Starting phenix.real_space_refine on Sat Aug 23 07:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymq_39403/08_2025/8ymq_39403_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymq_39403/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ymq_39403/08_2025/8ymq_39403_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymq_39403/08_2025/8ymq_39403_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ymq_39403/08_2025/8ymq_39403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymq_39403/08_2025/8ymq_39403.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.25, per 1000 atoms: 0.21 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: 1.02 Conformation dependent library (CDL) restraints added in 417.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.35 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: 1.58 Time building geometry restraints manager: 1.33 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.360 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.061 10806 Z= 0.809 Angle : 1.477 25.160 14672 Z= 0.947 Chirality : 0.114 0.631 1650 Planarity : 0.008 0.102 1826 Dihedral : 23.723 89.210 3890 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 2.18 % Allowed : 8.24 % Favored : 89.58 % Rotamer: Outliers : 32.64 % Allowed : 10.97 % Favored : 56.38 % Cbeta Deviations : 0.81 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 197 TYR 0.015 0.002 TYR B 618 PHE 0.018 0.002 PHE A 624 TRP 0.015 0.003 TRP B 625 HIS 0.008 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.01094 (10806) covalent geometry : angle 1.47715 (14672) hydrogen bonds : bond 0.19948 ( 645) hydrogen bonds : angle 7.24129 ( 1917) *********************** 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 : 0.274 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: 0.4760 time to fit residues: 248.5900 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 : 0.240 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.156435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103631 restraints weight = 11229.104| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.95 r_work: 0.3035 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3382 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= 0.191 Angle : 0.808 11.570 14672 Z= 0.419 Chirality : 0.047 0.213 1650 Planarity : 0.007 0.102 1826 Dihedral : 12.207 78.302 1558 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.93 % Favored : 91.91 % Rotamer: Outliers : 9.26 % Allowed : 21.67 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.23), residues: 1286 helix: 0.63 (0.18), residues: 824 sheet: -3.40 (0.56), residues: 42 loop : -3.01 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 556 TYR 0.020 0.002 TYR A 262 PHE 0.015 0.002 PHE A 421 TRP 0.024 0.002 TRP B 625 HIS 0.003 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00412 (10806) covalent geometry : angle 0.80830 (14672) hydrogen bonds : bond 0.06063 ( 645) hydrogen bonds : angle 4.76053 ( 1917) *********************** 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 : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7588 (mtp85) REVERT: A 61 PHE cc_start: 0.3038 (OUTLIER) cc_final: 0.2821 (m-80) REVERT: A 256 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: A 258 TRP cc_start: 0.6775 (OUTLIER) cc_final: 0.5415 (t60) REVERT: A 278 LYS cc_start: 0.2028 (OUTLIER) cc_final: 0.0854 (ttmm) REVERT: A 282 LEU cc_start: 0.2483 (OUTLIER) cc_final: 0.1080 (mm) REVERT: A 468 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7011 (mmp-170) REVERT: A 532 GLU cc_start: 0.8049 (tp30) cc_final: 0.7564 (tm-30) REVERT: A 535 MET cc_start: 0.8654 (mtp) cc_final: 0.8383 (mtt) REVERT: A 639 SER cc_start: 0.8542 (t) cc_final: 0.8164 (p) REVERT: A 644 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6580 (mtp) REVERT: A 660 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 671 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7575 (mmm160) REVERT: A 676 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7676 (tpt90) REVERT: B 36 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7587 (mtp85) REVERT: B 256 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: B 258 TRP cc_start: 0.6773 (OUTLIER) cc_final: 0.5411 (t60) REVERT: B 278 LYS cc_start: 0.2028 (OUTLIER) cc_final: 0.0853 (ttmm) REVERT: B 282 LEU cc_start: 0.2491 (OUTLIER) cc_final: 0.1085 (mm) REVERT: B 468 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7017 (mmp-170) REVERT: B 532 GLU cc_start: 0.8043 (tp30) cc_final: 0.7563 (tm-30) REVERT: B 535 MET cc_start: 0.8656 (mtp) cc_final: 0.8386 (mtt) REVERT: B 639 SER cc_start: 0.8539 (t) cc_final: 0.8159 (p) REVERT: B 644 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6577 (mtp) REVERT: B 660 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7873 (mp) REVERT: B 671 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7575 (mmm160) REVERT: B 676 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7661 (tpt90) outliers start: 103 outliers final: 41 residues processed: 256 average time/residue: 0.5093 time to fit residues: 142.0563 Evaluate side-chains 212 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 710 GLN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 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 2 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 575 GLN B 14 ASN B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.101425 restraints weight = 11382.954| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.98 r_work: 0.2999 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10806 Z= 0.173 Angle : 0.705 10.295 14672 Z= 0.359 Chirality : 0.044 0.161 1650 Planarity : 0.007 0.100 1826 Dihedral : 9.987 66.533 1512 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.16 % Favored : 91.68 % Rotamer: Outliers : 7.73 % Allowed : 21.85 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.23), residues: 1286 helix: 1.15 (0.18), residues: 834 sheet: -3.11 (0.62), residues: 42 loop : -2.91 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.012 0.001 TYR A 577 PHE 0.019 0.002 PHE B 421 TRP 0.022 0.001 TRP A 625 HIS 0.003 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00381 (10806) covalent geometry : angle 0.70452 (14672) hydrogen bonds : bond 0.05380 ( 645) hydrogen bonds : angle 4.40861 ( 1917) *********************** 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 246 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 160 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7852 (mtp85) REVERT: A 256 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6641 (tm-30) REVERT: A 258 TRP cc_start: 0.6748 (OUTLIER) cc_final: 0.5440 (t60) REVERT: A 278 LYS cc_start: 0.2059 (OUTLIER) cc_final: 0.0802 (tttp) REVERT: A 282 LEU cc_start: 0.2743 (OUTLIER) cc_final: 0.1290 (mm) REVERT: A 318 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7633 (mttt) REVERT: A 468 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7181 (mmp-170) REVERT: A 532 GLU cc_start: 0.8138 (tp30) cc_final: 0.7724 (tm-30) REVERT: A 535 MET cc_start: 0.8661 (mtp) cc_final: 0.8401 (mtt) REVERT: A 639 SER cc_start: 0.8662 (t) cc_final: 0.8255 (p) REVERT: A 642 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7257 (tt) REVERT: A 671 ARG cc_start: 0.7938 (mtp180) cc_final: 0.7668 (mmm160) REVERT: B 36 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7859 (mtp85) REVERT: B 256 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: B 258 TRP cc_start: 0.6750 (OUTLIER) cc_final: 0.5439 (t60) REVERT: B 278 LYS cc_start: 0.2060 (OUTLIER) cc_final: 0.0805 (tttp) REVERT: B 282 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.1304 (mm) REVERT: B 318 LYS cc_start: 0.8025 (mmmm) cc_final: 0.7625 (mttt) REVERT: B 468 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7180 (mmp-170) REVERT: B 532 GLU cc_start: 0.8139 (tp30) cc_final: 0.7730 (tm-30) REVERT: B 535 MET cc_start: 0.8666 (mtp) cc_final: 0.8411 (mtt) REVERT: B 639 SER cc_start: 0.8656 (t) cc_final: 0.8245 (p) REVERT: B 642 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7245 (tt) REVERT: B 671 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7655 (mmm160) outliers start: 86 outliers final: 39 residues processed: 224 average time/residue: 0.5220 time to fit residues: 127.3342 Evaluate side-chains 199 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 392 ILE 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 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 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 = 0.3758 r_free = 0.3758 target = 0.151683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097875 restraints weight = 11549.137| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.32 r_work: 0.2933 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10806 Z= 0.211 Angle : 0.696 8.618 14672 Z= 0.354 Chirality : 0.046 0.174 1650 Planarity : 0.006 0.087 1826 Dihedral : 9.444 62.973 1504 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.61 % Rotamer: Outliers : 8.27 % Allowed : 21.04 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.23), residues: 1286 helix: 1.26 (0.18), residues: 832 sheet: -3.02 (0.64), residues: 42 loop : -2.75 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 36 TYR 0.016 0.002 TYR A 577 PHE 0.016 0.002 PHE B 384 TRP 0.018 0.001 TRP B 625 HIS 0.004 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00496 (10806) covalent geometry : angle 0.69552 (14672) hydrogen bonds : bond 0.05498 ( 645) hydrogen bonds : angle 4.38434 ( 1917) *********************** 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: 92 poor density : 150 time to evaluate : 0.391 Fit side-chains REVERT: A 36 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7767 (mtp85) REVERT: A 278 LYS cc_start: 0.1979 (OUTLIER) cc_final: 0.0670 (mmtp) REVERT: A 468 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7240 (mmp-170) REVERT: A 532 GLU cc_start: 0.8175 (tp30) cc_final: 0.7764 (tm-30) REVERT: A 639 SER cc_start: 0.8631 (t) cc_final: 0.8187 (p) REVERT: A 671 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7676 (mmm160) REVERT: B 36 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7763 (mtp85) REVERT: B 278 LYS cc_start: 0.1984 (OUTLIER) cc_final: 0.0669 (mmtp) REVERT: B 468 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7246 (mmp-170) REVERT: B 532 GLU cc_start: 0.8172 (tp30) cc_final: 0.7768 (tm-30) REVERT: B 639 SER cc_start: 0.8626 (t) cc_final: 0.8178 (p) REVERT: B 671 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7656 (mmm160) outliers start: 92 outliers final: 46 residues processed: 217 average time/residue: 0.5095 time to fit residues: 120.8239 Evaluate side-chains 201 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 40 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 479 LEU 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 40 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 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 479 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 609 GLN ** B 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.098273 restraints weight = 11394.979| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.98 r_work: 0.2955 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4487 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= 0.182 Angle : 0.697 12.754 14672 Z= 0.346 Chirality : 0.044 0.148 1650 Planarity : 0.006 0.059 1826 Dihedral : 8.719 61.549 1488 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.61 % Rotamer: Outliers : 7.19 % Allowed : 22.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.24), residues: 1286 helix: 1.40 (0.18), residues: 832 sheet: -2.95 (0.66), residues: 42 loop : -2.67 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 36 TYR 0.014 0.001 TYR A 577 PHE 0.015 0.001 PHE B 384 TRP 0.019 0.001 TRP B 625 HIS 0.003 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00418 (10806) covalent geometry : angle 0.69665 (14672) hydrogen bonds : bond 0.05119 ( 645) hydrogen bonds : angle 4.27163 ( 1917) *********************** 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 238 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 158 time to evaluate : 0.364 Fit side-chains REVERT: A 36 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7682 (mtp85) REVERT: A 256 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: A 278 LYS cc_start: 0.1863 (OUTLIER) cc_final: 0.0596 (mmtp) REVERT: A 318 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7456 (mmtm) REVERT: A 468 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7152 (mmp-170) REVERT: A 532 GLU cc_start: 0.8101 (tp30) cc_final: 0.7683 (tm-30) REVERT: A 639 SER cc_start: 0.8574 (t) cc_final: 0.8159 (p) REVERT: A 671 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7453 (mmm160) REVERT: B 36 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7684 (mtp85) REVERT: B 256 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: B 278 LYS cc_start: 0.1857 (OUTLIER) cc_final: 0.0593 (mmtp) REVERT: B 318 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7461 (mmtm) REVERT: B 468 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7090 (mmp-170) REVERT: B 532 GLU cc_start: 0.8107 (tp30) cc_final: 0.7690 (tm-30) REVERT: B 639 SER cc_start: 0.8570 (t) cc_final: 0.8152 (p) REVERT: B 671 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7440 (mmm160) outliers start: 80 outliers final: 39 residues processed: 217 average time/residue: 0.5143 time to fit residues: 121.6797 Evaluate side-chains 199 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE 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 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 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 B 74 HIS B 190 GLN B 476 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099888 restraints weight = 11471.459| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.97 r_work: 0.2979 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4668 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= 0.149 Angle : 0.673 11.137 14672 Z= 0.335 Chirality : 0.043 0.200 1650 Planarity : 0.005 0.057 1826 Dihedral : 8.482 59.530 1482 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.39 % Favored : 92.46 % Rotamer: Outliers : 5.67 % Allowed : 24.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1286 helix: 1.61 (0.18), residues: 832 sheet: -2.85 (0.68), residues: 42 loop : -2.51 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 36 TYR 0.011 0.001 TYR A 577 PHE 0.017 0.001 PHE B 384 TRP 0.020 0.001 TRP A 625 HIS 0.002 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00333 (10806) covalent geometry : angle 0.67333 (14672) hydrogen bonds : bond 0.04710 ( 645) hydrogen bonds : angle 4.14482 ( 1917) *********************** 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 214 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 0.465 Fit side-chains REVERT: A 36 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7746 (mtp85) REVERT: A 256 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: A 258 TRP cc_start: 0.6689 (OUTLIER) cc_final: 0.5745 (t-100) REVERT: A 278 LYS cc_start: 0.1565 (OUTLIER) cc_final: 0.0330 (mmtp) REVERT: A 318 LYS cc_start: 0.8045 (mmmm) cc_final: 0.7469 (mmtm) REVERT: A 468 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6929 (mmp-170) REVERT: A 532 GLU cc_start: 0.8162 (tp30) cc_final: 0.7809 (tm-30) REVERT: A 535 MET cc_start: 0.8692 (mtp) cc_final: 0.8454 (mtt) REVERT: A 639 SER cc_start: 0.8660 (t) cc_final: 0.8443 (p) REVERT: B 36 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7748 (mtp85) REVERT: B 256 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: B 258 TRP cc_start: 0.6684 (OUTLIER) cc_final: 0.5742 (t-100) REVERT: B 278 LYS cc_start: 0.1567 (OUTLIER) cc_final: 0.0331 (mmtp) REVERT: B 318 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7479 (mmtm) REVERT: B 468 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6947 (mmp-170) REVERT: B 532 GLU cc_start: 0.8163 (tp30) cc_final: 0.7815 (tm-30) REVERT: B 535 MET cc_start: 0.8696 (mtp) cc_final: 0.8458 (mtt) REVERT: B 639 SER cc_start: 0.8655 (t) cc_final: 0.8438 (p) outliers start: 63 outliers final: 37 residues processed: 197 average time/residue: 0.4874 time to fit residues: 105.0588 Evaluate side-chains 195 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 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 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 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 190 GLN B 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.100446 restraints weight = 11330.862| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.95 r_work: 0.2954 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10806 Z= 0.146 Angle : 0.637 7.667 14672 Z= 0.319 Chirality : 0.043 0.188 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.890 59.634 1478 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 6.21 % Allowed : 23.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.24), residues: 1286 helix: 1.68 (0.18), residues: 836 sheet: -2.80 (0.69), residues: 42 loop : -2.44 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 36 TYR 0.012 0.001 TYR A 577 PHE 0.019 0.001 PHE B 384 TRP 0.018 0.001 TRP A 625 HIS 0.002 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00329 (10806) covalent geometry : angle 0.63750 (14672) hydrogen bonds : bond 0.04605 ( 645) hydrogen bonds : angle 4.08688 ( 1917) *********************** 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 210 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 141 time to evaluate : 0.297 Fit side-chains REVERT: A 36 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7917 (mtp85) REVERT: A 256 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: A 258 TRP cc_start: 0.6660 (OUTLIER) cc_final: 0.5739 (t-100) REVERT: A 278 LYS cc_start: 0.1542 (OUTLIER) cc_final: 0.0269 (mmtt) REVERT: A 318 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7645 (mtmt) REVERT: A 468 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7050 (mmp-170) REVERT: A 532 GLU cc_start: 0.8191 (tp30) cc_final: 0.7832 (tm-30) REVERT: A 535 MET cc_start: 0.8716 (mtp) cc_final: 0.8492 (mtt) REVERT: A 671 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7755 (mmm160) REVERT: B 36 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7909 (mtp85) REVERT: B 256 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: B 258 TRP cc_start: 0.6653 (OUTLIER) cc_final: 0.5734 (t-100) REVERT: B 278 LYS cc_start: 0.1551 (OUTLIER) cc_final: 0.0274 (mmtt) REVERT: B 318 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7648 (mtmt) REVERT: B 468 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.6998 (mmp-170) REVERT: B 532 GLU cc_start: 0.8187 (tp30) cc_final: 0.7836 (tm-30) REVERT: B 535 MET cc_start: 0.8716 (mtp) cc_final: 0.8496 (mtt) REVERT: B 671 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7745 (mmm160) outliers start: 69 outliers final: 35 residues processed: 194 average time/residue: 0.4930 time to fit residues: 104.1171 Evaluate side-chains 183 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 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 206 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 421 PHE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 126 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102289 restraints weight = 11303.991| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.32 r_work: 0.2968 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4966 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= 0.131 Angle : 0.624 7.972 14672 Z= 0.309 Chirality : 0.042 0.177 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.767 58.585 1478 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.92 % Favored : 92.92 % Rotamer: Outliers : 5.31 % Allowed : 25.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.24), residues: 1286 helix: 1.82 (0.18), residues: 836 sheet: -2.80 (0.69), residues: 42 loop : -2.45 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.010 0.001 TYR B 577 PHE 0.018 0.001 PHE A 384 TRP 0.018 0.001 TRP B 625 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00289 (10806) covalent geometry : angle 0.62410 (14672) hydrogen bonds : bond 0.04281 ( 645) hydrogen bonds : angle 4.00990 ( 1917) *********************** 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 201 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 142 time to evaluate : 0.440 Fit side-chains REVERT: A 4 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6600 (pt) REVERT: A 258 TRP cc_start: 0.6554 (OUTLIER) cc_final: 0.5696 (t-100) REVERT: A 278 LYS cc_start: 0.1526 (OUTLIER) cc_final: 0.0316 (mmmt) REVERT: A 318 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7614 (mtmt) REVERT: A 532 GLU cc_start: 0.8185 (tp30) cc_final: 0.7816 (tm-30) REVERT: A 671 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7766 (mmm160) REVERT: B 4 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6590 (pt) REVERT: B 258 TRP cc_start: 0.6543 (OUTLIER) cc_final: 0.5688 (t-100) REVERT: B 278 LYS cc_start: 0.1527 (OUTLIER) cc_final: 0.0314 (mmmt) REVERT: B 318 LYS cc_start: 0.7985 (mmmm) cc_final: 0.7605 (mtmt) REVERT: B 532 GLU cc_start: 0.8179 (tp30) cc_final: 0.7818 (tm-30) REVERT: B 671 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7755 (mmm160) outliers start: 59 outliers final: 32 residues processed: 187 average time/residue: 0.5246 time to fit residues: 106.8459 Evaluate side-chains 173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 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 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 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 121 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 702 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101814 restraints weight = 11348.072| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.97 r_work: 0.3003 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 0.061 10806 Z= 0.131 Angle : 0.612 7.832 14672 Z= 0.305 Chirality : 0.042 0.160 1650 Planarity : 0.005 0.057 1826 Dihedral : 7.706 59.333 1478 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.13 % Allowed : 24.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.24), residues: 1286 helix: 1.93 (0.18), residues: 834 sheet: -2.77 (0.70), residues: 42 loop : -2.38 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.011 0.001 TYR B 577 PHE 0.019 0.001 PHE B 384 TRP 0.017 0.001 TRP A 625 HIS 0.002 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00291 (10806) covalent geometry : angle 0.61214 (14672) hydrogen bonds : bond 0.04289 ( 645) hydrogen bonds : angle 3.98570 ( 1917) *********************** 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 196 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 258 TRP cc_start: 0.6520 (OUTLIER) cc_final: 0.5673 (t-100) REVERT: A 278 LYS cc_start: 0.1494 (OUTLIER) cc_final: 0.0655 (mmmt) REVERT: A 282 LEU cc_start: 0.3620 (OUTLIER) cc_final: 0.2645 (mt) REVERT: A 318 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7540 (mtmt) REVERT: A 508 MET cc_start: -0.0462 (mmt) cc_final: -0.0788 (ppp) REVERT: A 532 GLU cc_start: 0.8161 (tp30) cc_final: 0.7763 (tm-30) REVERT: A 671 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7685 (mmm160) REVERT: B 258 TRP cc_start: 0.6506 (OUTLIER) cc_final: 0.5664 (t-100) REVERT: B 278 LYS cc_start: 0.1491 (OUTLIER) cc_final: 0.0652 (mmmt) REVERT: B 282 LEU cc_start: 0.3618 (OUTLIER) cc_final: 0.2647 (mt) REVERT: B 318 LYS cc_start: 0.7914 (mmmm) cc_final: 0.7540 (mtmt) REVERT: B 508 MET cc_start: 0.0053 (mmp) cc_final: -0.0341 (ppp) REVERT: B 532 GLU cc_start: 0.8161 (tp30) cc_final: 0.7768 (tm-30) REVERT: B 671 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7672 (mmm160) outliers start: 57 outliers final: 33 residues processed: 187 average time/residue: 0.4996 time to fit residues: 102.1398 Evaluate side-chains 177 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 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 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 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 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 52 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 702 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101887 restraints weight = 11263.181| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.96 r_work: 0.3003 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5067 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= 0.132 Angle : 0.606 7.851 14672 Z= 0.304 Chirality : 0.042 0.169 1650 Planarity : 0.005 0.056 1826 Dihedral : 7.511 59.710 1476 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.50 % Allowed : 25.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.24), residues: 1286 helix: 1.98 (0.18), residues: 834 sheet: -2.74 (0.71), residues: 42 loop : -2.37 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.011 0.001 TYR A 577 PHE 0.020 0.001 PHE B 384 TRP 0.017 0.001 TRP B 625 HIS 0.002 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00294 (10806) covalent geometry : angle 0.60561 (14672) hydrogen bonds : bond 0.04292 ( 645) hydrogen bonds : angle 4.00012 ( 1917) ********************** 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 191 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.458 Fit side-chains REVERT: A 86 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: A 258 TRP cc_start: 0.6510 (OUTLIER) cc_final: 0.5628 (t-100) REVERT: A 278 LYS cc_start: 0.1345 (OUTLIER) cc_final: 0.0698 (mmmt) REVERT: A 282 LEU cc_start: 0.3658 (OUTLIER) cc_final: 0.2767 (mt) REVERT: A 318 LYS cc_start: 0.7873 (mmmm) cc_final: 0.7502 (mtmt) REVERT: A 508 MET cc_start: -0.0574 (mmt) cc_final: -0.0862 (ppp) REVERT: A 532 GLU cc_start: 0.8171 (tp30) cc_final: 0.7788 (tm-30) REVERT: A 671 ARG cc_start: 0.7972 (mtp180) cc_final: 0.7680 (mmm160) REVERT: B 86 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: B 258 TRP cc_start: 0.6504 (OUTLIER) cc_final: 0.5625 (t-100) REVERT: B 278 LYS cc_start: 0.1343 (OUTLIER) cc_final: 0.0694 (mmmt) REVERT: B 282 LEU cc_start: 0.3660 (OUTLIER) cc_final: 0.2770 (mt) REVERT: B 318 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7504 (mtmt) REVERT: B 532 GLU cc_start: 0.8168 (tp30) cc_final: 0.7788 (tm-30) REVERT: B 671 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7673 (mmm160) outliers start: 50 outliers final: 30 residues processed: 181 average time/residue: 0.5062 time to fit residues: 100.1649 Evaluate side-chains 176 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 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 50 SER Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 400 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 702 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 702 ASN B 190 GLN B 702 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.101306 restraints weight = 11356.160| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.99 r_work: 0.2993 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5065 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= 0.139 Angle : 0.620 7.895 14672 Z= 0.312 Chirality : 0.043 0.199 1650 Planarity : 0.005 0.056 1826 Dihedral : 7.169 58.163 1470 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.05 % Allowed : 26.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.24), residues: 1286 helix: 2.01 (0.18), residues: 834 sheet: -2.75 (0.71), residues: 42 loop : -2.36 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.011 0.001 TYR A 577 PHE 0.020 0.001 PHE B 27 TRP 0.019 0.001 TRP B 625 HIS 0.002 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00314 (10806) covalent geometry : angle 0.62044 (14672) hydrogen bonds : bond 0.04383 ( 645) hydrogen bonds : angle 4.04591 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5095.47 seconds wall clock time: 87 minutes 28.45 seconds (5248.45 seconds total)