Starting phenix.real_space_refine on Thu Oct 22 23:25:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21mw_67827/10_2026/21mw_67827.cif Found real_map, /net/cci-nas-00/data/ceres_data/21mw_67827/10_2026/21mw_67827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21mw_67827/10_2026/21mw_67827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21mw_67827/10_2026/21mw_67827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21mw_67827/10_2026/21mw_67827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21mw_67827/10_2026/21mw_67827.map" } resolution = 3.64 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= 0.004 sd= 0.063 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4363 2.51 5 N 1058 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6575 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3286 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3289 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 412} Time building chain proxies: 1.10, per 1000 atoms: 0.17 Number of scatterers: 6575 At special positions: 0 Unit cell: (71.02, 115.54, 69.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1106 8.00 N 1058 7.00 C 4363 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=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 287.3 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 62 through 86 removed outlier: 3.529A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 93 through 115 Processing helix chain 'A' and resid 124 through 139 removed outlier: 4.052A pdb=" N GLY A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 removed outlier: 4.307A pdb=" N GLU A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 171 Processing helix chain 'A' and resid 173 through 180 removed outlier: 4.021A pdb=" N LEU A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 207 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.599A pdb=" N VAL A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.878A pdb=" N SER A 256 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 307 removed outlier: 4.099A pdb=" N ARG A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 337 Processing helix chain 'A' and resid 341 through 356 removed outlier: 4.026A pdb=" N LEU A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 388 removed outlier: 4.104A pdb=" N LYS A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Proline residue: A 378 - end of helix removed outlier: 4.328A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.784A pdb=" N VAL A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.765A pdb=" N LYS A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 496 removed outlier: 3.657A pdb=" N ALA A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) Proline residue: A 482 - end of helix Proline residue: A 493 - end of helix removed outlier: 3.609A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 86 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 115 Processing helix chain 'B' and resid 124 through 139 removed outlier: 4.079A pdb=" N GLY B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 removed outlier: 4.311A pdb=" N GLU B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 171 Processing helix chain 'B' and resid 173 through 180 removed outlier: 4.082A pdb=" N LEU B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 207 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 225 through 240 removed outlier: 3.678A pdb=" N VAL B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Proline residue: B 231 - end of helix Processing helix chain 'B' and resid 246 through 270 removed outlier: 3.955A pdb=" N SER B 256 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 307 removed outlier: 4.024A pdb=" N ARG B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 338 Processing helix chain 'B' and resid 341 through 356 removed outlier: 3.950A pdb=" N LEU B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 388 removed outlier: 4.122A pdb=" N LYS B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Proline residue: B 378 - end of helix removed outlier: 4.335A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.765A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.797A pdb=" N LYS B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 458 Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 491 removed outlier: 3.701A pdb=" N ALA B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 481 " --> pdb=" O ILE B 477 " (cutoff:3.500A) Proline residue: B 482 - end of helix removed outlier: 3.614A pdb=" N GLY B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.581A pdb=" N LEU B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1916 1.34 - 1.46: 1227 1.46 - 1.58: 3504 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 6725 Sorted by residual: bond pdb=" N ARG B 412 " pdb=" CA ARG B 412 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.07e+00 bond pdb=" N ARG A 412 " pdb=" CA ARG A 412 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.65e+00 bond pdb=" N GLU A 453 " pdb=" CA GLU A 453 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.17e-02 7.31e+03 4.55e+00 bond pdb=" N LEU B 487 " pdb=" CA LEU B 487 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.55e+00 bond pdb=" N GLU B 453 " pdb=" CA GLU B 453 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.17e-02 7.31e+03 4.38e+00 ... (remaining 6720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 8849 2.22 - 4.45: 241 4.45 - 6.67: 49 6.67 - 8.89: 12 8.89 - 11.11: 9 Bond angle restraints: 9160 Sorted by residual: angle pdb=" CA ILE B 67 " pdb=" CB ILE B 67 " pdb=" CG1 ILE B 67 " ideal model delta sigma weight residual 110.40 116.73 -6.33 1.70e+00 3.46e-01 1.39e+01 angle pdb=" CB MET B 363 " pdb=" CG MET B 363 " pdb=" SD MET B 363 " ideal model delta sigma weight residual 112.70 123.49 -10.79 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CB MET A 80 " pdb=" CG MET A 80 " pdb=" SD MET A 80 " ideal model delta sigma weight residual 112.70 101.95 10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CA ILE A 67 " pdb=" CB ILE A 67 " pdb=" CG1 ILE A 67 " ideal model delta sigma weight residual 110.40 116.15 -5.75 1.70e+00 3.46e-01 1.15e+01 angle pdb=" N ILE A 337 " pdb=" CA ILE A 337 " pdb=" C ILE A 337 " ideal model delta sigma weight residual 112.29 109.13 3.16 9.40e-01 1.13e+00 1.13e+01 ... (remaining 9155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 3301 15.59 - 31.18: 442 31.18 - 46.78: 176 46.78 - 62.37: 28 62.37 - 77.96: 7 Dihedral angle restraints: 3954 sinusoidal: 1486 harmonic: 2468 Sorted by residual: dihedral pdb=" CD ARG B 412 " pdb=" NE ARG B 412 " pdb=" CZ ARG B 412 " pdb=" NH1 ARG B 412 " ideal model delta sinusoidal sigma weight residual 0.00 -46.91 46.91 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CD ARG A 412 " pdb=" NE ARG A 412 " pdb=" CZ ARG A 412 " pdb=" NH1 ARG A 412 " ideal model delta sinusoidal sigma weight residual 0.00 -44.08 44.08 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA SER B 225 " pdb=" C SER B 225 " pdb=" N PRO B 226 " pdb=" CA PRO B 226 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 3951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 954 0.067 - 0.134: 156 0.134 - 0.201: 14 0.201 - 0.268: 3 0.268 - 0.335: 2 Chirality restraints: 1129 Sorted by residual: chirality pdb=" CG LEU A 156 " pdb=" CB LEU A 156 " pdb=" CD1 LEU A 156 " pdb=" CD2 LEU A 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CG LEU B 156 " pdb=" CB LEU B 156 " pdb=" CD1 LEU B 156 " pdb=" CD2 LEU B 156 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE B 298 " pdb=" CA ILE B 298 " pdb=" CG1 ILE B 298 " pdb=" CG2 ILE B 298 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1126 not shown) Planarity restraints: 1112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 412 " 0.782 9.50e-02 1.11e+02 3.50e-01 7.48e+01 pdb=" NE ARG B 412 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 412 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 412 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 412 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " -0.752 9.50e-02 1.11e+02 3.37e-01 6.92e+01 pdb=" NE ARG A 412 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 117 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 118 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.029 5.00e-02 4.00e+02 ... (remaining 1109 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 277 2.73 - 3.27: 6997 3.27 - 3.81: 11520 3.81 - 4.36: 12345 4.36 - 4.90: 21320 Nonbonded interactions: 52459 Sorted by model distance: nonbonded pdb=" O PHE A 321 " pdb=" OG1 THR A 325 " model vdw 2.186 3.040 nonbonded pdb=" NH1 ARG A 319 " pdb=" OE1 GLU A 361 " model vdw 2.389 3.120 nonbonded pdb=" NH1 ARG B 319 " pdb=" OE1 GLU B 361 " model vdw 2.399 3.120 nonbonded pdb=" NH1 ARG A 157 " pdb=" OE1 GLU A 453 " model vdw 2.413 3.120 nonbonded pdb=" NH2 ARG B 157 " pdb=" OE1 GLU B 453 " model vdw 2.428 3.120 ... (remaining 52454 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 62 through 297 or (resid 298 and (name N or name CA or nam \ e C or name O or name CB )) or resid 299 through 496)) } 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 group one per residue 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 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 0.049 6725 Z= 0.211 Angle : 0.946 11.114 9160 Z= 0.478 Chirality : 0.051 0.335 1129 Planarity : 0.016 0.350 1112 Dihedral : 16.880 77.958 2366 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.26 % Allowed : 28.17 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.26 (0.28), residues: 866 helix: 0.68 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -1.42 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 157 TYR 0.009 0.001 TYR A 241 PHE 0.014 0.001 PHE A 266 TRP 0.014 0.002 TRP A 78 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 ( 6725) covalent geometry : angle 0.94593 / 0.48 ( 9160) hydrogen bonds : bond 0.10777 / 7.47 ( 530) hydrogen bonds : angle 5.48918 / 3.97 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 151 average time/residue: 0.0396 time to fit residues: 8.4681 Evaluate side-chains 145 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 412 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.200820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.180811 restraints weight = 10960.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.185398 restraints weight = 6162.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.188515 restraints weight = 3897.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.190709 restraints weight = 2697.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.192090 restraints weight = 2001.180| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6725 Z= 0.136 Angle : 0.621 7.514 9160 Z= 0.307 Chirality : 0.041 0.207 1129 Planarity : 0.005 0.046 1112 Dihedral : 6.147 52.842 921 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.88 % Allowed : 24.97 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.62 (0.29), residues: 866 helix: 1.69 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -1.05 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 305 TYR 0.011 0.001 TYR B 306 PHE 0.010 0.001 PHE A 303 TRP 0.012 0.001 TRP A 78 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6725) covalent geometry : angle 0.62059 / 0.31 ( 9160) hydrogen bonds : bond 0.03597 / 2.40 ( 530) hydrogen bonds : angle 4.28251 / 3.11 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8356 (tp) cc_final: 0.8065 (tp) REVERT: A 378 PRO cc_start: 0.9366 (Cg_exo) cc_final: 0.9077 (Cg_endo) REVERT: A 461 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6240 (p-80) REVERT: B 98 LEU cc_start: 0.7637 (tp) cc_final: 0.7238 (tp) REVERT: B 461 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.6342 (p-80) REVERT: B 470 MET cc_start: 0.8078 (tpp) cc_final: 0.7512 (tpp) outliers start: 35 outliers final: 17 residues processed: 164 average time/residue: 0.0552 time to fit residues: 12.8984 Evaluate side-chains 144 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 461 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [12, 19, 21, 43, 53, 27, 68, 32, 45, 80, 64] chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.200972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.180938 restraints weight = 10927.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.185488 restraints weight = 6213.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.188683 restraints weight = 3954.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.190622 restraints weight = 2718.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.192265 restraints weight = 2064.137| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6725 Z= 0.134 Angle : 0.622 8.990 9160 Z= 0.303 Chirality : 0.041 0.223 1129 Planarity : 0.004 0.047 1112 Dihedral : 5.328 50.464 911 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.02 % Allowed : 25.38 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.86 (0.29), residues: 866 helix: 1.83 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.04 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 412 TYR 0.007 0.001 TYR A 103 PHE 0.009 0.001 PHE A 303 TRP 0.011 0.001 TRP A 78 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 6725) covalent geometry : angle 0.62202 / 0.30 ( 9160) hydrogen bonds : bond 0.03411 / 2.28 ( 530) hydrogen bonds : angle 4.28488 / 3.11 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8066 (mtp) cc_final: 0.7785 (ttt) REVERT: A 378 PRO cc_start: 0.9390 (Cg_exo) cc_final: 0.9112 (Cg_endo) REVERT: A 461 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.6317 (p-80) REVERT: A 470 MET cc_start: 0.8168 (tpp) cc_final: 0.7655 (tpp) REVERT: B 98 LEU cc_start: 0.7758 (tp) cc_final: 0.7530 (tp) REVERT: B 461 HIS cc_start: 0.6833 (OUTLIER) cc_final: 0.6395 (p-80) REVERT: B 470 MET cc_start: 0.8123 (tpp) cc_final: 0.7647 (tpp) outliers start: 36 outliers final: 18 residues processed: 163 average time/residue: 0.0546 time to fit residues: 13.1395 Evaluate side-chains 145 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 461 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [19, 45, 15, 3, 1, 82, 76, 10, 35, 34, 55] chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.0070 chunk 76 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.202142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.182408 restraints weight = 11165.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.186925 restraints weight = 6393.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.190077 restraints weight = 4082.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.192182 restraints weight = 2818.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.193623 restraints weight = 2108.396| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6725 Z= 0.119 Angle : 0.608 7.969 9160 Z= 0.294 Chirality : 0.040 0.201 1129 Planarity : 0.004 0.043 1112 Dihedral : 4.562 46.212 907 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.46 % Allowed : 27.62 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.02 (0.29), residues: 866 helix: 1.94 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.97 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.007 0.001 TYR A 103 PHE 0.009 0.001 PHE A 303 TRP 0.010 0.001 TRP A 78 HIS 0.002 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 6725) covalent geometry : angle 0.60778 / 0.29 ( 9160) hydrogen bonds : bond 0.03187 / 2.12 ( 530) hydrogen bonds : angle 4.21735 / 3.07 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 PRO cc_start: 0.9377 (Cg_exo) cc_final: 0.9101 (Cg_endo) REVERT: A 461 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6298 (p-80) REVERT: A 470 MET cc_start: 0.8031 (tpp) cc_final: 0.7575 (tpp) REVERT: B 98 LEU cc_start: 0.7852 (tp) cc_final: 0.7645 (tp) REVERT: B 207 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7060 (mpp) REVERT: B 208 LYS cc_start: 0.4814 (OUTLIER) cc_final: 0.3874 (tppt) REVERT: B 461 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6317 (p-80) REVERT: B 470 MET cc_start: 0.7914 (tpp) cc_final: 0.7318 (tpp) outliers start: 32 outliers final: 18 residues processed: 160 average time/residue: 0.0553 time to fit residues: 12.8419 Evaluate side-chains 149 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 461 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [77, 67, 18, 68, 61, 38, 3, 14, 71, 30, 55] chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 0.0570 chunk 18 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.0060 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.1666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 HIS B 461 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.205263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.185396 restraints weight = 11341.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.190109 restraints weight = 6431.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.193245 restraints weight = 4069.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.195497 restraints weight = 2816.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.196772 restraints weight = 2073.701| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6725 Z= 0.112 Angle : 0.602 8.129 9160 Z= 0.289 Chirality : 0.040 0.200 1129 Planarity : 0.004 0.043 1112 Dihedral : 4.419 44.126 907 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.91 % Allowed : 28.31 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.14 (0.29), residues: 866 helix: 2.02 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -0.89 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 412 TYR 0.008 0.001 TYR A 103 PHE 0.009 0.001 PHE A 102 TRP 0.008 0.001 TRP A 78 HIS 0.001 0.000 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6725) covalent geometry : angle 0.60203 / 0.29 ( 9160) hydrogen bonds : bond 0.02957 / 1.95 ( 530) hydrogen bonds : angle 4.18783 / 3.05 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 PRO cc_start: 0.9404 (Cg_exo) cc_final: 0.9140 (Cg_endo) REVERT: A 461 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.6416 (p90) REVERT: A 470 MET cc_start: 0.7770 (tpp) cc_final: 0.7474 (tpp) REVERT: B 207 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6905 (mpp) REVERT: B 208 LYS cc_start: 0.4722 (OUTLIER) cc_final: 0.3791 (tppt) REVERT: B 461 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6441 (p90) REVERT: B 470 MET cc_start: 0.7879 (tpp) cc_final: 0.7389 (tpp) outliers start: 28 outliers final: 17 residues processed: 167 average time/residue: 0.0607 time to fit residues: 14.5358 Evaluate side-chains 151 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 461 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [56, 22, 79, 24, 60, 80, 34, 15, 54, 1, 64] chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.200652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.180706 restraints weight = 11501.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.185298 restraints weight = 6586.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.188386 restraints weight = 4200.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.190481 restraints weight = 2925.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.191924 restraints weight = 2196.703| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6725 Z= 0.144 Angle : 0.644 8.647 9160 Z= 0.311 Chirality : 0.042 0.240 1129 Planarity : 0.004 0.043 1112 Dihedral : 4.484 43.097 907 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.46 % Allowed : 28.31 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.00 (0.29), residues: 866 helix: 1.96 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.13 (0.41), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.008 0.001 TYR A 103 PHE 0.009 0.001 PHE A 303 TRP 0.007 0.001 TRP B 78 HIS 0.003 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 6725) covalent geometry : angle 0.64399 / 0.31 ( 9160) hydrogen bonds : bond 0.03204 / 2.12 ( 530) hydrogen bonds : angle 4.23964 / 3.08 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6915 (mpp) REVERT: A 378 PRO cc_start: 0.9453 (Cg_exo) cc_final: 0.9194 (Cg_endo) REVERT: B 207 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7011 (mpp) REVERT: B 208 LYS cc_start: 0.4842 (OUTLIER) cc_final: 0.3896 (tppt) REVERT: B 470 MET cc_start: 0.7946 (tpp) cc_final: 0.7458 (tpp) outliers start: 32 outliers final: 23 residues processed: 158 average time/residue: 0.0600 time to fit residues: 13.8321 Evaluate side-chains 155 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 461 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [85, 84, 64, 7, 21, 50, 22, 6, 61, 63, 55] chunk 85 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.200415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180521 restraints weight = 11337.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.185111 restraints weight = 6466.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.188176 restraints weight = 4124.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.190159 restraints weight = 2874.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.191717 restraints weight = 2190.522| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6725 Z= 0.136 Angle : 0.643 8.876 9160 Z= 0.313 Chirality : 0.042 0.235 1129 Planarity : 0.005 0.053 1112 Dihedral : 4.484 41.461 907 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.60 % Allowed : 28.73 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.07 (0.29), residues: 866 helix: 2.03 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.00 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.007 0.001 TYR A 306 PHE 0.010 0.001 PHE A 303 TRP 0.009 0.001 TRP B 78 HIS 0.004 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6725) covalent geometry : angle 0.64296 / 0.31 ( 9160) hydrogen bonds : bond 0.03266 / 2.16 ( 530) hydrogen bonds : angle 4.26913 / 3.11 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6979 (mpp) REVERT: A 208 LYS cc_start: 0.4852 (OUTLIER) cc_final: 0.3904 (tppt) REVERT: A 378 PRO cc_start: 0.9442 (Cg_exo) cc_final: 0.9179 (Cg_endo) REVERT: A 415 THR cc_start: 0.7407 (m) cc_final: 0.6934 (m) REVERT: A 470 MET cc_start: 0.7936 (tpp) cc_final: 0.7545 (tpp) REVERT: B 207 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7085 (mpp) REVERT: B 208 LYS cc_start: 0.4894 (OUTLIER) cc_final: 0.3943 (tppt) REVERT: B 415 THR cc_start: 0.7367 (m) cc_final: 0.6854 (m) REVERT: B 461 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6301 (p-80) REVERT: B 470 MET cc_start: 0.8055 (tpp) cc_final: 0.7648 (tpp) REVERT: B 488 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7223 (mmt) outliers start: 33 outliers final: 23 residues processed: 161 average time/residue: 0.0605 time to fit residues: 13.9938 Evaluate side-chains 159 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [59, 54, 60, 14, 27, 43, 69, 58, 82, 63, 62] chunk 59 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.200241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.180259 restraints weight = 11088.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.184948 restraints weight = 6218.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.188101 restraints weight = 3905.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.190315 restraints weight = 2678.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.191838 restraints weight = 1969.163| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6725 Z= 0.132 Angle : 0.654 11.415 9160 Z= 0.317 Chirality : 0.043 0.294 1129 Planarity : 0.005 0.045 1112 Dihedral : 4.493 39.781 907 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.88 % Allowed : 28.45 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.02 (0.29), residues: 866 helix: 2.00 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.006 0.001 TYR A 103 PHE 0.010 0.001 PHE A 303 TRP 0.009 0.001 TRP B 78 HIS 0.002 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 6725) covalent geometry : angle 0.65436 / 0.32 ( 9160) hydrogen bonds : bond 0.03232 / 2.14 ( 530) hydrogen bonds : angle 4.31060 / 3.15 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6976 (mpp) REVERT: A 208 LYS cc_start: 0.4838 (OUTLIER) cc_final: 0.3901 (tppt) REVERT: A 378 PRO cc_start: 0.9448 (Cg_exo) cc_final: 0.9183 (Cg_endo) REVERT: A 415 THR cc_start: 0.7403 (m) cc_final: 0.7090 (m) REVERT: A 470 MET cc_start: 0.8078 (tpp) cc_final: 0.7685 (tpp) REVERT: B 129 MET cc_start: 0.8548 (mtt) cc_final: 0.8340 (mtt) REVERT: B 207 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7086 (mpp) REVERT: B 208 LYS cc_start: 0.4881 (OUTLIER) cc_final: 0.3946 (tppt) REVERT: B 415 THR cc_start: 0.7359 (m) cc_final: 0.7026 (m) REVERT: B 461 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6461 (p-80) REVERT: B 488 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7179 (mmt) outliers start: 35 outliers final: 24 residues processed: 166 average time/residue: 0.0613 time to fit residues: 14.4783 Evaluate side-chains 162 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [25, 84, 62, 24, 45, 17, 81, 51, 23, 19, 65] chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.198345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178459 restraints weight = 11049.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.183090 restraints weight = 6228.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.186268 restraints weight = 3932.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.188437 restraints weight = 2691.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.189904 restraints weight = 1986.915| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6725 Z= 0.147 Angle : 0.683 11.030 9160 Z= 0.331 Chirality : 0.044 0.333 1129 Planarity : 0.005 0.048 1112 Dihedral : 4.526 39.237 907 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.46 % Allowed : 29.29 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.86 (0.29), residues: 866 helix: 1.89 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.006 0.001 TYR A 103 PHE 0.011 0.001 PHE A 303 TRP 0.009 0.001 TRP B 78 HIS 0.002 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 6725) covalent geometry : angle 0.68290 / 0.33 ( 9160) hydrogen bonds : bond 0.03369 / 2.24 ( 530) hydrogen bonds : angle 4.36994 / 3.19 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7029 (mpp) REVERT: A 208 LYS cc_start: 0.4900 (OUTLIER) cc_final: 0.3953 (tppt) REVERT: A 326 MET cc_start: 0.7854 (mmm) cc_final: 0.7649 (mmm) REVERT: A 378 PRO cc_start: 0.9452 (Cg_exo) cc_final: 0.9162 (Cg_endo) REVERT: A 415 THR cc_start: 0.7354 (m) cc_final: 0.7067 (m) REVERT: A 470 MET cc_start: 0.8066 (tpp) cc_final: 0.7383 (tpp) REVERT: B 207 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7151 (mpp) REVERT: B 208 LYS cc_start: 0.5051 (OUTLIER) cc_final: 0.4088 (tppt) REVERT: B 415 THR cc_start: 0.7423 (m) cc_final: 0.7109 (m) REVERT: B 461 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6337 (p-80) REVERT: B 470 MET cc_start: 0.8127 (tpp) cc_final: 0.7196 (tpp) REVERT: B 488 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7238 (mmt) outliers start: 32 outliers final: 24 residues processed: 159 average time/residue: 0.0601 time to fit residues: 13.8626 Evaluate side-chains 161 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [73, 45, 56, 48, 62, 15, 75, 57, 69, 68, 41] chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 62 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 57 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 461 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.201874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182019 restraints weight = 10900.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.186714 restraints weight = 6129.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.189953 restraints weight = 3839.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.192175 restraints weight = 2614.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.193504 restraints weight = 1909.203| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6725 Z= 0.125 Angle : 0.670 11.355 9160 Z= 0.321 Chirality : 0.043 0.309 1129 Planarity : 0.004 0.042 1112 Dihedral : 4.433 38.330 907 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.18 % Allowed : 30.26 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.83 (0.29), residues: 866 helix: 1.83 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.011 0.001 TYR A 232 PHE 0.014 0.001 PHE A 303 TRP 0.010 0.001 TRP B 78 HIS 0.001 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6725) covalent geometry : angle 0.67046 / 0.32 ( 9160) hydrogen bonds : bond 0.03151 / 2.09 ( 530) hydrogen bonds : angle 4.35192 / 3.17 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6922 (mpp) REVERT: A 378 PRO cc_start: 0.9442 (Cg_exo) cc_final: 0.9177 (Cg_endo) REVERT: A 415 THR cc_start: 0.7456 (m) cc_final: 0.6997 (m) REVERT: A 470 MET cc_start: 0.7908 (tpp) cc_final: 0.7659 (tpp) REVERT: B 207 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7069 (mpp) REVERT: B 208 LYS cc_start: 0.4832 (OUTLIER) cc_final: 0.3916 (tppt) REVERT: B 405 LEU cc_start: 0.7499 (tp) cc_final: 0.7244 (tt) REVERT: B 415 THR cc_start: 0.7496 (m) cc_final: 0.7066 (m) REVERT: B 461 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.6446 (p90) REVERT: B 470 MET cc_start: 0.8024 (tpp) cc_final: 0.7421 (tpp) outliers start: 30 outliers final: 23 residues processed: 157 average time/residue: 0.0604 time to fit residues: 13.7009 Evaluate side-chains 158 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [42, 44, 61, 49, 62, 55, 53, 26, 52, 71, 20] chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.201229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.181285 restraints weight = 11301.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.185906 restraints weight = 6418.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.189056 restraints weight = 4069.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.191241 restraints weight = 2817.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.192689 restraints weight = 2093.176| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6725 Z= 0.133 Angle : 0.689 12.262 9160 Z= 0.328 Chirality : 0.044 0.301 1129 Planarity : 0.005 0.042 1112 Dihedral : 4.452 38.078 907 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.32 % Allowed : 29.99 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.81 (0.29), residues: 866 helix: 1.82 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 137 TYR 0.010 0.001 TYR A 232 PHE 0.016 0.001 PHE A 321 TRP 0.008 0.001 TRP B 78 HIS 0.003 0.001 HIS B 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 6725) covalent geometry : angle 0.68901 / 0.33 ( 9160) hydrogen bonds : bond 0.03208 / 2.13 ( 530) hydrogen bonds : angle 4.37362 / 3.19 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1028.77 seconds wall clock time: 18 minutes 25.26 seconds (1105.26 seconds total)