.66 35.34 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 109.00 73.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N SER A 291 " pdb=" CA SER A 291 " pdb=" HA SER A 291 " ideal model delta sigma weight residual 110.00 74.79 35.21 3.00e+00 1.11e-01 1.38e+02 ... (remaining 27681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 6309 17.21 - 34.43: 569 34.43 - 51.64: 220 51.64 - 68.85: 56 68.85 - 86.06: 16 Dihedral angle restraints: 7170 sinusoidal: 3866 harmonic: 3304 Sorted by residual: dihedral pdb=" CA TYR A 353 " pdb=" C TYR A 353 " pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta harmonic sigma weight residual -180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA TYR B 353 " pdb=" C TYR B 353 " pdb=" N VAL B 354 " pdb=" CA VAL B 354 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA THR B 225 " pdb=" C THR B 225 " pdb=" N GLY B 226 " pdb=" CA GLY B 226 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 1228 0.343 - 0.686: 4 0.686 - 1.029: 0 1.029 - 1.372: 0 1.372 - 1.715: 16 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CG LEU A 22 " pdb=" CB LEU A 22 " pdb=" CD1 LEU A 22 " pdb=" CD2 LEU A 22 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.71 2.00e-01 2.50e+01 7.35e+01 chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.71 2.00e-01 2.50e+01 7.35e+01 chirality pdb=" CG LEU A 23 " pdb=" CB LEU A 23 " pdb=" CD1 LEU A 23 " pdb=" CD2 LEU A 23 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.10e+01 ... (remaining 1245 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO B 229 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 228 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 229 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 374 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 375 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.015 5.00e-02 4.00e+02 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1091 2.20 - 2.80: 30724 2.80 - 3.40: 42031 3.40 - 4.00: 53114 4.00 - 4.60: 84039 Nonbonded interactions: 210999 Sorted by model distance: nonbonded pdb=" HA VAL B 263 " pdb=" HB VAL B 263 " model vdw 1.602 1.952 nonbonded pdb=" HA VAL A 263 " pdb=" HB VAL A 263 " model vdw 1.603 1.952 nonbonded pdb=" HB THR A 351 " pdb=" HG1 THR A 351 " model vdw 1.627 1.816 nonbonded pdb=" HB THR B 351 " pdb=" HG1 THR B 351 " model vdw 1.627 1.816 nonbonded pdb=" HE3 LYS B 352 " pdb=" HZ2 LYS B 352 " model vdw 1.631 1.816 ... (remaining 210994 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.004 0.071 7536 Z= 0.175 Angle : 1.093 26.434 10280 Z= 0.475 Chirality : 0.181 1.715 1248 Planarity : 0.004 0.035 1230 Dihedral : 16.225 79.816 2690 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.31 % Favored : 92.58 % Rotamer: Outliers : 1.75 % Allowed : 27.93 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.28), residues: 916 helix: 0.78 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -2.47 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.005 0.001 TYR B 353 PHE 0.016 0.001 PHE B 362 TRP 0.010 0.001 TRP A 138 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 7534) covalent geometry : angle 1.08988 / 0.47 (10274) hydrogen bonds : bond 0.14994 / 8.81 ( 476) hydrogen bonds : angle 6.10716 / 4.35 ( 1410) link_NAG-ASN : bond 0.00970 / 0.49 ( 2) link_NAG-ASN : angle 3.64090 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 0.304 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 248 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8320 (p) REVERT: A 267 PHE cc_start: 0.8002 (m-10) cc_final: 0.7625 (m-80) REVERT: A 531 ILE cc_start: 0.8348 (mm) cc_final: 0.8021 (mp) REVERT: A 535 ILE cc_start: 0.8762 (mm) cc_final: 0.8535 (mm) REVERT: B 153 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 248 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8570 (p) REVERT: B 267 PHE cc_start: 0.7825 (m-10) cc_final: 0.7462 (m-10) REVERT: B 531 ILE cc_start: 0.8071 (mm) cc_final: 0.7791 (mp) outliers start: 14 outliers final: 10 residues processed: 240 average time/residue: 0.5537 time to fit residues: 147.1149 Evaluate side-chains 181 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 491 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 519 HIS B 556 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.117377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.093156 restraints weight = 49849.154| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.85 r_work: 0.3442 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7536 Z= 0.206 Angle : 1.098 26.198 10280 Z= 0.487 Chirality : 0.183 1.707 1248 Planarity : 0.005 0.076 1230 Dihedral : 5.936 53.542 1034 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.99 % Allowed : 27.43 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.29), residues: 916 helix: 1.31 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.31 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 307 TYR 0.009 0.001 TYR B 214 PHE 0.011 0.001 PHE A 258 TRP 0.014 0.001 TRP A 547 HIS 0.003 0.001 HIS B 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 ( 7534) covalent geometry : angle 1.09564 / 0.49 (10274) hydrogen bonds : bond 0.04155 / 2.60 ( 476) hydrogen bonds : angle 4.56991 / 3.26 ( 1410) link_NAG-ASN : bond 0.00698 / 0.35 ( 2) link_NAG-ASN : angle 3.17379 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.255 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8968 (p) REVERT: A 500 PHE cc_start: 0.8641 (m-10) cc_final: 0.8415 (m-10) REVERT: A 531 ILE cc_start: 0.8471 (mm) cc_final: 0.8109 (mp) REVERT: A 535 ILE cc_start: 0.9223 (mm) cc_final: 0.8948 (mm) REVERT: B 248 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 455 LEU cc_start: 0.9254 (tm) cc_final: 0.8697 (mt) outliers start: 40 outliers final: 14 residues processed: 185 average time/residue: 0.4622 time to fit residues: 96.0754 Evaluate side-chains 156 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.114069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089821 restraints weight = 49725.804| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.78 r_work: 0.3377 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7536 Z= 0.163 Angle : 1.087 26.592 10280 Z= 0.472 Chirality : 0.182 1.709 1248 Planarity : 0.005 0.071 1230 Dihedral : 5.253 54.810 1024 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.49 % Allowed : 29.43 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.30), residues: 916 helix: 1.76 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.13 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 307 TYR 0.013 0.001 TYR B 214 PHE 0.013 0.001 PHE B 258 TRP 0.011 0.001 TRP A 49 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7534) covalent geometry : angle 1.08473 / 0.47 (10274) hydrogen bonds : bond 0.03917 / 2.45 ( 476) hydrogen bonds : angle 4.42389 / 3.16 ( 1410) link_NAG-ASN : bond 0.00762 / 0.38 ( 2) link_NAG-ASN : angle 2.93101 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.299 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: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.7004 (ttm) cc_final: 0.6759 (tmm) REVERT: B 277 MET cc_start: 0.7129 (mmm) cc_final: 0.6717 (mmp) REVERT: B 455 LEU cc_start: 0.9153 (tm) cc_final: 0.8754 (mt) REVERT: B 500 PHE cc_start: 0.8618 (m-10) cc_final: 0.8355 (m-80) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.4599 time to fit residues: 87.3626 Evaluate side-chains 146 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 469 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 42 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.111611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087322 restraints weight = 49797.581| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.78 r_work: 0.3333 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 7536 Z= 0.182 Angle : 1.089 27.494 10280 Z= 0.476 Chirality : 0.182 1.742 1248 Planarity : 0.005 0.039 1230 Dihedral : 5.228 52.559 1022 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.87 % Allowed : 28.55 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.30), residues: 916 helix: 1.88 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.01 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 307 TYR 0.008 0.001 TYR A 82 PHE 0.056 0.001 PHE B 459 TRP 0.011 0.001 TRP B 138 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 7534) covalent geometry : angle 1.08672 / 0.48 (10274) hydrogen bonds : bond 0.03772 / 2.38 ( 476) hydrogen bonds : angle 4.34761 / 3.10 ( 1410) link_NAG-ASN : bond 0.00744 / 0.37 ( 2) link_NAG-ASN : angle 2.88808 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.395 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 392 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5880 (t80) REVERT: A 525 MET cc_start: 0.6976 (ttm) cc_final: 0.6752 (tmm) REVERT: B 210 LEU cc_start: 0.9206 (mt) cc_final: 0.8936 (tm) REVERT: B 392 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.6433 (t80) REVERT: B 525 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6591 (tmm) outliers start: 31 outliers final: 13 residues processed: 146 average time/residue: 0.4474 time to fit residues: 74.4083 Evaluate side-chains 135 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 88 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.108251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.084163 restraints weight = 50206.418| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.68 r_work: 0.3276 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7536 Z= 0.169 Angle : 1.078 26.442 10280 Z= 0.469 Chirality : 0.182 1.719 1248 Planarity : 0.005 0.038 1230 Dihedral : 5.146 50.490 1022 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.36 % Allowed : 26.81 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.30), residues: 916 helix: 1.95 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.10 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 307 TYR 0.009 0.001 TYR A 82 PHE 0.011 0.001 PHE B 314 TRP 0.012 0.001 TRP A 138 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 7534) covalent geometry : angle 1.07626 / 0.47 (10274) hydrogen bonds : bond 0.03669 / 2.29 ( 476) hydrogen bonds : angle 4.22364 / 3.03 ( 1410) link_NAG-ASN : bond 0.00709 / 0.36 ( 2) link_NAG-ASN : angle 2.85370 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6520 (t80) REVERT: A 525 MET cc_start: 0.6968 (ttm) cc_final: 0.6754 (tmm) outliers start: 35 outliers final: 17 residues processed: 142 average time/residue: 0.6959 time to fit residues: 109.6374 Evaluate side-chains 126 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.107641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.083725 restraints weight = 50007.736| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.68 r_work: 0.3244 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7536 Z= 0.145 Angle : 1.082 26.754 10280 Z= 0.466 Chirality : 0.183 1.749 1248 Planarity : 0.005 0.037 1230 Dihedral : 4.981 50.647 1020 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.24 % Allowed : 26.56 % Favored : 69.20 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.30), residues: 916 helix: 2.02 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.04 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.008 0.001 TYR B 48 PHE 0.009 0.001 PHE B 314 TRP 0.012 0.001 TRP A 138 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 7534) covalent geometry : angle 1.07972 / 0.47 (10274) hydrogen bonds : bond 0.03530 / 2.18 ( 476) hydrogen bonds : angle 4.15925 / 2.99 ( 1410) link_NAG-ASN : bond 0.00749 / 0.38 ( 2) link_NAG-ASN : angle 2.83130 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9405 (p) REVERT: A 392 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6727 (t80) REVERT: B 211 CYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9346 (p) outliers start: 34 outliers final: 22 residues processed: 139 average time/residue: 0.5978 time to fit residues: 93.7284 Evaluate side-chains 133 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.107537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083890 restraints weight = 49775.119| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.62 r_work: 0.3281 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7536 Z= 0.136 Angle : 1.081 26.606 10280 Z= 0.463 Chirality : 0.182 1.713 1248 Planarity : 0.004 0.037 1230 Dihedral : 4.913 51.059 1020 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.24 % Allowed : 26.43 % Favored : 69.33 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.30), residues: 916 helix: 2.09 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -2.01 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.012 0.001 TYR A 214 PHE 0.009 0.001 PHE B 314 TRP 0.012 0.001 TRP A 138 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7534) covalent geometry : angle 1.07885 / 0.46 (10274) hydrogen bonds : bond 0.03402 / 2.11 ( 476) hydrogen bonds : angle 4.10435 / 2.95 ( 1410) link_NAG-ASN : bond 0.00772 / 0.39 ( 2) link_NAG-ASN : angle 2.82589 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.9302 (mt) cc_final: 0.9053 (mp) REVERT: A 211 CYS cc_start: 0.9650 (OUTLIER) cc_final: 0.9359 (p) REVERT: A 392 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6778 (t80) REVERT: B 83 MET cc_start: 0.8782 (mmt) cc_final: 0.8553 (tpt) REVERT: B 211 CYS cc_start: 0.9621 (OUTLIER) cc_final: 0.9226 (p) outliers start: 34 outliers final: 22 residues processed: 136 average time/residue: 0.5427 time to fit residues: 83.9947 Evaluate side-chains 133 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.107454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.083466 restraints weight = 50642.945| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.71 r_work: 0.3275 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7536 Z= 0.134 Angle : 1.085 26.595 10280 Z= 0.463 Chirality : 0.182 1.711 1248 Planarity : 0.004 0.037 1230 Dihedral : 4.713 51.190 1018 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.49 % Allowed : 28.05 % Favored : 68.45 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.30), residues: 916 helix: 2.16 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.92 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.010 0.001 TYR A 214 PHE 0.009 0.001 PHE B 314 TRP 0.012 0.001 TRP B 138 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 7534) covalent geometry : angle 1.08364 / 0.46 (10274) hydrogen bonds : bond 0.03334 / 2.06 ( 476) hydrogen bonds : angle 4.05007 / 2.91 ( 1410) link_NAG-ASN : bond 0.00777 / 0.39 ( 2) link_NAG-ASN : angle 2.82163 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.9272 (mt) cc_final: 0.9019 (mp) REVERT: A 211 CYS cc_start: 0.9652 (OUTLIER) cc_final: 0.9362 (p) REVERT: A 392 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6918 (t80) REVERT: B 16 ILE cc_start: 0.8863 (tt) cc_final: 0.8622 (tp) REVERT: B 83 MET cc_start: 0.8761 (mmt) cc_final: 0.8532 (tpt) REVERT: B 211 CYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9208 (p) outliers start: 28 outliers final: 19 residues processed: 131 average time/residue: 0.5255 time to fit residues: 78.7783 Evaluate side-chains 127 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 525 MET Chi-restraints excluded: chain B residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.104211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080167 restraints weight = 50976.859| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.62 r_work: 0.3198 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7536 Z= 0.194 Angle : 1.101 26.118 10280 Z= 0.479 Chirality : 0.182 1.721 1248 Planarity : 0.005 0.037 1230 Dihedral : 4.840 51.518 1018 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.24 % Allowed : 28.18 % Favored : 68.58 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.30), residues: 916 helix: 2.01 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 37 TYR 0.009 0.001 TYR A 214 PHE 0.009 0.001 PHE B 472 TRP 0.013 0.001 TRP A 138 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 7534) covalent geometry : angle 1.09937 / 0.48 (10274) hydrogen bonds : bond 0.03651 / 2.25 ( 476) hydrogen bonds : angle 4.15612 / 2.99 ( 1410) link_NAG-ASN : bond 0.00641 / 0.32 ( 2) link_NAG-ASN : angle 2.76326 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.9342 (mt) cc_final: 0.9126 (mp) REVERT: A 211 CYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9386 (p) REVERT: A 392 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.7264 (t80) REVERT: B 16 ILE cc_start: 0.8976 (tt) cc_final: 0.8751 (tp) REVERT: B 211 CYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9333 (p) outliers start: 26 outliers final: 14 residues processed: 127 average time/residue: 0.5538 time to fit residues: 80.2204 Evaluate side-chains 126 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.104971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081369 restraints weight = 50490.183| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.59 r_work: 0.3247 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7536 Z= 0.137 Angle : 1.102 26.614 10280 Z= 0.472 Chirality : 0.181 1.700 1248 Planarity : 0.004 0.038 1230 Dihedral : 4.780 52.209 1018 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.00 % Allowed : 29.55 % Favored : 68.45 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.30), residues: 916 helix: 2.08 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -1.83 (0.45), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.018 0.001 TYR B 214 PHE 0.007 0.001 PHE A 502 TRP 0.013 0.001 TRP B 138 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7534) covalent geometry : angle 1.10016 / 0.47 (10274) hydrogen bonds : bond 0.03362 / 2.05 ( 476) hydrogen bonds : angle 4.05813 / 2.92 ( 1410) link_NAG-ASN : bond 0.00789 / 0.40 ( 2) link_NAG-ASN : angle 2.79839 / 1.27 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LEU cc_start: 0.9287 (mt) cc_final: 0.9057 (mp) REVERT: A 211 CYS cc_start: 0.9609 (OUTLIER) cc_final: 0.9378 (p) REVERT: A 264 MET cc_start: 0.8929 (ttm) cc_final: 0.8720 (mtm) REVERT: A 271 TRP cc_start: 0.9063 (t-100) cc_final: 0.8797 (t-100) REVERT: B 16 ILE cc_start: 0.8885 (tt) cc_final: 0.8656 (tp) REVERT: B 211 CYS cc_start: 0.9611 (OUTLIER) cc_final: 0.9303 (p) REVERT: B 264 MET cc_start: 0.8872 (ttm) cc_final: 0.8637 (mtm) outliers start: 16 outliers final: 13 residues processed: 128 average time/residue: 0.5414 time to fit residues: 79.0338 Evaluate side-chains 123 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 525 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.0270 chunk 82 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.105469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082034 restraints weight = 50327.228| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.62 r_work: 0.3259 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7536 Z= 0.131 Angle : 1.092 26.571 10280 Z= 0.465 Chirality : 0.181 1.714 1248 Planarity : 0.004 0.037 1230 Dihedral : 4.722 52.635 1018 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.12 % Allowed : 29.80 % Favored : 68.08 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.30), residues: 916 helix: 2.11 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.86 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 307 TYR 0.012 0.001 TYR B 214 PHE 0.008 0.001 PHE B 472 TRP 0.012 0.001 TRP B 138 HIS 0.002 0.001 HIS A 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7534) covalent geometry : angle 1.09009 / 0.46 (10274) hydrogen bonds : bond 0.03266 / 1.98 ( 476) hydrogen bonds : angle 4.03207 / 2.90 ( 1410) link_NAG-ASN : bond 0.00791 / 0.40 ( 2) link_NAG-ASN : angle 2.80412 / 1.28 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4911.61 seconds wall clock time: 83 minutes 56.65 seconds (5036.65 seconds total)