Starting phenix.real_space_refine on Mon Jun 9 11:24:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymq_39403/06_2025/8ymq_39403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymq_39403/06_2025/8ymq_39403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymq_39403/06_2025/8ymq_39403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymq_39403/06_2025/8ymq_39403.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymq_39403/06_2025/8ymq_39403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymq_39403/06_2025/8ymq_39403_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6964 2.51 5 N 1720 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10524 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5244 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 33, 'TRANS': 617} Chain breaks: 3 Chain: "B" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5244 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 33, 'TRANS': 617} Chain breaks: 3 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 8.67, per 1000 atoms: 0.82 Number of scatterers: 10524 At special positions: 0 Unit cell: (151.05, 86.07, 90.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1788 8.00 N 1720 7.00 C 6964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 69.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.540A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.677A pdb=" N GLU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 92 through 120 removed outlier: 3.546A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 160 through 195 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.604A pdb=" N LEU A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.523A pdb=" N ALA A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.778A pdb=" N ALA A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 367 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 408 removed outlier: 4.137A pdb=" N THR A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.559A pdb=" N ALA A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 removed outlier: 3.679A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 476 Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.761A pdb=" N ILE A 533 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 566 through 585 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 591 through 613 Processing helix chain 'A' and resid 624 through 647 Processing helix chain 'A' and resid 654 through 677 removed outlier: 3.942A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Proline residue: A 663 - end of helix Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 704 through 711 removed outlier: 3.669A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 31 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 39 through 45 removed outlier: 3.540A pdb=" N TYR B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.677A pdb=" N GLU B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 92 through 120 removed outlier: 3.546A pdb=" N ILE B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 160 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.604A pdb=" N LEU B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 315 Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.523A pdb=" N ALA B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.778A pdb=" N ALA B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 367 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 408 removed outlier: 4.137A pdb=" N THR B 373 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Proline residue: B 393 - end of helix removed outlier: 3.798A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 removed outlier: 3.559A pdb=" N ALA B 431 " --> pdb=" O GLN B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.679A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 476 Processing helix chain 'B' and resid 513 through 525 Processing helix chain 'B' and resid 526 through 534 removed outlier: 3.761A pdb=" N ILE B 533 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'B' and resid 566 through 585 Proline residue: B 572 - end of helix Processing helix chain 'B' and resid 591 through 613 Processing helix chain 'B' and resid 624 through 647 Processing helix chain 'B' and resid 654 through 677 removed outlier: 3.942A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 704 through 711 removed outlier: 3.669A pdb=" N TYR B 708 " --> pdb=" O ASN B 704 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 235 removed outlier: 4.775A pdb=" N VAL A 239 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 235 Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 235 removed outlier: 4.775A pdb=" N VAL B 239 " --> pdb=" O MET B 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 233 through 235 649 hydrogen bonds defined for protein. 1917 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: 4.61 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1770 1.32 - 1.44: 2975 1.44 - 1.56: 5969 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 10806 Sorted by residual: bond pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.32e-02 5.74e+03 2.17e+01 bond pdb=" CA TRP B 258 " pdb=" C TRP B 258 " ideal model delta sigma weight residual 1.524 1.462 0.061 1.32e-02 5.74e+03 2.17e+01 bond pdb=" CA HIS A 294 " pdb=" C HIS A 294 " ideal model delta sigma weight residual 1.529 1.483 0.045 1.26e-02 6.30e+03 1.30e+01 bond pdb=" CA HIS B 294 " pdb=" C HIS B 294 " ideal model delta sigma weight residual 1.529 1.483 0.045 1.26e-02 6.30e+03 1.30e+01 bond pdb=" CA TYR B 262 " pdb=" C TYR B 262 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.10e-02 8.26e+03 1.24e+01 ... (remaining 10801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 14448 5.03 - 10.06: 208 10.06 - 15.10: 14 15.10 - 20.13: 0 20.13 - 25.16: 2 Bond angle restraints: 14672 Sorted by residual: angle pdb=" N ASP B 260 " pdb=" CA ASP B 260 " pdb=" C ASP B 260 " ideal model delta sigma weight residual 113.41 88.25 25.16 1.22e+00 6.72e-01 4.25e+02 angle pdb=" N ASP A 260 " pdb=" CA ASP A 260 " pdb=" C ASP A 260 " ideal model delta sigma weight residual 113.41 88.25 25.16 1.22e+00 6.72e-01 4.25e+02 angle pdb=" N LYS B 318 " pdb=" CA LYS B 318 " pdb=" C LYS B 318 " ideal model delta sigma weight residual 113.97 102.29 11.68 1.28e+00 6.10e-01 8.32e+01 angle pdb=" N LYS A 318 " pdb=" CA LYS A 318 " pdb=" C LYS A 318 " ideal model delta sigma weight residual 113.97 102.29 11.68 1.28e+00 6.10e-01 8.32e+01 angle pdb=" N LYS B 265 " pdb=" CA LYS B 265 " pdb=" C LYS B 265 " ideal model delta sigma weight residual 111.14 101.32 9.82 1.08e+00 8.57e-01 8.27e+01 ... (remaining 14667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5072 17.84 - 35.68: 633 35.68 - 53.53: 478 53.53 - 71.37: 160 71.37 - 89.21: 23 Dihedral angle restraints: 6366 sinusoidal: 2540 harmonic: 3826 Sorted by residual: dihedral pdb=" C VAL B 121 " pdb=" N VAL B 121 " pdb=" CA VAL B 121 " pdb=" CB VAL B 121 " ideal model delta harmonic sigma weight residual -122.00 -135.56 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C VAL A 121 " pdb=" N VAL A 121 " pdb=" CA VAL A 121 " pdb=" CB VAL A 121 " ideal model delta harmonic sigma weight residual -122.00 -135.56 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C LEU B 259 " pdb=" N LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual -122.60 -135.77 13.17 0 2.50e+00 1.60e-01 2.77e+01 ... (remaining 6363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1320 0.126 - 0.252: 250 0.252 - 0.378: 68 0.378 - 0.505: 8 0.505 - 0.631: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA LEU A 259 " pdb=" N LEU A 259 " pdb=" C LEU A 259 " pdb=" CB LEU A 259 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.94e+00 chirality pdb=" CA LEU B 259 " pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CB LEU B 259 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.94e+00 chirality pdb=" CA TRP A 625 " pdb=" N TRP A 625 " pdb=" C TRP A 625 " pdb=" CB TRP A 625 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.88e+00 ... (remaining 1647 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 392 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 393 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 393 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 393 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 392 " 0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 393 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 571 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 572 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 572 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 572 " 0.036 5.00e-02 4.00e+02 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 62 2.57 - 3.15: 8217 3.15 - 3.73: 17786 3.73 - 4.32: 26338 4.32 - 4.90: 40290 Nonbonded interactions: 92693 Sorted by model distance: nonbonded pdb=" OD1 ASN B 241 " pdb=" CB ALA B 366 " model vdw 1.982 3.460 nonbonded pdb=" OD1 ASN A 241 " pdb=" CB ALA A 366 " model vdw 1.982 3.460 nonbonded pdb=" CG1 VAL A 9 " pdb=" CD1 LEU A 425 " model vdw 2.046 3.880 nonbonded pdb=" CG1 VAL B 9 " pdb=" CD1 LEU B 425 " model vdw 2.046 3.880 nonbonded pdb=" N ASP B 260 " pdb=" N TYR B 261 " model vdw 2.177 2.560 ... (remaining 92688 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.960 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:15.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.011 0.061 10806 Z= 0.809 Angle : 1.477 25.160 14672 Z= 0.947 Chirality : 0.114 0.631 1650 Planarity : 0.008 0.102 1826 Dihedral : 23.723 89.210 3890 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 2.18 % Allowed : 8.24 % Favored : 89.58 % Rotamer: Outliers : 32.64 % Allowed : 10.97 % Favored : 56.38 % Cbeta Deviations : 0.81 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.20), residues: 1286 helix: -1.56 (0.15), residues: 834 sheet: -3.68 (0.58), residues: 46 loop : -3.36 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 625 HIS 0.008 0.002 HIS A 90 PHE 0.018 0.002 PHE A 624 TYR 0.015 0.002 TYR B 618 ARG 0.005 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.19948 ( 645) hydrogen bonds : angle 7.24129 ( 1917) covalent geometry : bond 0.01094 (10806) covalent geometry : angle 1.47715 (14672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 363 poor density : 212 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.3686 (OUTLIER) cc_final: 0.3469 (m-10) REVERT: A 220 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7653 (mt) REVERT: A 278 LYS cc_start: 0.1921 (OUTLIER) cc_final: 0.0490 (mptm) REVERT: A 377 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6130 (tp) REVERT: A 442 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7822 (tp) REVERT: A 659 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6930 (mt) REVERT: A 692 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7580 (tttp) REVERT: B 220 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7648 (mt) REVERT: B 278 LYS cc_start: 0.1932 (OUTLIER) cc_final: 0.0488 (mptm) REVERT: B 377 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.6136 (tp) REVERT: B 659 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6917 (mt) REVERT: B 692 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7583 (tttp) outliers start: 363 outliers final: 40 residues processed: 483 average time/residue: 1.1166 time to fit residues: 583.2236 Evaluate side-chains 214 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 MET Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 692 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS A 190 GLN A 228 ASN A 294 HIS A 339 GLN A 476 ASN A 568 ASN A 573 GLN A 616 GLN A 687 GLN A 704 ASN A 715 HIS B 90 HIS B 190 GLN B 228 ASN B 294 HIS B 339 GLN B 476 ASN B 568 ASN B 573 GLN B 616 GLN B 687 GLN B 704 ASN B 715 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103799 restraints weight = 11217.355| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.95 r_work: 0.3039 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10806 Z= 0.185 Angle : 0.804 12.432 14672 Z= 0.414 Chirality : 0.047 0.204 1650 Planarity : 0.007 0.103 1826 Dihedral : 12.098 77.386 1558 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.78 % Favored : 92.07 % Rotamer: Outliers : 9.26 % Allowed : 21.40 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1286 helix: 0.66 (0.18), residues: 824 sheet: -3.37 (0.57), residues: 42 loop : -2.99 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 625 HIS 0.003 0.001 HIS A 715 PHE 0.014 0.002 PHE A 421 TYR 0.021 0.001 TYR A 262 ARG 0.009 0.001 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.05792 ( 645) hydrogen bonds : angle 4.72733 ( 1917) covalent geometry : bond 0.00399 (10806) covalent geometry : angle 0.80430 (14672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 187 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7619 (mtp85) REVERT: A 256 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: A 258 TRP cc_start: 0.6751 (OUTLIER) cc_final: 0.5400 (t60) REVERT: A 278 LYS cc_start: 0.2022 (OUTLIER) cc_final: 0.0851 (ttmm) REVERT: A 282 LEU cc_start: 0.2410 (OUTLIER) cc_final: 0.0968 (mm) REVERT: A 468 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7002 (mmp-170) REVERT: A 532 GLU cc_start: 0.8065 (tp30) cc_final: 0.7576 (tm-30) REVERT: A 639 SER cc_start: 0.8550 (t) cc_final: 0.8184 (p) REVERT: A 644 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6544 (mtp) REVERT: A 659 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 660 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 671 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7579 (mmm160) REVERT: B 36 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7621 (mtp85) REVERT: B 256 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6625 (tm-30) REVERT: B 258 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5400 (t60) REVERT: B 278 LYS cc_start: 0.2022 (OUTLIER) cc_final: 0.0850 (ttmm) REVERT: B 282 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.0962 (mm) REVERT: B 468 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7017 (mmp-170) REVERT: B 532 GLU cc_start: 0.8059 (tp30) cc_final: 0.7572 (tm-30) REVERT: B 639 SER cc_start: 0.8542 (t) cc_final: 0.8173 (p) REVERT: B 644 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6536 (mtp) REVERT: B 659 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 660 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7868 (mp) REVERT: B 671 ARG cc_start: 0.7850 (mtp180) cc_final: 0.7585 (mmm160) outliers start: 103 outliers final: 43 residues processed: 257 average time/residue: 1.3627 time to fit residues: 380.3496 Evaluate side-chains 220 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 710 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 0.0000 chunk 86 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 116 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 190 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN A 609 GLN B 14 ASN B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 609 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.104131 restraints weight = 11367.957| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.97 r_work: 0.3038 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10806 Z= 0.150 Angle : 0.686 10.640 14672 Z= 0.349 Chirality : 0.043 0.158 1650 Planarity : 0.006 0.100 1826 Dihedral : 9.999 66.080 1514 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.78 % Favored : 92.07 % Rotamer: Outliers : 7.91 % Allowed : 22.21 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1286 helix: 1.26 (0.18), residues: 832 sheet: -3.10 (0.63), residues: 42 loop : -2.91 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 625 HIS 0.003 0.001 HIS B 74 PHE 0.022 0.001 PHE A 421 TYR 0.013 0.001 TYR A 262 ARG 0.003 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 645) hydrogen bonds : angle 4.34319 ( 1917) covalent geometry : bond 0.00309 (10806) covalent geometry : angle 0.68641 (14672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 163 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8512 (mtp180) REVERT: A 61 PHE cc_start: 0.3144 (OUTLIER) cc_final: 0.2706 (m-10) REVERT: A 86 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: A 256 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: A 258 TRP cc_start: 0.6633 (OUTLIER) cc_final: 0.5782 (t-100) REVERT: A 278 LYS cc_start: 0.2087 (OUTLIER) cc_final: 0.0839 (tttp) REVERT: A 282 LEU cc_start: 0.2745 (OUTLIER) cc_final: 0.1213 (mm) REVERT: A 318 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7472 (mmtm) REVERT: A 371 SER cc_start: 0.7950 (t) cc_final: 0.7650 (m) REVERT: A 468 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7125 (mmp-170) REVERT: A 532 GLU cc_start: 0.8112 (tp30) cc_final: 0.7678 (tm-30) REVERT: A 639 SER cc_start: 0.8676 (t) cc_final: 0.8305 (p) REVERT: A 642 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7217 (tt) REVERT: A 660 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7873 (mp) REVERT: A 671 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7670 (mmm160) REVERT: A 676 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7793 (tpt90) REVERT: B 36 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8514 (mtp180) REVERT: B 86 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 256 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: B 258 TRP cc_start: 0.6634 (OUTLIER) cc_final: 0.5779 (t-100) REVERT: B 278 LYS cc_start: 0.2091 (OUTLIER) cc_final: 0.0844 (tttp) REVERT: B 282 LEU cc_start: 0.2750 (OUTLIER) cc_final: 0.1223 (mm) REVERT: B 318 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7471 (mmtm) REVERT: B 371 SER cc_start: 0.7948 (t) cc_final: 0.7649 (m) REVERT: B 468 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7120 (mmp-170) REVERT: B 532 GLU cc_start: 0.8111 (tp30) cc_final: 0.7679 (tm-30) REVERT: B 639 SER cc_start: 0.8665 (t) cc_final: 0.8290 (p) REVERT: B 642 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7197 (tt) REVERT: B 660 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7867 (mp) REVERT: B 671 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7659 (mmm160) REVERT: B 676 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7779 (tpt90) outliers start: 88 outliers final: 33 residues processed: 231 average time/residue: 1.3262 time to fit residues: 334.3849 Evaluate side-chains 201 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 710 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 190 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098101 restraints weight = 11387.329| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.20 r_work: 0.2916 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10806 Z= 0.242 Angle : 0.721 8.332 14672 Z= 0.368 Chirality : 0.047 0.176 1650 Planarity : 0.006 0.066 1826 Dihedral : 9.365 62.963 1502 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.39 % Favored : 92.46 % Rotamer: Outliers : 8.09 % Allowed : 20.50 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1286 helix: 1.20 (0.18), residues: 834 sheet: -3.02 (0.64), residues: 42 loop : -2.77 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 625 HIS 0.005 0.001 HIS A 670 PHE 0.017 0.002 PHE B 384 TYR 0.018 0.002 TYR A 577 ARG 0.003 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.05764 ( 645) hydrogen bonds : angle 4.42947 ( 1917) covalent geometry : bond 0.00572 (10806) covalent geometry : angle 0.72110 (14672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 152 time to evaluate : 1.682 Fit side-chains REVERT: A 30 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7489 (mp) REVERT: A 36 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7721 (mtp85) REVERT: A 278 LYS cc_start: 0.2048 (OUTLIER) cc_final: 0.0749 (mmtp) REVERT: A 318 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7579 (mmtm) REVERT: A 468 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7229 (mmp-170) REVERT: A 532 GLU cc_start: 0.8206 (tp30) cc_final: 0.7783 (tm-30) REVERT: A 639 SER cc_start: 0.8628 (t) cc_final: 0.8165 (p) REVERT: A 642 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7253 (tt) REVERT: A 671 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7680 (mmm160) REVERT: B 30 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7474 (mp) REVERT: B 36 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7723 (mtp85) REVERT: B 278 LYS cc_start: 0.2052 (OUTLIER) cc_final: 0.0749 (mmtp) REVERT: B 318 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7578 (mmtm) REVERT: B 468 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7228 (mmp-170) REVERT: B 532 GLU cc_start: 0.8197 (tp30) cc_final: 0.7783 (tm-30) REVERT: B 639 SER cc_start: 0.8620 (t) cc_final: 0.8152 (p) REVERT: B 642 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7247 (tt) REVERT: B 671 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7667 (mmm160) outliers start: 90 outliers final: 46 residues processed: 218 average time/residue: 1.0770 time to fit residues: 257.3789 Evaluate side-chains 207 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101386 restraints weight = 11319.770| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.09 r_work: 0.2968 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10806 Z= 0.155 Angle : 0.679 13.309 14672 Z= 0.337 Chirality : 0.043 0.141 1650 Planarity : 0.006 0.061 1826 Dihedral : 8.689 61.282 1486 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 7.01 % Allowed : 21.76 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1286 helix: 1.56 (0.18), residues: 828 sheet: -2.92 (0.67), residues: 42 loop : -2.56 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.002 0.001 HIS B 90 PHE 0.013 0.001 PHE A 384 TYR 0.012 0.001 TYR A 577 ARG 0.003 0.000 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 645) hydrogen bonds : angle 4.18792 ( 1917) covalent geometry : bond 0.00334 (10806) covalent geometry : angle 0.67915 (14672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 156 time to evaluate : 1.169 Fit side-chains REVERT: A 36 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7691 (mtp85) REVERT: A 61 PHE cc_start: 0.3240 (OUTLIER) cc_final: 0.2713 (m-10) REVERT: A 256 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: A 258 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.5732 (t-100) REVERT: A 278 LYS cc_start: 0.1902 (OUTLIER) cc_final: 0.0635 (mmtp) REVERT: A 318 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7476 (mmtm) REVERT: A 468 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7077 (mmp-170) REVERT: A 532 GLU cc_start: 0.8186 (tp30) cc_final: 0.7781 (tm-30) REVERT: A 639 SER cc_start: 0.8635 (t) cc_final: 0.8416 (p) REVERT: A 671 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7568 (mmm160) REVERT: B 36 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7695 (mtp85) REVERT: B 256 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: B 258 TRP cc_start: 0.6688 (OUTLIER) cc_final: 0.5732 (t-100) REVERT: B 278 LYS cc_start: 0.1896 (OUTLIER) cc_final: 0.0631 (mmtp) REVERT: B 318 LYS cc_start: 0.8086 (mmmm) cc_final: 0.7490 (mmtm) REVERT: B 468 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7008 (mmp-170) REVERT: B 532 GLU cc_start: 0.8183 (tp30) cc_final: 0.7785 (tm-30) REVERT: B 639 SER cc_start: 0.8628 (t) cc_final: 0.8407 (p) REVERT: B 671 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7547 (mmm160) outliers start: 78 outliers final: 31 residues processed: 212 average time/residue: 1.0065 time to fit residues: 233.2049 Evaluate side-chains 192 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 119 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.0010 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 190 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102096 restraints weight = 11377.869| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.97 r_work: 0.3010 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10806 Z= 0.134 Angle : 0.657 11.249 14672 Z= 0.326 Chirality : 0.042 0.206 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.810 59.283 1476 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.15 % Favored : 92.69 % Rotamer: Outliers : 5.49 % Allowed : 23.38 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1286 helix: 1.76 (0.18), residues: 834 sheet: -2.78 (0.70), residues: 42 loop : -2.46 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.003 0.001 HIS B 651 PHE 0.016 0.001 PHE B 384 TYR 0.010 0.001 TYR A 577 ARG 0.002 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 645) hydrogen bonds : angle 4.04917 ( 1917) covalent geometry : bond 0.00286 (10806) covalent geometry : angle 0.65680 (14672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 1.238 Fit side-chains REVERT: A 36 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: A 61 PHE cc_start: 0.3267 (OUTLIER) cc_final: 0.2761 (m-10) REVERT: A 256 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 258 TRP cc_start: 0.6563 (OUTLIER) cc_final: 0.5705 (t-100) REVERT: A 278 LYS cc_start: 0.1557 (OUTLIER) cc_final: 0.0316 (mmtp) REVERT: A 403 ILE cc_start: 0.2301 (OUTLIER) cc_final: 0.2070 (mm) REVERT: A 532 GLU cc_start: 0.8180 (tp30) cc_final: 0.7795 (tm-30) REVERT: A 639 SER cc_start: 0.8646 (t) cc_final: 0.8440 (p) REVERT: A 671 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7589 (mmm160) REVERT: B 36 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7807 (mtp85) REVERT: B 256 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: B 258 TRP cc_start: 0.6560 (OUTLIER) cc_final: 0.5703 (t-100) REVERT: B 278 LYS cc_start: 0.1562 (OUTLIER) cc_final: 0.0318 (mmtp) REVERT: B 468 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6571 (mtp180) REVERT: B 532 GLU cc_start: 0.8178 (tp30) cc_final: 0.7804 (tm-30) REVERT: B 639 SER cc_start: 0.8638 (t) cc_final: 0.8428 (p) REVERT: B 671 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7573 (mmm160) outliers start: 61 outliers final: 27 residues processed: 194 average time/residue: 1.0311 time to fit residues: 218.8921 Evaluate side-chains 181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 HIS A 702 ASN B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 HIS B 702 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.150810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.096578 restraints weight = 11497.438| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.96 r_work: 0.2928 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10806 Z= 0.247 Angle : 0.708 8.808 14672 Z= 0.356 Chirality : 0.047 0.186 1650 Planarity : 0.006 0.058 1826 Dihedral : 8.006 59.530 1476 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.08 % Favored : 92.77 % Rotamer: Outliers : 6.38 % Allowed : 23.11 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1286 helix: 1.55 (0.18), residues: 834 sheet: -2.85 (0.66), residues: 42 loop : -2.50 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 625 HIS 0.005 0.001 HIS A 670 PHE 0.022 0.002 PHE B 384 TYR 0.018 0.002 TYR A 577 ARG 0.003 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.05500 ( 645) hydrogen bonds : angle 4.27180 ( 1917) covalent geometry : bond 0.00600 (10806) covalent geometry : angle 0.70780 (14672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 150 time to evaluate : 1.119 Fit side-chains REVERT: A 36 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7654 (mtp85) REVERT: A 61 PHE cc_start: 0.3259 (OUTLIER) cc_final: 0.2676 (m-10) REVERT: A 256 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: A 278 LYS cc_start: 0.1578 (OUTLIER) cc_final: 0.0313 (mmtt) REVERT: A 318 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7570 (mmtm) REVERT: A 532 GLU cc_start: 0.8203 (tp30) cc_final: 0.7835 (tm-30) REVERT: B 36 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: B 256 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: B 278 LYS cc_start: 0.1579 (OUTLIER) cc_final: 0.0313 (mmtt) REVERT: B 318 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7573 (mmtm) REVERT: B 468 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7273 (mmp-170) REVERT: B 532 GLU cc_start: 0.8202 (tp30) cc_final: 0.7835 (tm-30) outliers start: 71 outliers final: 43 residues processed: 197 average time/residue: 1.0010 time to fit residues: 215.6194 Evaluate side-chains 193 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 476 ASN A 702 ASN B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100372 restraints weight = 11324.758| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.94 r_work: 0.2980 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10806 Z= 0.146 Angle : 0.644 7.525 14672 Z= 0.323 Chirality : 0.042 0.172 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.913 59.860 1476 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 5.31 % Allowed : 24.37 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1286 helix: 1.76 (0.18), residues: 834 sheet: -2.77 (0.69), residues: 42 loop : -2.43 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.002 0.001 HIS B 90 PHE 0.016 0.001 PHE A 27 TYR 0.011 0.001 TYR B 577 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 645) hydrogen bonds : angle 4.08147 ( 1917) covalent geometry : bond 0.00328 (10806) covalent geometry : angle 0.64432 (14672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 1.223 Fit side-chains REVERT: A 4 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6620 (pt) REVERT: A 36 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7719 (mtp85) REVERT: A 61 PHE cc_start: 0.3364 (OUTLIER) cc_final: 0.2805 (m-10) REVERT: A 256 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: A 278 LYS cc_start: 0.1522 (OUTLIER) cc_final: 0.0371 (mmmt) REVERT: A 282 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.2205 (mm) REVERT: A 318 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7721 (mtpt) REVERT: A 532 GLU cc_start: 0.8181 (tp30) cc_final: 0.7793 (tm-30) REVERT: A 639 SER cc_start: 0.8661 (t) cc_final: 0.8452 (p) REVERT: A 671 ARG cc_start: 0.7982 (mtp180) cc_final: 0.7693 (mmm160) REVERT: B 4 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6615 (pt) REVERT: B 36 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7721 (mtp85) REVERT: B 256 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 278 LYS cc_start: 0.1524 (OUTLIER) cc_final: 0.0374 (mmmt) REVERT: B 282 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.2206 (mm) REVERT: B 318 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7717 (mtpt) REVERT: B 468 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.6841 (mmp-170) REVERT: B 532 GLU cc_start: 0.8180 (tp30) cc_final: 0.7797 (tm-30) REVERT: B 671 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7692 (mmm160) outliers start: 59 outliers final: 33 residues processed: 197 average time/residue: 0.9583 time to fit residues: 207.3457 Evaluate side-chains 189 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 117 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 476 ASN A 702 ASN B 190 GLN B 476 ASN B 702 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100142 restraints weight = 11487.216| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.96 r_work: 0.2952 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10806 Z= 0.143 Angle : 0.648 9.266 14672 Z= 0.320 Chirality : 0.042 0.164 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.772 59.343 1476 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.22 % Allowed : 25.09 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1286 helix: 1.85 (0.18), residues: 836 sheet: -2.74 (0.69), residues: 42 loop : -2.41 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.002 0.001 HIS A 74 PHE 0.020 0.001 PHE A 384 TYR 0.012 0.001 TYR A 577 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 645) hydrogen bonds : angle 4.04628 ( 1917) covalent geometry : bond 0.00323 (10806) covalent geometry : angle 0.64780 (14672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7799 (mtp85) REVERT: A 61 PHE cc_start: 0.3443 (OUTLIER) cc_final: 0.2850 (m-10) REVERT: A 258 TRP cc_start: 0.6708 (OUTLIER) cc_final: 0.5770 (t-100) REVERT: A 278 LYS cc_start: 0.1555 (OUTLIER) cc_final: 0.0378 (mmmt) REVERT: A 318 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7671 (mtpt) REVERT: A 468 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6626 (mtp180) REVERT: A 532 GLU cc_start: 0.8188 (tp30) cc_final: 0.7865 (tm-30) REVERT: A 671 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7761 (mmm160) REVERT: B 36 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7762 (mtp85) REVERT: B 258 TRP cc_start: 0.6701 (OUTLIER) cc_final: 0.5765 (t-100) REVERT: B 278 LYS cc_start: 0.1556 (OUTLIER) cc_final: 0.0377 (mmmt) REVERT: B 318 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7668 (mtpt) REVERT: B 468 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6994 (mmp-170) REVERT: B 532 GLU cc_start: 0.8194 (tp30) cc_final: 0.7870 (tm-30) REVERT: B 671 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7753 (mmm160) outliers start: 58 outliers final: 34 residues processed: 188 average time/residue: 1.0147 time to fit residues: 208.9370 Evaluate side-chains 181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 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 190 GLN A 702 ASN B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101390 restraints weight = 11327.461| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.95 r_work: 0.2995 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10806 Z= 0.133 Angle : 0.621 8.962 14672 Z= 0.310 Chirality : 0.042 0.157 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.647 59.547 1474 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.68 % Allowed : 25.63 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1286 helix: 1.93 (0.18), residues: 834 sheet: -2.72 (0.70), residues: 42 loop : -2.39 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.002 0.001 HIS A 74 PHE 0.020 0.001 PHE A 384 TYR 0.011 0.001 TYR A 577 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 645) hydrogen bonds : angle 4.01217 ( 1917) covalent geometry : bond 0.00295 (10806) covalent geometry : angle 0.62092 (14672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 142 time to evaluate : 1.065 Fit side-chains REVERT: A 36 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7730 (mtp85) REVERT: A 61 PHE cc_start: 0.3477 (OUTLIER) cc_final: 0.2892 (m-10) REVERT: A 258 TRP cc_start: 0.6632 (OUTLIER) cc_final: 0.5737 (t-100) REVERT: A 278 LYS cc_start: 0.1355 (OUTLIER) cc_final: 0.0708 (mmmt) REVERT: A 282 LEU cc_start: 0.3588 (OUTLIER) cc_final: 0.2710 (mt) REVERT: A 318 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7579 (mtpt) REVERT: A 468 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6584 (mtp180) REVERT: A 508 MET cc_start: -0.0464 (OUTLIER) cc_final: -0.0813 (ppp) REVERT: A 532 GLU cc_start: 0.8139 (tp30) cc_final: 0.7802 (tm-30) REVERT: A 671 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7710 (mmm160) REVERT: B 36 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: B 258 TRP cc_start: 0.6631 (OUTLIER) cc_final: 0.5733 (t-100) REVERT: B 278 LYS cc_start: 0.1355 (OUTLIER) cc_final: 0.0706 (mmmt) REVERT: B 282 LEU cc_start: 0.3590 (OUTLIER) cc_final: 0.2716 (mt) REVERT: B 318 LYS cc_start: 0.7983 (mmmm) cc_final: 0.7572 (mtpt) REVERT: B 508 MET cc_start: -0.0484 (OUTLIER) cc_final: -0.0790 (ppp) REVERT: B 532 GLU cc_start: 0.8144 (tp30) cc_final: 0.7806 (tm-30) REVERT: B 671 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7700 (mmm160) outliers start: 52 outliers final: 31 residues processed: 186 average time/residue: 0.9681 time to fit residues: 196.9106 Evaluate side-chains 182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 702 ASN Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 702 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 118 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 702 ASN B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100355 restraints weight = 11273.547| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.96 r_work: 0.2980 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10806 Z= 0.152 Angle : 0.642 8.908 14672 Z= 0.321 Chirality : 0.044 0.177 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.115 57.478 1466 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.14 % Allowed : 26.17 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1286 helix: 1.90 (0.18), residues: 836 sheet: -2.68 (0.70), residues: 42 loop : -2.44 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.003 0.001 HIS A 90 PHE 0.020 0.001 PHE B 384 TYR 0.013 0.001 TYR A 577 ARG 0.001 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 645) hydrogen bonds : angle 4.07402 ( 1917) covalent geometry : bond 0.00348 (10806) covalent geometry : angle 0.64194 (14672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10928.05 seconds wall clock time: 190 minutes 45.68 seconds (11445.68 seconds total)