Starting phenix.real_space_refine on Sun Apr 5 13:20:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0x_65520/04_2026/9w0x_65520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0x_65520/04_2026/9w0x_65520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w0x_65520/04_2026/9w0x_65520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0x_65520/04_2026/9w0x_65520.map" model { file = "/net/cci-nas-00/data/ceres_data/9w0x_65520/04_2026/9w0x_65520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0x_65520/04_2026/9w0x_65520.cif" } resolution = 2.9 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= -0.001 sd= 0.077 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 P 8 5.49 5 S 44 5.16 5 C 6950 2.51 5 N 1694 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10436 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 5028 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 19, 'TRANS': 575} Chain breaks: 3 Chain: "A" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 190 Unusual residues: {'8PE': 1, 'PO4': 3, 'POV': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-1': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 45 Restraints were copied for chains: D Time building chain proxies: 4.12, per 1000 atoms: 0.39 Number of scatterers: 10436 At special positions: 0 Unit cell: (109.787, 118.483, 100.004, 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 44 16.00 P 8 15.00 O 1740 8.00 N 1694 7.00 C 6950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 448 " - pdb=" SG CYS A 460 " distance=2.03 Simple disulfide: pdb=" SG CYS D 448 " - pdb=" SG CYS D 460 " distance=2.03 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: 0.62 Conformation dependent library (CDL) restraints added in 530.9 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 75.0% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 66 through 112 removed outlier: 3.530A pdb=" N GLU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 206 Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.040A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 247 removed outlier: 3.889A pdb=" N THR A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.590A pdb=" N ALA A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 296 through 329 removed outlier: 3.654A pdb=" N SER A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.739A pdb=" N ILE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 370 Processing helix chain 'A' and resid 379 through 393 Processing helix chain 'A' and resid 400 through 416 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.777A pdb=" N CYS A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 3.972A pdb=" N LEU A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 removed outlier: 3.513A pdb=" N LEU A 459 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 491 removed outlier: 4.334A pdb=" N GLY A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 493 through 519 removed outlier: 3.560A pdb=" N VAL A 498 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 547 Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 586 through 592 removed outlier: 3.932A pdb=" N CYS A 590 " --> pdb=" O PHE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 635 removed outlier: 4.041A pdb=" N PHE A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 66 through 112 removed outlier: 3.529A pdb=" N GLU D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 165 through 206 Processing helix chain 'D' and resid 214 through 222 removed outlier: 4.040A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 247 removed outlier: 3.889A pdb=" N THR D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.590A pdb=" N ALA D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 296 through 329 removed outlier: 3.653A pdb=" N SER D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.740A pdb=" N ILE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 370 Processing helix chain 'D' and resid 379 through 393 Processing helix chain 'D' and resid 400 through 416 Processing helix chain 'D' and resid 423 through 435 Processing helix chain 'D' and resid 436 through 441 removed outlier: 3.777A pdb=" N CYS D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 452 removed outlier: 3.972A pdb=" N LEU D 445 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 452 " --> pdb=" O CYS D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 460 removed outlier: 3.513A pdb=" N LEU D 459 " --> pdb=" O GLN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 491 removed outlier: 4.334A pdb=" N GLY D 469 " --> pdb=" O SER D 465 " (cutoff:3.500A) Proline residue: D 475 - end of helix Processing helix chain 'D' and resid 493 through 519 removed outlier: 3.560A pdb=" N VAL D 498 " --> pdb=" O PHE D 494 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN D 499 " --> pdb=" O PRO D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 547 Processing helix chain 'D' and resid 570 through 584 Processing helix chain 'D' and resid 586 through 592 removed outlier: 3.932A pdb=" N CYS D 590 " --> pdb=" O PHE D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 635 removed outlier: 4.041A pdb=" N PHE D 604 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.681A pdb=" N TYR A 147 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AA3, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.681A pdb=" N TYR D 147 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 551 through 553 669 hydrogen bonds defined for protein. 2001 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: 1.69 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1506 1.28 - 1.41: 3131 1.41 - 1.55: 5991 1.55 - 1.68: 14 1.68 - 1.82: 70 Bond restraints: 10712 Sorted by residual: bond pdb=" C MET D 612 " pdb=" O MET D 612 " ideal model delta sigma weight residual 1.237 1.351 -0.114 1.17e-02 7.31e+03 9.50e+01 bond pdb=" C MET A 612 " pdb=" O MET A 612 " ideal model delta sigma weight residual 1.237 1.351 -0.114 1.17e-02 7.31e+03 9.48e+01 bond pdb=" CA ASN A 632 " pdb=" C ASN A 632 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.32e-02 5.74e+03 9.07e+01 bond pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.32e-02 5.74e+03 9.07e+01 bond pdb=" CA ARG D 630 " pdb=" C ARG D 630 " ideal model delta sigma weight residual 1.524 1.416 0.107 1.27e-02 6.20e+03 7.13e+01 ... (remaining 10707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 13860 2.80 - 5.61: 386 5.61 - 8.41: 92 8.41 - 11.22: 32 11.22 - 14.02: 4 Bond angle restraints: 14374 Sorted by residual: angle pdb=" N ASN D 632 " pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 113.50 101.61 11.89 1.23e+00 6.61e-01 9.34e+01 angle pdb=" N ASN A 632 " pdb=" CA ASN A 632 " pdb=" C ASN A 632 " ideal model delta sigma weight residual 113.50 101.62 11.88 1.23e+00 6.61e-01 9.33e+01 angle pdb=" N GLU A 631 " pdb=" CA GLU A 631 " pdb=" C GLU A 631 " ideal model delta sigma weight residual 113.01 122.61 -9.60 1.20e+00 6.94e-01 6.39e+01 angle pdb=" N GLU D 631 " pdb=" CA GLU D 631 " pdb=" C GLU D 631 " ideal model delta sigma weight residual 113.01 122.58 -9.57 1.20e+00 6.94e-01 6.36e+01 angle pdb=" N GLU D 610 " pdb=" CA GLU D 610 " pdb=" C GLU D 610 " ideal model delta sigma weight residual 111.28 118.94 -7.66 1.09e+00 8.42e-01 4.94e+01 ... (remaining 14369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 5396 23.05 - 46.10: 751 46.10 - 69.16: 119 69.16 - 92.21: 22 92.21 - 115.26: 6 Dihedral angle restraints: 6294 sinusoidal: 2758 harmonic: 3536 Sorted by residual: dihedral pdb=" CA ASN A 294 " pdb=" C ASN A 294 " pdb=" N ALA A 295 " pdb=" CA ALA A 295 " ideal model delta harmonic sigma weight residual -180.00 -145.51 -34.49 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ASN D 294 " pdb=" C ASN D 294 " pdb=" N ALA D 295 " pdb=" CA ALA D 295 " ideal model delta harmonic sigma weight residual -180.00 -145.54 -34.46 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" C ASN D 632 " pdb=" N ASN D 632 " pdb=" CA ASN D 632 " pdb=" CB ASN D 632 " ideal model delta harmonic sigma weight residual -122.60 -107.47 -15.13 0 2.50e+00 1.60e-01 3.66e+01 ... (remaining 6291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1365 0.093 - 0.186: 71 0.186 - 0.279: 32 0.279 - 0.371: 10 0.371 - 0.464: 4 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA LEU D 620 " pdb=" N LEU D 620 " pdb=" C LEU D 620 " pdb=" CB LEU D 620 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA LEU A 620 " pdb=" N LEU A 620 " pdb=" C LEU A 620 " pdb=" CB LEU A 620 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA ARG D 614 " pdb=" N ARG D 614 " pdb=" C ARG D 614 " pdb=" CB ARG D 614 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 1479 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 620 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LEU A 620 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU A 620 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG A 621 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 620 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LEU D 620 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU D 620 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG D 621 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 602 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C ILE A 602 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 602 " -0.018 2.00e-02 2.50e+03 pdb=" N SER A 603 " -0.017 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3682 2.86 - 3.37: 9808 3.37 - 3.88: 16823 3.88 - 4.39: 19576 4.39 - 4.90: 33114 Nonbonded interactions: 83003 Sorted by model distance: nonbonded pdb=" N ASN D 632 " pdb=" N LEU D 633 " model vdw 2.348 2.560 nonbonded pdb=" N ASN A 632 " pdb=" N LEU A 633 " model vdw 2.348 2.560 nonbonded pdb=" CB SER D 154 " pdb=" N VAL D 155 " model vdw 2.375 2.816 nonbonded pdb=" CB SER A 154 " pdb=" N VAL A 155 " model vdw 2.375 2.816 nonbonded pdb=" OG SER D 154 " pdb=" N VAL D 155 " model vdw 2.417 3.120 ... (remaining 82998 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 'D' } 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: 3.350 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.870 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.012 0.127 10714 Z= 0.754 Angle : 1.170 14.022 14378 Z= 0.670 Chirality : 0.064 0.464 1482 Planarity : 0.006 0.046 1774 Dihedral : 20.226 115.262 3996 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.94 % Favored : 94.21 % Rotamer: Outliers : 4.72 % Allowed : 31.67 % Favored : 63.61 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.82 (0.25), residues: 1174 helix: 1.69 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -2.94 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 614 TYR 0.023 0.001 TYR D 628 PHE 0.024 0.001 PHE A 275 TRP 0.014 0.002 TRP D 217 HIS 0.007 0.001 HIS A 624 Details of bonding type rmsd covalent geometry : bond 0.01155 (10712) covalent geometry : angle 1.17012 (14374) SS BOND : bond 0.00253 ( 2) SS BOND : angle 1.33744 ( 4) hydrogen bonds : bond 0.13877 ( 669) hydrogen bonds : angle 5.13499 ( 2001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7500 (mmm160) REVERT: A 172 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8264 (tptm) REVERT: A 343 LYS cc_start: 0.8765 (mmmt) cc_final: 0.7584 (tttt) REVERT: A 431 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8661 (m-30) REVERT: A 562 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7834 (mm-30) REVERT: A 610 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: A 616 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8445 (ptt) REVERT: D 167 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7509 (mmm160) REVERT: D 343 LYS cc_start: 0.8724 (mmmt) cc_final: 0.7491 (tttt) REVERT: D 431 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: D 610 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: D 613 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7285 (ttp80) REVERT: D 616 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8449 (ptt) outliers start: 51 outliers final: 26 residues processed: 152 average time/residue: 0.7236 time to fit residues: 116.4911 Evaluate side-chains 135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 610 GLU Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 613 ARG Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 616 MET Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 642 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.1980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN D 191 GLN D 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.167299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130360 restraints weight = 12243.095| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.59 r_work: 0.3403 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10714 Z= 0.140 Angle : 0.537 6.297 14378 Z= 0.290 Chirality : 0.039 0.200 1482 Planarity : 0.004 0.034 1774 Dihedral : 13.351 94.156 1678 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.94 % Favored : 94.38 % Rotamer: Outliers : 6.85 % Allowed : 26.85 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.40 (0.25), residues: 1174 helix: 2.13 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 405 TYR 0.014 0.001 TYR A 628 PHE 0.022 0.001 PHE A 275 TRP 0.011 0.001 TRP D 217 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00277 (10712) covalent geometry : angle 0.53627 (14374) SS BOND : bond 0.00354 ( 2) SS BOND : angle 1.33823 ( 4) hydrogen bonds : bond 0.06470 ( 669) hydrogen bonds : angle 3.91879 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 116 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.6051 (tp) REVERT: A 95 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: A 142 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7335 (mtt180) REVERT: A 229 PHE cc_start: 0.7682 (m-10) cc_final: 0.7282 (m-80) REVERT: A 343 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8534 (mtmt) REVERT: A 431 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8629 (m-30) REVERT: A 562 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 610 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: D 95 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: D 142 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7343 (mtt180) REVERT: D 156 PRO cc_start: 0.8918 (Cg_endo) cc_final: 0.8713 (Cg_endo) REVERT: D 343 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8509 (mtmt) REVERT: D 431 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8622 (m-30) REVERT: D 555 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: D 610 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7858 (mm-30) outliers start: 74 outliers final: 24 residues processed: 177 average time/residue: 0.6476 time to fit residues: 122.0625 Evaluate side-chains 133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 610 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 499 ASN D 191 GLN D 499 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128734 restraints weight = 12296.520| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.59 r_work: 0.3362 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10714 Z= 0.151 Angle : 0.541 6.816 14378 Z= 0.289 Chirality : 0.039 0.196 1482 Planarity : 0.004 0.032 1774 Dihedral : 12.209 84.954 1612 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.37 % Favored : 93.95 % Rotamer: Outliers : 6.02 % Allowed : 29.35 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.25), residues: 1174 helix: 2.37 (0.17), residues: 854 sheet: None (None), residues: 0 loop : -2.54 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.014 0.002 TYR D 224 PHE 0.020 0.001 PHE A 275 TRP 0.009 0.001 TRP D 217 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00320 (10712) covalent geometry : angle 0.54100 (14374) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.25439 ( 4) hydrogen bonds : bond 0.06769 ( 669) hydrogen bonds : angle 3.85657 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 105 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.6337 (OUTLIER) cc_final: 0.6126 (tp) REVERT: A 95 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7245 (m-30) REVERT: A 130 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6614 (tp) REVERT: A 499 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8231 (t0) REVERT: A 562 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 583 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7963 (mtt-85) REVERT: A 610 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: D 95 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: D 130 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6614 (tp) REVERT: D 499 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8220 (t0) REVERT: D 557 ARG cc_start: 0.7502 (mpp80) cc_final: 0.7266 (mpp80) REVERT: D 583 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7997 (mtt-85) REVERT: D 610 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7829 (mm-30) outliers start: 65 outliers final: 37 residues processed: 161 average time/residue: 0.6775 time to fit residues: 115.9556 Evaluate side-chains 143 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 499 ASN Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 610 GLU Chi-restraints excluded: chain D residue 633 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS D 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.162509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125073 restraints weight = 12404.114| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.54 r_work: 0.3337 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10714 Z= 0.189 Angle : 0.570 7.113 14378 Z= 0.305 Chirality : 0.041 0.196 1482 Planarity : 0.004 0.031 1774 Dihedral : 12.217 85.451 1604 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.54 % Favored : 93.78 % Rotamer: Outliers : 6.57 % Allowed : 28.43 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.58 (0.24), residues: 1174 helix: 2.24 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -2.55 (0.29), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 637 TYR 0.018 0.002 TYR D 503 PHE 0.022 0.002 PHE A 446 TRP 0.009 0.002 TRP D 454 HIS 0.006 0.001 HIS D 598 Details of bonding type rmsd covalent geometry : bond 0.00429 (10712) covalent geometry : angle 0.56987 (14374) SS BOND : bond 0.00490 ( 2) SS BOND : angle 1.36694 ( 4) hydrogen bonds : bond 0.07692 ( 669) hydrogen bonds : angle 3.96244 ( 2001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 101 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.6065 (tp) REVERT: A 95 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: A 133 ARG cc_start: 0.6704 (tpt-90) cc_final: 0.5655 (ttt180) REVERT: A 562 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 583 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8010 (mtt-85) REVERT: A 610 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: D 95 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: D 130 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6681 (tp) REVERT: D 131 ARG cc_start: 0.5049 (ttt180) cc_final: 0.4835 (tpt170) REVERT: D 133 ARG cc_start: 0.6708 (tpt-90) cc_final: 0.5663 (ttt180) REVERT: D 562 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 583 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8039 (mtt-85) REVERT: D 610 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7950 (mm-30) outliers start: 71 outliers final: 37 residues processed: 160 average time/residue: 0.6728 time to fit residues: 114.4195 Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 610 GLU Chi-restraints excluded: chain D residue 633 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS A 350 HIS D 191 GLN D 350 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128063 restraints weight = 12410.971| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.64 r_work: 0.3382 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10714 Z= 0.143 Angle : 0.520 7.383 14378 Z= 0.278 Chirality : 0.039 0.199 1482 Planarity : 0.003 0.030 1774 Dihedral : 11.635 81.600 1604 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.86 % Favored : 94.46 % Rotamer: Outliers : 6.76 % Allowed : 28.52 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.97 (0.25), residues: 1174 helix: 2.50 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -2.29 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 557 TYR 0.017 0.001 TYR D 19 PHE 0.018 0.001 PHE A 446 TRP 0.009 0.001 TRP A 570 HIS 0.005 0.001 HIS D 598 Details of bonding type rmsd covalent geometry : bond 0.00300 (10712) covalent geometry : angle 0.51936 (14374) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.17598 ( 4) hydrogen bonds : bond 0.06622 ( 669) hydrogen bonds : angle 3.78176 ( 2001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 103 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7875 (m-80) cc_final: 0.7281 (m-80) REVERT: A 28 ILE cc_start: 0.6232 (OUTLIER) cc_final: 0.6026 (tp) REVERT: A 95 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: A 163 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: A 562 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 583 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8084 (mtt-85) REVERT: A 610 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: D 19 TYR cc_start: 0.7886 (m-80) cc_final: 0.7158 (m-80) REVERT: D 95 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: D 130 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6684 (tp) REVERT: D 133 ARG cc_start: 0.6645 (tpt-90) cc_final: 0.5610 (ttp-170) REVERT: D 137 ILE cc_start: 0.7964 (mm) cc_final: 0.7617 (mp) REVERT: D 163 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7581 (mpp) REVERT: D 562 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7691 (mm-30) REVERT: D 583 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8096 (mtt-85) REVERT: D 610 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7863 (mm-30) outliers start: 73 outliers final: 38 residues processed: 164 average time/residue: 0.6293 time to fit residues: 110.0650 Evaluate side-chains 144 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 610 GLU Chi-restraints excluded: chain D residue 633 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 0.0020 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS D 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127776 restraints weight = 12588.506| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.81 r_work: 0.3386 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10714 Z= 0.140 Angle : 0.524 8.195 14378 Z= 0.276 Chirality : 0.039 0.219 1482 Planarity : 0.003 0.028 1774 Dihedral : 11.233 79.980 1604 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.86 % Favored : 94.46 % Rotamer: Outliers : 5.93 % Allowed : 29.44 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 2.04 (0.25), residues: 1174 helix: 2.54 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -2.29 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.015 0.001 TYR D 19 PHE 0.018 0.001 PHE A 446 TRP 0.008 0.001 TRP A 347 HIS 0.005 0.001 HIS D 598 Details of bonding type rmsd covalent geometry : bond 0.00292 (10712) covalent geometry : angle 0.52348 (14374) SS BOND : bond 0.00351 ( 2) SS BOND : angle 1.10642 ( 4) hydrogen bonds : bond 0.06495 ( 669) hydrogen bonds : angle 3.75080 ( 2001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 101 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6583 (tp) REVERT: A 167 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7527 (mmm160) REVERT: A 402 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.6980 (mmm160) REVERT: A 562 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 583 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8100 (mtt-85) REVERT: A 610 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: A 616 MET cc_start: 0.8615 (ttp) cc_final: 0.8301 (ptt) REVERT: D 130 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6606 (tp) REVERT: D 133 ARG cc_start: 0.6615 (tpt-90) cc_final: 0.5673 (ttp-170) REVERT: D 163 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: D 167 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7517 (mmm160) REVERT: D 402 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6987 (mmm160) REVERT: D 562 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7716 (mm-30) REVERT: D 583 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8073 (mtt-85) REVERT: D 610 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: D 616 MET cc_start: 0.8601 (ttp) cc_final: 0.8261 (ptt) outliers start: 64 outliers final: 34 residues processed: 155 average time/residue: 0.6306 time to fit residues: 104.2645 Evaluate side-chains 142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 112 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 610 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 49 optimal weight: 0.0000 chunk 103 optimal weight: 0.0030 chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130720 restraints weight = 12394.914| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.60 r_work: 0.3414 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10714 Z= 0.126 Angle : 0.511 8.849 14378 Z= 0.271 Chirality : 0.038 0.234 1482 Planarity : 0.003 0.028 1774 Dihedral : 10.792 77.832 1604 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.86 % Favored : 94.63 % Rotamer: Outliers : 5.46 % Allowed : 30.19 % Favored : 64.35 % 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: 2.23 (0.25), residues: 1174 helix: 2.67 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -2.18 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 405 TYR 0.020 0.001 TYR A 19 PHE 0.019 0.001 PHE A 275 TRP 0.009 0.001 TRP A 570 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00251 (10712) covalent geometry : angle 0.51055 (14374) SS BOND : bond 0.00264 ( 2) SS BOND : angle 1.04239 ( 4) hydrogen bonds : bond 0.05871 ( 669) hydrogen bonds : angle 3.63770 ( 2001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 106 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: A 130 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6610 (tp) REVERT: A 167 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7433 (mmm160) REVERT: A 402 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6916 (mmm160) REVERT: A 562 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 95 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: D 130 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6540 (tm) REVERT: D 167 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7438 (mmm160) REVERT: D 402 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.6909 (mmm160) REVERT: D 562 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7769 (mm-30) outliers start: 59 outliers final: 30 residues processed: 154 average time/residue: 0.6329 time to fit residues: 104.1031 Evaluate side-chains 134 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 402 ARG Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 566 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127531 restraints weight = 12448.442| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.68 r_work: 0.3371 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10714 Z= 0.153 Angle : 0.538 9.563 14378 Z= 0.285 Chirality : 0.040 0.233 1482 Planarity : 0.003 0.028 1774 Dihedral : 10.785 83.062 1596 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.03 % Favored : 94.46 % Rotamer: Outliers : 5.09 % Allowed : 31.11 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 2.10 (0.25), residues: 1174 helix: 2.57 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -2.19 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 583 TYR 0.028 0.002 TYR A 19 PHE 0.019 0.001 PHE A 446 TRP 0.008 0.001 TRP A 347 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00329 (10712) covalent geometry : angle 0.53754 (14374) SS BOND : bond 0.00404 ( 2) SS BOND : angle 1.24722 ( 4) hydrogen bonds : bond 0.06812 ( 669) hydrogen bonds : angle 3.78654 ( 2001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: A 130 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6742 (tp) REVERT: A 167 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7488 (mmm160) REVERT: A 562 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7756 (mm-30) REVERT: A 583 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8140 (mtt-85) REVERT: D 27 LYS cc_start: 0.7530 (tmmt) cc_final: 0.7132 (ttpt) REVERT: D 95 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: D 130 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6566 (tm) REVERT: D 562 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7690 (mm-30) outliers start: 55 outliers final: 35 residues processed: 149 average time/residue: 0.6493 time to fit residues: 103.4841 Evaluate side-chains 139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 566 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 55 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127800 restraints weight = 12378.992| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.62 r_work: 0.3374 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10714 Z= 0.149 Angle : 0.536 9.677 14378 Z= 0.284 Chirality : 0.039 0.229 1482 Planarity : 0.003 0.029 1774 Dihedral : 10.753 83.760 1594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.11 % Favored : 94.38 % Rotamer: Outliers : 4.35 % Allowed : 32.13 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.25), residues: 1174 helix: 2.55 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -2.22 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 557 TYR 0.022 0.002 TYR A 19 PHE 0.019 0.001 PHE D 446 TRP 0.008 0.001 TRP A 347 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00318 (10712) covalent geometry : angle 0.53550 (14374) SS BOND : bond 0.00389 ( 2) SS BOND : angle 1.21519 ( 4) hydrogen bonds : bond 0.06682 ( 669) hydrogen bonds : angle 3.78637 ( 2001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: A 167 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7496 (mmm160) REVERT: A 562 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 583 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8129 (mtt-85) REVERT: D 95 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: D 167 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7491 (mmm160) REVERT: D 562 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7646 (mm-30) outliers start: 47 outliers final: 35 residues processed: 138 average time/residue: 0.6489 time to fit residues: 95.6349 Evaluate side-chains 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129698 restraints weight = 12310.343| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.82 r_work: 0.3382 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10714 Z= 0.144 Angle : 0.534 10.145 14378 Z= 0.283 Chirality : 0.039 0.235 1482 Planarity : 0.004 0.029 1774 Dihedral : 10.692 83.260 1594 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.11 % Favored : 94.38 % Rotamer: Outliers : 3.98 % Allowed : 32.50 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 2.08 (0.25), residues: 1174 helix: 2.56 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -2.24 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 402 TYR 0.021 0.002 TYR A 19 PHE 0.018 0.001 PHE D 446 TRP 0.008 0.001 TRP A 570 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00302 (10712) covalent geometry : angle 0.53349 (14374) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.19280 ( 4) hydrogen bonds : bond 0.06550 ( 669) hydrogen bonds : angle 3.76910 ( 2001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: A 562 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7763 (mm-30) REVERT: D 95 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: D 167 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7524 (mmm160) REVERT: D 562 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7688 (mm-30) outliers start: 43 outliers final: 35 residues processed: 136 average time/residue: 0.6730 time to fit residues: 97.3635 Evaluate side-chains 133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 267 HIS Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 548 TRP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 142 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 167 ARG Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 267 HIS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 543 ASP Chi-restraints excluded: chain D residue 548 TRP Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 110 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN D 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.167222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130726 restraints weight = 12372.425| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.80 r_work: 0.3409 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10714 Z= 0.138 Angle : 0.533 10.079 14378 Z= 0.282 Chirality : 0.039 0.229 1482 Planarity : 0.004 0.030 1774 Dihedral : 10.528 81.723 1594 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.03 % Favored : 94.46 % Rotamer: Outliers : 4.17 % Allowed : 32.59 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 2.22 (0.25), residues: 1174 helix: 2.66 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 402 TYR 0.020 0.001 TYR A 19 PHE 0.021 0.001 PHE A 275 TRP 0.008 0.001 TRP A 570 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00287 (10712) covalent geometry : angle 0.53265 (14374) SS BOND : bond 0.00339 ( 2) SS BOND : angle 1.15211 ( 4) hydrogen bonds : bond 0.06284 ( 669) hydrogen bonds : angle 3.71935 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3924.05 seconds wall clock time: 67 minutes 21.30 seconds (4041.30 seconds total)