Starting phenix.real_space_refine on Fri Jan 17 07:59:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymq_39403/01_2025/8ymq_39403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymq_39403/01_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_39403/01_2025/8ymq_39403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymq_39403/01_2025/8ymq_39403.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymq_39403/01_2025/8ymq_39403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymq_39403/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.77, per 1000 atoms: 0.93 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: 3.04 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: 1.07 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: 3.18 Time building geometry restraints manager: 3.23 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: 39.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.820 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.560 ------------------------------------------------------------------------------- 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= 0.699 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 *********************** 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 : 1.196 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: 1.0934 time to fit residues: 571.9484 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 : 1.229 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3816 r_free = 0.3816 target = 0.156786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103837 restraints weight = 11213.069| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.95 r_work: 0.3038 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10806 Z= 0.259 Angle : 0.805 12.277 14672 Z= 0.414 Chirality : 0.047 0.204 1650 Planarity : 0.007 0.102 1826 Dihedral : 12.076 77.162 1558 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.65 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: 0.64 (0.18), residues: 826 sheet: -3.37 (0.57), residues: 42 loop : -2.99 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 625 HIS 0.003 0.001 HIS B 670 PHE 0.015 0.002 PHE A 421 TYR 0.021 0.001 TYR A 262 ARG 0.009 0.001 ARG A 556 *********************** 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 289 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 186 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7615 (mtp85) REVERT: A 256 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6608 (tm-30) REVERT: A 258 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5416 (t60) REVERT: A 278 LYS cc_start: 0.2029 (OUTLIER) cc_final: 0.0896 (tttp) REVERT: A 282 LEU cc_start: 0.2393 (OUTLIER) cc_final: 0.0943 (mm) REVERT: A 468 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7006 (mmp-170) REVERT: A 532 GLU cc_start: 0.8059 (tp30) cc_final: 0.7571 (tm-30) REVERT: A 639 SER cc_start: 0.8545 (t) cc_final: 0.8179 (p) REVERT: A 660 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 671 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7576 (mmm160) REVERT: B 36 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7618 (mtp85) REVERT: B 256 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: B 258 TRP cc_start: 0.6751 (OUTLIER) cc_final: 0.5413 (t60) REVERT: B 278 LYS cc_start: 0.2030 (OUTLIER) cc_final: 0.0897 (tttp) REVERT: B 282 LEU cc_start: 0.2394 (OUTLIER) cc_final: 0.0944 (mm) REVERT: B 468 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7010 (mmp-170) REVERT: B 532 GLU cc_start: 0.8055 (tp30) cc_final: 0.7568 (tm-30) REVERT: B 639 SER cc_start: 0.8538 (t) cc_final: 0.8169 (p) REVERT: B 660 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7877 (mp) REVERT: B 671 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7582 (mmm160) outliers start: 103 outliers final: 45 residues processed: 258 average time/residue: 1.0699 time to fit residues: 300.1501 Evaluate side-chains 221 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 654 SER 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 654 SER 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: 4.9990 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.156499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102854 restraints weight = 11377.417| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.97 r_work: 0.3019 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10806 Z= 0.219 Angle : 0.687 10.431 14672 Z= 0.351 Chirality : 0.043 0.158 1650 Planarity : 0.006 0.100 1826 Dihedral : 9.869 65.946 1510 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.85 % Favored : 91.99 % Rotamer: Outliers : 7.73 % Allowed : 21.94 % 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: -0.22 (0.24), residues: 1286 helix: 1.25 (0.18), residues: 834 sheet: -3.10 (0.63), residues: 42 loop : -2.87 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 625 HIS 0.003 0.001 HIS B 74 PHE 0.021 0.002 PHE A 421 TYR 0.011 0.001 TYR A 262 ARG 0.003 0.000 ARG B 556 *********************** 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 249 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 163 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8522 (mtp180) REVERT: A 61 PHE cc_start: 0.3163 (OUTLIER) cc_final: 0.2705 (m-10) REVERT: A 256 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: A 258 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.5818 (t-100) REVERT: A 278 LYS cc_start: 0.2086 (OUTLIER) cc_final: 0.0823 (tttp) REVERT: A 282 LEU cc_start: 0.2731 (OUTLIER) cc_final: 0.1206 (mm) REVERT: A 318 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7485 (mmtm) REVERT: A 468 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7137 (mmp-170) REVERT: A 532 GLU cc_start: 0.8123 (tp30) cc_final: 0.7692 (tm-30) REVERT: A 639 SER cc_start: 0.8672 (t) cc_final: 0.8283 (p) REVERT: A 642 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7232 (tt) REVERT: A 671 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7665 (mmm160) REVERT: A 676 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7804 (tpt90) REVERT: B 36 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8525 (mtp180) REVERT: B 256 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: B 258 TRP cc_start: 0.6703 (OUTLIER) cc_final: 0.5814 (t-100) REVERT: B 278 LYS cc_start: 0.2088 (OUTLIER) cc_final: 0.0826 (tttp) REVERT: B 282 LEU cc_start: 0.2730 (OUTLIER) cc_final: 0.1213 (mm) REVERT: B 318 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7485 (mmtm) REVERT: B 371 SER cc_start: 0.7954 (t) cc_final: 0.7647 (m) REVERT: B 468 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7130 (mmp-170) REVERT: B 532 GLU cc_start: 0.8125 (tp30) cc_final: 0.7696 (tm-30) REVERT: B 639 SER cc_start: 0.8661 (t) cc_final: 0.8268 (p) REVERT: B 642 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7211 (tt) REVERT: B 671 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7652 (mmm160) REVERT: B 676 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7789 (tpt90) outliers start: 86 outliers final: 35 residues processed: 229 average time/residue: 1.0422 time to fit residues: 259.8405 Evaluate side-chains 197 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.154534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100441 restraints weight = 11373.519| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.97 r_work: 0.2984 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10806 Z= 0.237 Angle : 0.661 9.105 14672 Z= 0.336 Chirality : 0.044 0.156 1650 Planarity : 0.006 0.064 1826 Dihedral : 9.187 61.920 1502 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 7.91 % Allowed : 20.68 % 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: 0.04 (0.24), residues: 1286 helix: 1.44 (0.18), residues: 832 sheet: -3.03 (0.65), residues: 42 loop : -2.72 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 625 HIS 0.003 0.001 HIS B 670 PHE 0.015 0.001 PHE B 384 TYR 0.013 0.001 TYR A 577 ARG 0.002 0.000 ARG A 36 *********************** 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: 88 poor density : 154 time to evaluate : 0.959 Fit side-chains REVERT: A 36 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7704 (mtp85) REVERT: A 61 PHE cc_start: 0.3207 (OUTLIER) cc_final: 0.2686 (m-10) REVERT: A 258 TRP cc_start: 0.6676 (OUTLIER) cc_final: 0.5796 (t-100) REVERT: A 278 LYS cc_start: 0.1974 (OUTLIER) cc_final: 0.0669 (mmtp) REVERT: A 318 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7564 (mtmt) REVERT: A 468 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7109 (mmp-170) REVERT: A 532 GLU cc_start: 0.8106 (tp30) cc_final: 0.7684 (tm-30) REVERT: A 535 MET cc_start: 0.8591 (mtp) cc_final: 0.8388 (mtt) REVERT: A 639 SER cc_start: 0.8610 (t) cc_final: 0.8191 (p) REVERT: A 671 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7612 (mmm160) REVERT: B 36 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7698 (mtp85) REVERT: B 258 TRP cc_start: 0.6671 (OUTLIER) cc_final: 0.5792 (t-100) REVERT: B 278 LYS cc_start: 0.1979 (OUTLIER) cc_final: 0.0672 (mmtp) REVERT: B 318 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7571 (mtmt) REVERT: B 371 SER cc_start: 0.7938 (t) cc_final: 0.7611 (m) REVERT: B 468 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7111 (mmp-170) REVERT: B 532 GLU cc_start: 0.8111 (tp30) cc_final: 0.7690 (tm-30) REVERT: B 639 SER cc_start: 0.8601 (t) cc_final: 0.8190 (p) REVERT: B 642 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7173 (tt) REVERT: B 671 ARG cc_start: 0.7864 (mtp180) cc_final: 0.7597 (mmm160) outliers start: 88 outliers final: 29 residues processed: 218 average time/residue: 1.1110 time to fit residues: 263.8799 Evaluate side-chains 191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 258 TRP 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 479 LEU Chi-restraints excluded: chain A residue 588 THR 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 258 TRP 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 479 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 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: 1.9990 chunk 15 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 129 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7938 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.155106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100490 restraints weight = 11331.090| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.98 r_work: 0.2990 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10806 Z= 0.220 Angle : 0.667 12.979 14672 Z= 0.331 Chirality : 0.043 0.146 1650 Planarity : 0.006 0.060 1826 Dihedral : 8.020 59.536 1482 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.61 % Favored : 93.23 % Rotamer: Outliers : 7.28 % Allowed : 22.12 % Favored : 70.59 % 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: 0.28 (0.24), residues: 1286 helix: 1.62 (0.18), residues: 830 sheet: -2.90 (0.67), residues: 42 loop : -2.57 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 625 HIS 0.002 0.001 HIS A 670 PHE 0.017 0.001 PHE B 384 TYR 0.013 0.001 TYR A 577 ARG 0.010 0.000 ARG B 274 *********************** 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 231 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 150 time to evaluate : 1.245 Fit side-chains REVERT: A 36 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7709 (mtp85) REVERT: A 61 PHE cc_start: 0.3224 (OUTLIER) cc_final: 0.2702 (m-10) REVERT: A 256 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: A 258 TRP cc_start: 0.6601 (OUTLIER) cc_final: 0.5767 (t-100) REVERT: A 278 LYS cc_start: 0.1774 (OUTLIER) cc_final: 0.0542 (mmtp) REVERT: A 318 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7558 (mtmt) REVERT: A 403 ILE cc_start: 0.2233 (OUTLIER) cc_final: 0.2019 (mm) REVERT: A 468 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7110 (mmp-170) REVERT: A 532 GLU cc_start: 0.8152 (tp30) cc_final: 0.7749 (tm-30) REVERT: A 639 SER cc_start: 0.8642 (t) cc_final: 0.8423 (p) REVERT: A 671 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7545 (mmm160) REVERT: B 36 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7710 (mtp85) REVERT: B 256 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: B 258 TRP cc_start: 0.6597 (OUTLIER) cc_final: 0.5765 (t-100) REVERT: B 278 LYS cc_start: 0.1769 (OUTLIER) cc_final: 0.0537 (mmtp) REVERT: B 318 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7572 (mtmt) REVERT: B 468 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7027 (mmp-170) REVERT: B 532 GLU cc_start: 0.8156 (tp30) cc_final: 0.7736 (tm-30) REVERT: B 639 SER cc_start: 0.8626 (t) cc_final: 0.8403 (p) REVERT: B 671 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7528 (mmm160) outliers start: 81 outliers final: 39 residues processed: 214 average time/residue: 1.0265 time to fit residues: 240.2657 Evaluate side-chains 198 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 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 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 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 646 LEU 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 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 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 Chi-restraints excluded: chain B residue 710 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 119 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 0.0170 chunk 127 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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** 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 = 0.3817 r_free = 0.3817 target = 0.157222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102691 restraints weight = 11371.816| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.37 r_work: 0.3004 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10806 Z= 0.183 Angle : 0.643 10.571 14672 Z= 0.321 Chirality : 0.042 0.214 1650 Planarity : 0.005 0.056 1826 Dihedral : 7.770 59.370 1476 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 6.38 % Allowed : 23.47 % Favored : 70.14 % 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: 0.51 (0.24), residues: 1286 helix: 1.78 (0.18), residues: 834 sheet: -2.91 (0.69), residues: 42 loop : -2.47 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 625 HIS 0.002 0.001 HIS B 294 PHE 0.018 0.001 PHE A 384 TYR 0.010 0.001 TYR B 577 ARG 0.002 0.000 ARG B 36 *********************** 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 220 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 1.154 Fit side-chains REVERT: A 36 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7728 (mtp85) REVERT: A 61 PHE cc_start: 0.3195 (OUTLIER) cc_final: 0.2702 (m-10) REVERT: A 86 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: A 256 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: A 258 TRP cc_start: 0.6493 (OUTLIER) cc_final: 0.5743 (t-100) REVERT: A 278 LYS cc_start: 0.1612 (OUTLIER) cc_final: 0.0397 (mmtp) REVERT: A 318 LYS cc_start: 0.7929 (mmmm) cc_final: 0.7519 (mtmt) REVERT: A 371 SER cc_start: 0.7886 (t) cc_final: 0.7550 (m) REVERT: A 403 ILE cc_start: 0.2223 (OUTLIER) cc_final: 0.2005 (mm) REVERT: A 532 GLU cc_start: 0.8138 (tp30) cc_final: 0.7727 (tm-30) REVERT: A 639 SER cc_start: 0.8629 (t) cc_final: 0.8423 (p) REVERT: A 671 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7549 (mmm160) REVERT: B 36 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7725 (mtp85) REVERT: B 74 HIS cc_start: 0.7961 (t70) cc_final: 0.7590 (m170) REVERT: B 86 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: B 256 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: B 258 TRP cc_start: 0.6487 (OUTLIER) cc_final: 0.5737 (t-100) REVERT: B 278 LYS cc_start: 0.1616 (OUTLIER) cc_final: 0.0401 (mmtp) REVERT: B 318 LYS cc_start: 0.7933 (mmmm) cc_final: 0.7520 (mtmt) REVERT: B 371 SER cc_start: 0.7882 (t) cc_final: 0.7547 (m) REVERT: B 532 GLU cc_start: 0.8132 (tp30) cc_final: 0.7726 (tm-30) REVERT: B 639 SER cc_start: 0.8599 (t) cc_final: 0.8390 (p) REVERT: B 671 ARG cc_start: 0.7920 (mtp180) cc_final: 0.7536 (mmm160) outliers start: 71 outliers final: 29 residues processed: 206 average time/residue: 1.0240 time to fit residues: 230.7049 Evaluate side-chains 185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 273 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 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 35 ASP 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 273 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 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: 4.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3772 r_free = 0.3772 target = 0.153030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098706 restraints weight = 11516.830| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.98 r_work: 0.2963 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10806 Z= 0.274 Angle : 0.660 7.759 14672 Z= 0.331 Chirality : 0.044 0.175 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.832 59.842 1476 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.84 % Favored : 93.00 % Rotamer: Outliers : 5.76 % Allowed : 24.10 % Favored : 70.14 % 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: 0.47 (0.24), residues: 1286 helix: 1.74 (0.18), residues: 832 sheet: -2.89 (0.66), residues: 42 loop : -2.44 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 625 HIS 0.004 0.001 HIS A 670 PHE 0.022 0.001 PHE B 384 TYR 0.015 0.001 TYR A 577 ARG 0.002 0.000 ARG B 274 *********************** 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 214 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 150 time to evaluate : 1.054 Fit side-chains REVERT: A 4 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6633 (pt) REVERT: A 36 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7685 (mtp85) REVERT: A 61 PHE cc_start: 0.3239 (OUTLIER) cc_final: 0.2675 (m-10) REVERT: A 256 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: A 258 TRP cc_start: 0.6689 (OUTLIER) cc_final: 0.5767 (t-100) REVERT: A 278 LYS cc_start: 0.1572 (OUTLIER) cc_final: 0.0328 (mmtt) REVERT: A 318 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7612 (mtmt) REVERT: A 532 GLU cc_start: 0.8209 (tp30) cc_final: 0.7835 (tm-30) REVERT: A 639 SER cc_start: 0.8663 (t) cc_final: 0.8442 (p) REVERT: B 4 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6629 (pt) REVERT: B 36 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7702 (mtp85) REVERT: B 256 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: B 258 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.5769 (t-100) REVERT: B 278 LYS cc_start: 0.1575 (OUTLIER) cc_final: 0.0329 (mmtt) REVERT: B 318 LYS cc_start: 0.8033 (mmmm) cc_final: 0.7609 (mtmt) REVERT: B 532 GLU cc_start: 0.8199 (tp30) cc_final: 0.7811 (tm-30) REVERT: B 639 SER cc_start: 0.8662 (t) cc_final: 0.8447 (p) outliers start: 64 outliers final: 38 residues processed: 203 average time/residue: 1.0289 time to fit residues: 228.3758 Evaluate side-chains 191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 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 A residue 710 GLN 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 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 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 Chi-restraints excluded: chain B residue 710 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.155219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101159 restraints weight = 11340.412| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.97 r_work: 0.2963 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10806 Z= 0.200 Angle : 0.622 7.245 14672 Z= 0.313 Chirality : 0.042 0.168 1650 Planarity : 0.005 0.056 1826 Dihedral : 7.733 58.068 1476 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 5.22 % Allowed : 24.82 % Favored : 69.96 % 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: 1.86 (0.18), residues: 834 sheet: -2.85 (0.68), residues: 42 loop : -2.40 (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 74 PHE 0.017 0.001 PHE B 384 TYR 0.011 0.001 TYR B 577 ARG 0.002 0.000 ARG B 36 *********************** 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 203 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 1.084 Fit side-chains REVERT: A 4 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6620 (pt) REVERT: A 36 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7807 (mtp85) REVERT: A 61 PHE cc_start: 0.3297 (OUTLIER) cc_final: 0.2726 (m-10) REVERT: A 74 HIS cc_start: 0.8074 (t70) cc_final: 0.7626 (m170) REVERT: A 256 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: A 258 TRP cc_start: 0.6588 (OUTLIER) cc_final: 0.5726 (t-100) REVERT: A 278 LYS cc_start: 0.1564 (OUTLIER) cc_final: 0.0322 (mmmt) REVERT: A 318 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7635 (mtmt) REVERT: A 532 GLU cc_start: 0.8199 (tp30) cc_final: 0.7824 (tm-30) REVERT: A 671 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7764 (mmm160) REVERT: B 4 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6619 (pt) REVERT: B 36 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7790 (mtp85) REVERT: B 74 HIS cc_start: 0.8065 (t70) cc_final: 0.7617 (m170) REVERT: B 256 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6959 (tm-30) REVERT: B 258 TRP cc_start: 0.6579 (OUTLIER) cc_final: 0.5722 (t-100) REVERT: B 278 LYS cc_start: 0.1565 (OUTLIER) cc_final: 0.0323 (mmmt) REVERT: B 318 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7640 (mtmt) REVERT: B 532 GLU cc_start: 0.8196 (tp30) cc_final: 0.7826 (tm-30) REVERT: B 671 ARG cc_start: 0.8032 (mtp180) cc_final: 0.7753 (mmm160) outliers start: 58 outliers final: 33 residues processed: 192 average time/residue: 1.0200 time to fit residues: 215.2039 Evaluate side-chains 182 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 159 PHE Chi-restraints excluded: chain A residue 163 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 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 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 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 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: 0.9980 chunk 63 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.155207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101044 restraints weight = 11482.381| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.98 r_work: 0.2994 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10806 Z= 0.197 Angle : 0.619 8.503 14672 Z= 0.309 Chirality : 0.042 0.161 1650 Planarity : 0.005 0.056 1826 Dihedral : 7.633 59.203 1476 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.85 % Allowed : 24.37 % Favored : 69.78 % 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: 0.73 (0.24), residues: 1286 helix: 1.95 (0.18), residues: 834 sheet: -2.84 (0.68), residues: 42 loop : -2.37 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 625 HIS 0.003 0.001 HIS B 74 PHE 0.021 0.001 PHE B 384 TYR 0.012 0.001 TYR A 577 ARG 0.001 0.000 ARG A 36 *********************** 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 206 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 1.110 Fit side-chains REVERT: A 4 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6562 (pt) REVERT: A 36 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7751 (mtp85) REVERT: A 61 PHE cc_start: 0.3423 (OUTLIER) cc_final: 0.2849 (m-10) REVERT: A 74 HIS cc_start: 0.8060 (t70) cc_final: 0.7597 (m170) REVERT: A 258 TRP cc_start: 0.6578 (OUTLIER) cc_final: 0.5687 (t-100) REVERT: A 278 LYS cc_start: 0.1564 (OUTLIER) cc_final: 0.0730 (mmmt) REVERT: A 282 LEU cc_start: 0.3629 (OUTLIER) cc_final: 0.2691 (mt) REVERT: A 318 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7587 (mtmt) REVERT: A 532 GLU cc_start: 0.8157 (tp30) cc_final: 0.7802 (tm-30) REVERT: A 671 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7703 (mmm160) REVERT: B 4 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6562 (pt) REVERT: B 36 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7755 (mtp85) REVERT: B 74 HIS cc_start: 0.8075 (t70) cc_final: 0.7599 (m170) REVERT: B 258 TRP cc_start: 0.6574 (OUTLIER) cc_final: 0.5686 (t-100) REVERT: B 278 LYS cc_start: 0.1567 (OUTLIER) cc_final: 0.0731 (mmmt) REVERT: B 282 LEU cc_start: 0.3625 (OUTLIER) cc_final: 0.2689 (mt) REVERT: B 318 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7583 (mtmt) REVERT: B 468 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.6580 (mtp180) REVERT: B 532 GLU cc_start: 0.8171 (tp30) cc_final: 0.7823 (tm-30) REVERT: B 671 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7692 (mmm160) outliers start: 65 outliers final: 31 residues processed: 189 average time/residue: 1.0590 time to fit residues: 218.4269 Evaluate side-chains 183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 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 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 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 400 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 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 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 400 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.154488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100277 restraints weight = 11396.332| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.30 r_work: 0.2992 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4994 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= 0.188 Angle : 0.617 8.344 14672 Z= 0.310 Chirality : 0.042 0.196 1650 Planarity : 0.005 0.056 1826 Dihedral : 7.323 58.278 1472 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.13 % Allowed : 25.18 % 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: 0.77 (0.24), residues: 1286 helix: 1.97 (0.18), residues: 834 sheet: -2.82 (0.69), residues: 42 loop : -2.37 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.002 0.001 HIS B 670 PHE 0.019 0.001 PHE B 384 TYR 0.011 0.001 TYR A 577 ARG 0.002 0.000 ARG A 100 ********************** 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 196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.099 Fit side-chains REVERT: A 36 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7761 (mtp85) REVERT: A 61 PHE cc_start: 0.3369 (OUTLIER) cc_final: 0.2830 (m-10) REVERT: A 74 HIS cc_start: 0.8080 (t70) cc_final: 0.7619 (m170) REVERT: A 258 TRP cc_start: 0.6623 (OUTLIER) cc_final: 0.5738 (t-100) REVERT: A 278 LYS cc_start: 0.1354 (OUTLIER) cc_final: 0.0724 (mmmt) REVERT: A 282 LEU cc_start: 0.3696 (OUTLIER) cc_final: 0.2788 (mt) REVERT: A 318 LYS cc_start: 0.7961 (mmmm) cc_final: 0.7572 (mtmt) REVERT: A 532 GLU cc_start: 0.8185 (tp30) cc_final: 0.7820 (tm-30) REVERT: A 671 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7724 (mmm160) REVERT: B 4 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6540 (pt) REVERT: B 36 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7769 (mtp85) REVERT: B 74 HIS cc_start: 0.8080 (t70) cc_final: 0.7617 (m170) REVERT: B 258 TRP cc_start: 0.6616 (OUTLIER) cc_final: 0.5736 (t-100) REVERT: B 278 LYS cc_start: 0.1353 (OUTLIER) cc_final: 0.0722 (mmmt) REVERT: B 282 LEU cc_start: 0.3695 (OUTLIER) cc_final: 0.2792 (mt) REVERT: B 318 LYS cc_start: 0.7964 (mmmm) cc_final: 0.7571 (mtmt) REVERT: B 468 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6606 (mtp180) REVERT: B 532 GLU cc_start: 0.8180 (tp30) cc_final: 0.7838 (tm-30) REVERT: B 671 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7714 (mmm160) outliers start: 57 outliers final: 32 residues processed: 187 average time/residue: 1.0212 time to fit residues: 208.5316 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 : 1.063 ------------------------------------------------------------------------------- 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 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 165 MET 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 400 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 A residue 702 ASN 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 165 MET 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 400 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 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: 1.9990 chunk 90 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.155010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100493 restraints weight = 11271.032| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.97 r_work: 0.2954 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10806 Z= 0.234 Angle : 0.634 8.346 14672 Z= 0.319 Chirality : 0.044 0.211 1650 Planarity : 0.005 0.056 1826 Dihedral : 7.125 58.047 1468 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.32 % Allowed : 26.08 % Favored : 69.60 % 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: 0.76 (0.24), residues: 1286 helix: 1.96 (0.18), residues: 834 sheet: -2.79 (0.68), residues: 42 loop : -2.37 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 625 HIS 0.003 0.001 HIS A 670 PHE 0.041 0.001 PHE B 421 TYR 0.013 0.001 TYR B 577 ARG 0.003 0.000 ARG B 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9925.04 seconds wall clock time: 177 minutes 15.06 seconds (10635.06 seconds total)