Starting phenix.real_space_refine on Sat Aug 23 11:27:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grn_34209/08_2025/8grn_34209_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grn_34209/08_2025/8grn_34209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8grn_34209/08_2025/8grn_34209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grn_34209/08_2025/8grn_34209.map" model { file = "/net/cci-nas-00/data/ceres_data/8grn_34209/08_2025/8grn_34209_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grn_34209/08_2025/8grn_34209_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 52 5.16 5 C 7648 2.51 5 N 1898 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 11602 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5770 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 37, 'TRANS': 678} Chain: "B" Number of atoms: 5770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5770 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 37, 'TRANS': 678} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LPC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LPC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.35, per 1000 atoms: 0.20 Number of scatterers: 11602 At special positions: 0 Unit cell: (153.669, 111.219, 106.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 2 15.00 O 2002 8.00 N 1898 7.00 C 7648 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 485.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 2 sheets defined 62.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.589A pdb=" N TRP A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 92 through 126 removed outlier: 3.841A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 111 - end of helix Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.558A pdb=" N HIS A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 193 Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.578A pdb=" N VAL A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 296 through 316 Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.623A pdb=" N CYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.543A pdb=" N ASN A 364 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 402 removed outlier: 4.110A pdb=" N LEU A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 393 - end of helix removed outlier: 3.880A pdb=" N LEU A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 451 removed outlier: 4.160A pdb=" N SER A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 457 through 496 removed outlier: 3.637A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 533 Proline residue: A 511 - end of helix removed outlier: 3.774A pdb=" N ILE A 533 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 547 removed outlier: 3.592A pdb=" N TYR A 542 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 Processing helix chain 'A' and resid 591 through 612 Processing helix chain 'A' and resid 623 through 650 Processing helix chain 'A' and resid 655 through 683 Proline residue: A 663 - end of helix Proline residue: A 679 - end of helix removed outlier: 3.573A pdb=" N ARG A 683 " --> pdb=" O PRO A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 694 removed outlier: 3.757A pdb=" N ALA A 689 " --> pdb=" O PRO A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 removed outlier: 4.254A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 30 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.589A pdb=" N TRP B 42 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'B' and resid 92 through 126 removed outlier: 3.841A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Proline residue: B 111 - end of helix Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.558A pdb=" N HIS B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 193 Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.578A pdb=" N VAL B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.545A pdb=" N ALA B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.751A pdb=" N SER B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.623A pdb=" N CYS B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.543A pdb=" N ASN B 364 " --> pdb=" O TYR B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 402 removed outlier: 4.110A pdb=" N LEU B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 393 - end of helix removed outlier: 3.880A pdb=" N LEU B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 451 removed outlier: 4.160A pdb=" N SER B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 425 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Proline residue: B 443 - end of helix Processing helix chain 'B' and resid 457 through 496 removed outlier: 3.637A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 533 Proline residue: B 511 - end of helix removed outlier: 3.774A pdb=" N ILE B 533 " --> pdb=" O VAL B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 547 removed outlier: 3.592A pdb=" N TYR B 542 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 591 through 612 Processing helix chain 'B' and resid 623 through 650 Processing helix chain 'B' and resid 655 through 683 Proline residue: B 663 - end of helix Proline residue: B 679 - end of helix removed outlier: 3.573A pdb=" N ARG B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 694 removed outlier: 3.757A pdb=" N ALA B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 711 removed outlier: 4.254A pdb=" N TYR B 708 " --> pdb=" O ASN B 704 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 710 " --> pdb=" O LYS B 706 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 240 removed outlier: 6.888A pdb=" N THR A 235 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 325 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN A 237 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 323 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 239 " --> pdb=" O MET A 321 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 207 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 235 through 240 removed outlier: 6.888A pdb=" N THR B 235 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE B 325 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN B 237 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA B 323 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL B 239 " --> pdb=" O MET B 321 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 207 " --> pdb=" O LEU B 350 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1896 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: 1.68 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1499 1.25 - 1.39: 3422 1.39 - 1.53: 6426 1.53 - 1.67: 472 1.67 - 1.81: 97 Bond restraints: 11916 Sorted by residual: bond pdb=" C LEU B 437 " pdb=" O LEU B 437 " ideal model delta sigma weight residual 1.236 1.521 -0.285 1.16e-02 7.43e+03 6.04e+02 bond pdb=" C LEU A 437 " pdb=" O LEU A 437 " ideal model delta sigma weight residual 1.236 1.521 -0.285 1.16e-02 7.43e+03 6.04e+02 bond pdb=" C ALA A 623 " pdb=" O ALA A 623 " ideal model delta sigma weight residual 1.236 1.546 -0.309 1.32e-02 5.74e+03 5.49e+02 bond pdb=" C ALA B 623 " pdb=" O ALA B 623 " ideal model delta sigma weight residual 1.236 1.546 -0.309 1.32e-02 5.74e+03 5.49e+02 bond pdb=" C ILE B 440 " pdb=" O ILE B 440 " ideal model delta sigma weight residual 1.237 1.495 -0.259 1.12e-02 7.97e+03 5.34e+02 ... (remaining 11911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.23: 15704 8.23 - 16.46: 448 16.46 - 24.69: 34 24.69 - 32.92: 7 32.92 - 41.15: 3 Bond angle restraints: 16196 Sorted by residual: angle pdb=" N GLU A 298 " pdb=" CA GLU A 298 " pdb=" C GLU A 298 " ideal model delta sigma weight residual 111.69 70.54 41.15 1.23e+00 6.61e-01 1.12e+03 angle pdb=" C ALA B 585 " pdb=" N PRO B 586 " pdb=" CA PRO B 586 " ideal model delta sigma weight residual 120.83 99.27 21.56 1.02e+00 9.61e-01 4.47e+02 angle pdb=" C ALA A 585 " pdb=" N PRO A 586 " pdb=" CA PRO A 586 " ideal model delta sigma weight residual 120.83 99.27 21.56 1.02e+00 9.61e-01 4.47e+02 angle pdb=" N ASP A 316 " pdb=" CA ASP A 316 " pdb=" C ASP A 316 " ideal model delta sigma weight residual 112.92 138.48 -25.56 1.23e+00 6.61e-01 4.32e+02 angle pdb=" N LYS A 81 " pdb=" CA LYS A 81 " pdb=" C LYS A 81 " ideal model delta sigma weight residual 113.21 135.17 -21.96 1.15e+00 7.56e-01 3.65e+02 ... (remaining 16191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5490 17.88 - 35.76: 850 35.76 - 53.64: 542 53.64 - 71.52: 157 71.52 - 89.40: 17 Dihedral angle restraints: 7056 sinusoidal: 2842 harmonic: 4214 Sorted by residual: 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 -159.94 37.34 0 2.50e+00 1.60e-01 2.23e+02 dihedral pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual 122.80 158.36 -35.56 0 2.50e+00 1.60e-01 2.02e+02 dihedral pdb=" C ASN A 568 " pdb=" N ASN A 568 " pdb=" CA ASN A 568 " pdb=" CB ASN A 568 " ideal model delta harmonic sigma weight residual -122.60 -153.57 30.97 0 2.50e+00 1.60e-01 1.53e+02 ... (remaining 7053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 1510 0.337 - 0.674: 273 0.674 - 1.012: 29 1.012 - 1.349: 5 1.349 - 1.686: 1 Chirality restraints: 1818 Sorted by residual: 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 0.82 1.69 2.00e-01 2.50e+01 7.10e+01 chirality pdb=" CA ASN A 568 " pdb=" N ASN A 568 " pdb=" C ASN A 568 " pdb=" CB ASN A 568 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" CA ASN B 568 " pdb=" N ASN B 568 " pdb=" C ASN B 568 " pdb=" CB ASN B 568 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.19e+01 ... (remaining 1815 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 240 " 0.055 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C CYS A 240 " -0.174 2.00e-02 2.50e+03 pdb=" O CYS A 240 " 0.064 2.00e-02 2.50e+03 pdb=" N ASN A 241 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 296 " 0.052 2.00e-02 2.50e+03 9.63e-02 9.27e+01 pdb=" C ILE A 296 " -0.167 2.00e-02 2.50e+03 pdb=" O ILE A 296 " 0.063 2.00e-02 2.50e+03 pdb=" N ALA A 297 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 499 " -0.046 2.00e-02 2.50e+03 8.53e-02 7.27e+01 pdb=" C PRO B 499 " 0.148 2.00e-02 2.50e+03 pdb=" O PRO B 499 " -0.052 2.00e-02 2.50e+03 pdb=" N ASN B 500 " -0.050 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 181 2.45 - 3.07: 8023 3.07 - 3.68: 17337 3.68 - 4.29: 25999 4.29 - 4.90: 43127 Nonbonded interactions: 94667 Sorted by model distance: nonbonded pdb=" N GLU A 298 " pdb=" N VAL A 299 " model vdw 1.842 2.560 nonbonded pdb=" O TYR A 295 " pdb=" N ALA A 297 " model vdw 1.958 3.120 nonbonded pdb=" N ARG B 198 " pdb=" O ARG B 198 " model vdw 2.125 2.496 nonbonded pdb=" N ARG A 198 " pdb=" O ARG A 198 " model vdw 2.125 2.496 nonbonded pdb=" C0B LPC B 801 " pdb=" C3 LPC B 801 " model vdw 2.133 3.088 ... (remaining 94662 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.530 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 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 : 0.033 0.370 11918 Z= 2.426 Angle : 3.219 41.152 16196 Z= 2.122 Chirality : 0.257 1.686 1818 Planarity : 0.022 0.189 2024 Dihedral : 23.949 89.397 4328 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 7.42 % Allowed : 14.78 % Favored : 77.80 % Rotamer: Outliers : 36.57 % Allowed : 16.18 % Favored : 47.25 % Cbeta Deviations : 12.98 % 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: -5.62 (0.16), residues: 1428 helix: -3.22 (0.12), residues: 900 sheet: -2.13 (0.68), residues: 44 loop : -4.65 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 463 TYR 0.035 0.004 TYR B 618 PHE 0.047 0.005 PHE B 624 TRP 0.038 0.005 TRP B 75 HIS 0.015 0.004 HIS B 236 Details of bonding type rmsd covalent geometry : bond 0.03261 (11916) covalent geometry : angle 3.21901 (16196) hydrogen bonds : bond 0.16807 ( 638) hydrogen bonds : angle 9.43256 ( 1896) Misc. bond : bond 0.13751 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 452 poor density : 183 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5523 (tttm) REVERT: A 76 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6853 (mtt) REVERT: A 115 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6737 (mt) REVERT: A 122 PRO cc_start: 0.6814 (OUTLIER) cc_final: 0.6109 (Cg_exo) REVERT: A 178 MET cc_start: 0.6288 (ttp) cc_final: 0.6080 (ttp) REVERT: A 205 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8250 (tp) REVERT: A 212 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5873 (t70) REVERT: A 278 LYS cc_start: 0.3059 (OUTLIER) cc_final: 0.1568 (ttpt) REVERT: A 301 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.5249 (ptmt) REVERT: A 370 VAL cc_start: 0.5164 (OUTLIER) cc_final: 0.4871 (m) REVERT: A 379 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6850 (mmp) REVERT: A 394 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.5982 (mp) REVERT: A 400 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 457 SER cc_start: 0.7703 (OUTLIER) cc_final: 0.7179 (p) REVERT: A 491 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.4473 (tp) REVERT: A 572 PRO cc_start: 0.7827 (OUTLIER) cc_final: 0.7416 (Cg_exo) REVERT: A 590 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.6226 (ttt) REVERT: A 659 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6686 (mt) REVERT: A 660 ILE cc_start: 0.6213 (OUTLIER) cc_final: 0.5967 (mp) REVERT: A 709 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8126 (mt) REVERT: B 5 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5521 (tttm) REVERT: B 76 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6854 (mtt) REVERT: B 115 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6737 (mt) REVERT: B 122 PRO cc_start: 0.6813 (OUTLIER) cc_final: 0.6111 (Cg_exo) REVERT: B 178 MET cc_start: 0.6292 (ttp) cc_final: 0.6079 (ttp) REVERT: B 205 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8255 (tp) REVERT: B 212 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5872 (t70) REVERT: B 278 LYS cc_start: 0.3081 (OUTLIER) cc_final: 0.1501 (ttpt) REVERT: B 294 HIS cc_start: 0.5879 (OUTLIER) cc_final: 0.5074 (m90) REVERT: B 370 VAL cc_start: 0.5163 (OUTLIER) cc_final: 0.4871 (m) REVERT: B 379 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6857 (mmp) REVERT: B 394 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.5986 (mp) REVERT: B 400 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 457 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7180 (p) REVERT: B 491 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.4464 (tp) REVERT: B 572 PRO cc_start: 0.7830 (OUTLIER) cc_final: 0.7418 (Cg_exo) REVERT: B 590 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6235 (ttt) REVERT: B 659 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6687 (mt) REVERT: B 660 ILE cc_start: 0.6210 (OUTLIER) cc_final: 0.5965 (mp) REVERT: B 709 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8127 (mt) outliers start: 452 outliers final: 134 residues processed: 560 average time/residue: 0.4069 time to fit residues: 250.1117 Evaluate side-chains 325 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 153 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 111 PRO Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 PRO Chi-restraints excluded: chain A residue 137 LYS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 503 PRO Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 546 ASN Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 572 PRO Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 111 PRO Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 PRO Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 250 SER 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 278 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 PRO Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 546 ASN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 572 PRO Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 GLN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 699 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 90 HIS A 124 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 490 GLN A 497 GLN A 500 ASN A 543 HIS A 568 ASN A 573 GLN A 575 GLN A 616 GLN A 687 GLN B 63 ASN B 90 HIS B 124 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN B 490 GLN B 500 ASN B 543 HIS B 568 ASN B 573 GLN B 575 GLN B 616 GLN B 687 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134620 restraints weight = 13303.912| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.47 r_work: 0.3550 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11918 Z= 0.249 Angle : 0.988 14.625 16196 Z= 0.521 Chirality : 0.056 0.343 1818 Planarity : 0.009 0.101 2024 Dihedral : 15.798 73.157 1980 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.32 % Favored : 86.62 % Rotamer: Outliers : 11.97 % Allowed : 24.84 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.84 (0.21), residues: 1428 helix: -0.48 (0.17), residues: 876 sheet: -3.52 (0.53), residues: 46 loop : -4.34 (0.22), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 36 TYR 0.022 0.002 TYR B 98 PHE 0.023 0.002 PHE B 136 TRP 0.027 0.002 TRP A 625 HIS 0.005 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00498 (11916) covalent geometry : angle 0.98782 (16196) hydrogen bonds : bond 0.09590 ( 638) hydrogen bonds : angle 5.89372 ( 1896) Misc. bond : bond 0.00387 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 173 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5665 (tptp) REVERT: A 71 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6787 (pptt) REVERT: A 137 LYS cc_start: 0.5420 (mtmm) cc_final: 0.5194 (mtmt) REVERT: A 212 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7429 (t70) REVERT: A 214 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.6165 (p0) REVERT: A 273 ILE cc_start: 0.5126 (OUTLIER) cc_final: 0.4828 (pp) REVERT: A 292 ILE cc_start: 0.0824 (OUTLIER) cc_final: 0.0444 (tt) REVERT: A 318 LYS cc_start: 0.7042 (tmtt) cc_final: 0.6700 (tmmt) REVERT: A 379 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6346 (mmp) REVERT: A 457 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7692 (p) REVERT: A 491 LEU cc_start: 0.2103 (OUTLIER) cc_final: 0.1417 (tt) REVERT: A 532 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6913 (mt-10) REVERT: A 535 MET cc_start: 0.7443 (mmm) cc_final: 0.7228 (mmp) REVERT: A 590 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7420 (ttp) REVERT: A 660 ILE cc_start: 0.6408 (mm) cc_final: 0.6155 (mt) REVERT: B 5 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5668 (tptp) REVERT: B 71 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6736 (pptt) REVERT: B 137 LYS cc_start: 0.5437 (mtmm) cc_final: 0.5209 (mtmt) REVERT: B 212 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7408 (t70) REVERT: B 214 ASP cc_start: 0.6493 (OUTLIER) cc_final: 0.6152 (p0) REVERT: B 256 GLN cc_start: 0.5228 (tp40) cc_final: 0.4824 (tm-30) REVERT: B 379 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6341 (mmp) REVERT: B 457 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 491 LEU cc_start: 0.2154 (OUTLIER) cc_final: 0.1527 (tt) REVERT: B 532 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6887 (mt-10) REVERT: B 535 MET cc_start: 0.7416 (mmm) cc_final: 0.7199 (mmp) REVERT: B 590 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7440 (ttp) outliers start: 148 outliers final: 55 residues processed: 293 average time/residue: 0.4386 time to fit residues: 140.7290 Evaluate side-chains 227 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 154 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 141 optimal weight: 0.0970 chunk 70 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 294 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.182150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129659 restraints weight = 12938.781| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.49 r_work: 0.3447 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11918 Z= 0.198 Angle : 0.856 11.448 16196 Z= 0.446 Chirality : 0.048 0.218 1818 Planarity : 0.008 0.087 2024 Dihedral : 12.449 65.224 1722 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.78 % Favored : 88.31 % Rotamer: Outliers : 8.41 % Allowed : 26.78 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -1.52 (0.22), residues: 1428 helix: 0.56 (0.18), residues: 890 sheet: -3.34 (0.55), residues: 46 loop : -3.87 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 556 TYR 0.021 0.001 TYR B 98 PHE 0.019 0.001 PHE B 33 TRP 0.020 0.001 TRP A 75 HIS 0.006 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00387 (11916) covalent geometry : angle 0.85580 (16196) hydrogen bonds : bond 0.07924 ( 638) hydrogen bonds : angle 5.32175 ( 1896) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 155 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5634 (tptp) REVERT: A 137 LYS cc_start: 0.5319 (mtmm) cc_final: 0.5074 (mtmt) REVERT: A 212 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7151 (t70) REVERT: A 214 ASP cc_start: 0.6416 (m-30) cc_final: 0.6057 (p0) REVERT: A 273 ILE cc_start: 0.5167 (OUTLIER) cc_final: 0.4963 (pp) REVERT: A 318 LYS cc_start: 0.6842 (tmtt) cc_final: 0.6444 (tmmt) REVERT: A 457 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7332 (p) REVERT: A 491 LEU cc_start: 0.1653 (OUTLIER) cc_final: 0.1073 (tt) REVERT: A 522 MET cc_start: 0.6112 (ttm) cc_final: 0.5891 (mtm) REVERT: A 532 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 590 MET cc_start: 0.7514 (ttt) cc_final: 0.7166 (ttp) REVERT: A 691 MET cc_start: 0.6871 (mtm) cc_final: 0.6583 (mtp) REVERT: A 697 ARG cc_start: 0.7644 (tpt170) cc_final: 0.6547 (mtm110) REVERT: B 5 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5608 (tptp) REVERT: B 137 LYS cc_start: 0.5332 (mtmm) cc_final: 0.5086 (mtmt) REVERT: B 212 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7138 (t70) REVERT: B 214 ASP cc_start: 0.6374 (m-30) cc_final: 0.6015 (p0) REVERT: B 256 GLN cc_start: 0.5032 (tp40) cc_final: 0.4678 (tm-30) REVERT: B 294 HIS cc_start: 0.5215 (OUTLIER) cc_final: 0.4685 (m-70) REVERT: B 304 LYS cc_start: 0.6059 (mmtt) cc_final: 0.5698 (mtmm) REVERT: B 457 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7310 (p) REVERT: B 491 LEU cc_start: 0.1910 (OUTLIER) cc_final: 0.1381 (tt) REVERT: B 522 MET cc_start: 0.6121 (ttm) cc_final: 0.5900 (mtm) REVERT: B 532 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7000 (mt-10) REVERT: B 590 MET cc_start: 0.7526 (ttt) cc_final: 0.7173 (ttp) REVERT: B 691 MET cc_start: 0.6872 (mtm) cc_final: 0.6588 (mtp) REVERT: B 697 ARG cc_start: 0.7638 (tpt170) cc_final: 0.6540 (mtm110) outliers start: 104 outliers final: 41 residues processed: 242 average time/residue: 0.4818 time to fit residues: 127.1820 Evaluate side-chains 193 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN B 74 HIS ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.182162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130659 restraints weight = 13644.618| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.53 r_work: 0.3509 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 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 : 0.004 0.068 11918 Z= 0.186 Angle : 0.782 10.879 16196 Z= 0.406 Chirality : 0.047 0.191 1818 Planarity : 0.007 0.073 2024 Dihedral : 10.672 61.954 1673 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.36 % Favored : 88.87 % Rotamer: Outliers : 9.14 % Allowed : 25.97 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.04 (0.23), residues: 1428 helix: 0.93 (0.18), residues: 896 sheet: -3.29 (0.55), residues: 46 loop : -3.68 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 556 TYR 0.016 0.001 TYR B 98 PHE 0.024 0.002 PHE A 33 TRP 0.018 0.001 TRP A 625 HIS 0.014 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00378 (11916) covalent geometry : angle 0.78178 (16196) hydrogen bonds : bond 0.07597 ( 638) hydrogen bonds : angle 5.12717 ( 1896) Misc. bond : bond 0.00325 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 144 time to evaluate : 0.307 Fit side-chains REVERT: A 60 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.3091 (ptm160) REVERT: A 137 LYS cc_start: 0.5794 (mtmm) cc_final: 0.5504 (mtmt) REVERT: A 212 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7191 (t70) REVERT: A 214 ASP cc_start: 0.6526 (m-30) cc_final: 0.6242 (p0) REVERT: A 318 LYS cc_start: 0.7035 (tmtt) cc_final: 0.6623 (ttmt) REVERT: A 390 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.4939 (t80) REVERT: A 491 LEU cc_start: 0.1554 (OUTLIER) cc_final: 0.0907 (tt) REVERT: A 522 MET cc_start: 0.6411 (ttm) cc_final: 0.6133 (mtm) REVERT: A 532 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 590 MET cc_start: 0.7594 (ttt) cc_final: 0.7302 (ttp) REVERT: A 642 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5809 (mp) REVERT: A 669 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.4090 (t80) REVERT: A 697 ARG cc_start: 0.7676 (tpt170) cc_final: 0.6569 (mtm110) REVERT: B 60 ARG cc_start: 0.3606 (OUTLIER) cc_final: 0.3094 (ptm160) REVERT: B 137 LYS cc_start: 0.5853 (mtmm) cc_final: 0.5562 (mtmt) REVERT: B 212 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7178 (t70) REVERT: B 214 ASP cc_start: 0.6542 (m-30) cc_final: 0.6267 (p0) REVERT: B 256 GLN cc_start: 0.5303 (tp40) cc_final: 0.4870 (tm-30) REVERT: B 294 HIS cc_start: 0.5348 (OUTLIER) cc_final: 0.4904 (m-70) REVERT: B 390 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.4951 (t80) REVERT: B 491 LEU cc_start: 0.1448 (OUTLIER) cc_final: 0.0866 (tt) REVERT: B 522 MET cc_start: 0.6419 (ttm) cc_final: 0.6138 (mtm) REVERT: B 532 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7069 (mt-10) REVERT: B 590 MET cc_start: 0.7590 (ttt) cc_final: 0.7298 (ttp) REVERT: B 642 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5818 (mp) REVERT: B 669 PHE cc_start: 0.5613 (OUTLIER) cc_final: 0.4102 (t80) REVERT: B 697 ARG cc_start: 0.7672 (tpt170) cc_final: 0.6563 (mtm110) outliers start: 113 outliers final: 42 residues processed: 241 average time/residue: 0.4689 time to fit residues: 123.7590 Evaluate side-chains 186 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 100 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 127 ASN B 263 GLN B 270 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.181891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130973 restraints weight = 13600.761| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.51 r_work: 0.3479 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11918 Z= 0.197 Angle : 0.799 10.894 16196 Z= 0.410 Chirality : 0.047 0.197 1818 Planarity : 0.007 0.074 2024 Dihedral : 9.983 59.663 1654 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.57 % Favored : 88.87 % Rotamer: Outliers : 7.69 % Allowed : 26.70 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.83 (0.23), residues: 1428 helix: 1.08 (0.18), residues: 896 sheet: -3.24 (0.55), residues: 46 loop : -3.57 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 556 TYR 0.015 0.001 TYR B 98 PHE 0.023 0.002 PHE B 33 TRP 0.020 0.001 TRP B 625 HIS 0.004 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00415 (11916) covalent geometry : angle 0.79899 (16196) hydrogen bonds : bond 0.07970 ( 638) hydrogen bonds : angle 5.09176 ( 1896) Misc. bond : bond 0.00226 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 130 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5970 (tttp) REVERT: A 85 ARG cc_start: 0.7445 (tpt90) cc_final: 0.7059 (tpp-160) REVERT: A 137 LYS cc_start: 0.5600 (mtmm) cc_final: 0.5369 (mtmt) REVERT: A 212 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7131 (t70) REVERT: A 214 ASP cc_start: 0.6504 (m-30) cc_final: 0.6214 (p0) REVERT: A 318 LYS cc_start: 0.7024 (tmtt) cc_final: 0.6566 (tmmt) REVERT: A 390 PHE cc_start: 0.5524 (OUTLIER) cc_final: 0.4907 (t80) REVERT: A 391 ILE cc_start: 0.4852 (OUTLIER) cc_final: 0.4630 (tt) REVERT: A 491 LEU cc_start: 0.1422 (OUTLIER) cc_final: 0.0777 (tt) REVERT: A 522 MET cc_start: 0.6616 (ttm) cc_final: 0.6359 (mtm) REVERT: A 532 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 642 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5728 (mp) REVERT: A 669 PHE cc_start: 0.5617 (OUTLIER) cc_final: 0.4065 (t80) REVERT: A 697 ARG cc_start: 0.7580 (tpt170) cc_final: 0.6471 (mtm110) REVERT: B 5 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5962 (tttp) REVERT: B 60 ARG cc_start: 0.3766 (OUTLIER) cc_final: 0.3257 (ptm160) REVERT: B 85 ARG cc_start: 0.7436 (tpt90) cc_final: 0.7046 (tpp-160) REVERT: B 137 LYS cc_start: 0.5667 (mtmm) cc_final: 0.5430 (mtmt) REVERT: B 212 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7111 (t70) REVERT: B 214 ASP cc_start: 0.6511 (m-30) cc_final: 0.6219 (p0) REVERT: B 256 GLN cc_start: 0.5457 (tp40) cc_final: 0.4989 (tm-30) REVERT: B 294 HIS cc_start: 0.5240 (OUTLIER) cc_final: 0.4556 (m-70) REVERT: B 390 PHE cc_start: 0.5505 (OUTLIER) cc_final: 0.4882 (t80) REVERT: B 391 ILE cc_start: 0.4824 (OUTLIER) cc_final: 0.4601 (tt) REVERT: B 491 LEU cc_start: 0.1455 (OUTLIER) cc_final: 0.0891 (tt) REVERT: B 522 MET cc_start: 0.6630 (ttm) cc_final: 0.6362 (mtm) REVERT: B 532 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 642 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5747 (mp) REVERT: B 669 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.4083 (t80) REVERT: B 697 ARG cc_start: 0.7586 (tpt170) cc_final: 0.6476 (mtm110) outliers start: 95 outliers final: 44 residues processed: 213 average time/residue: 0.4675 time to fit residues: 109.2892 Evaluate side-chains 183 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 123 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 568 ASN Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 90 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 88 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.182530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130956 restraints weight = 13717.133| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.56 r_work: 0.3515 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11918 Z= 0.171 Angle : 0.742 10.103 16196 Z= 0.381 Chirality : 0.045 0.188 1818 Planarity : 0.007 0.080 2024 Dihedral : 9.562 59.668 1651 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.73 % Favored : 89.71 % Rotamer: Outliers : 6.72 % Allowed : 28.07 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.50 (0.23), residues: 1428 helix: 1.36 (0.18), residues: 898 sheet: -3.32 (0.53), residues: 46 loop : -3.49 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 556 TYR 0.015 0.001 TYR B 98 PHE 0.027 0.001 PHE B 33 TRP 0.019 0.001 TRP B 625 HIS 0.004 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00346 (11916) covalent geometry : angle 0.74232 (16196) hydrogen bonds : bond 0.06972 ( 638) hydrogen bonds : angle 4.93198 ( 1896) Misc. bond : bond 0.00356 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 134 time to evaluate : 0.444 Fit side-chains REVERT: A 5 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5901 (tptp) REVERT: A 60 ARG cc_start: 0.3820 (OUTLIER) cc_final: 0.3425 (ptm160) REVERT: A 85 ARG cc_start: 0.7317 (tpt90) cc_final: 0.6989 (tpp-160) REVERT: A 137 LYS cc_start: 0.5743 (mtmm) cc_final: 0.5517 (mtmt) REVERT: A 212 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7158 (t70) REVERT: A 214 ASP cc_start: 0.6843 (m-30) cc_final: 0.6618 (p0) REVERT: A 318 LYS cc_start: 0.7055 (tmtt) cc_final: 0.6610 (ttmt) REVERT: A 390 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.4880 (t80) REVERT: A 457 SER cc_start: 0.7821 (m) cc_final: 0.7311 (p) REVERT: A 491 LEU cc_start: 0.1198 (OUTLIER) cc_final: 0.0586 (tt) REVERT: A 532 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 537 LYS cc_start: 0.6542 (tttp) cc_final: 0.6258 (tttm) REVERT: A 669 PHE cc_start: 0.5542 (OUTLIER) cc_final: 0.3953 (t80) REVERT: A 697 ARG cc_start: 0.7524 (tpt170) cc_final: 0.6379 (mtm110) REVERT: B 5 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5900 (tptp) REVERT: B 60 ARG cc_start: 0.3815 (OUTLIER) cc_final: 0.3422 (ptm160) REVERT: B 85 ARG cc_start: 0.7325 (tpt90) cc_final: 0.6992 (tpp-160) REVERT: B 137 LYS cc_start: 0.5767 (mtmm) cc_final: 0.5538 (mtmt) REVERT: B 212 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7147 (t70) REVERT: B 214 ASP cc_start: 0.6817 (m-30) cc_final: 0.6589 (p0) REVERT: B 256 GLN cc_start: 0.5227 (tp40) cc_final: 0.4813 (tm-30) REVERT: B 260 ASP cc_start: 0.3768 (p0) cc_final: 0.3394 (p0) REVERT: B 390 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.4859 (t80) REVERT: B 491 LEU cc_start: 0.1240 (OUTLIER) cc_final: 0.0702 (tt) REVERT: B 522 MET cc_start: 0.6400 (ttm) cc_final: 0.6190 (ttp) REVERT: B 532 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7020 (mt-10) REVERT: B 669 PHE cc_start: 0.5566 (OUTLIER) cc_final: 0.3970 (t80) REVERT: B 697 ARG cc_start: 0.7514 (tpt170) cc_final: 0.6370 (mtm110) outliers start: 83 outliers final: 35 residues processed: 203 average time/residue: 0.4504 time to fit residues: 100.0091 Evaluate side-chains 170 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A 710 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.181120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129448 restraints weight = 13631.411| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.54 r_work: 0.3498 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11918 Z= 0.192 Angle : 0.820 13.762 16196 Z= 0.424 Chirality : 0.048 0.447 1818 Planarity : 0.007 0.071 2024 Dihedral : 9.401 60.552 1644 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.38 % Favored : 90.06 % Rotamer: Outliers : 5.26 % Allowed : 29.69 % Favored : 65.05 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.42 (0.23), residues: 1428 helix: 1.44 (0.18), residues: 896 sheet: -3.27 (0.53), residues: 46 loop : -3.45 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 556 TYR 0.013 0.001 TYR B 98 PHE 0.026 0.001 PHE A 33 TRP 0.018 0.001 TRP B 625 HIS 0.004 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00406 (11916) covalent geometry : angle 0.82050 (16196) hydrogen bonds : bond 0.07367 ( 638) hydrogen bonds : angle 4.96171 ( 1896) Misc. bond : bond 0.00985 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 130 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5951 (tttp) REVERT: A 60 ARG cc_start: 0.3844 (OUTLIER) cc_final: 0.3469 (ptm160) REVERT: A 137 LYS cc_start: 0.5759 (mtmm) cc_final: 0.5532 (mtmt) REVERT: A 212 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7248 (t70) REVERT: A 260 ASP cc_start: 0.4286 (p0) cc_final: 0.3746 (p0) REVERT: A 318 LYS cc_start: 0.7095 (tmtt) cc_final: 0.6647 (ttmt) REVERT: A 390 PHE cc_start: 0.5495 (OUTLIER) cc_final: 0.4908 (t80) REVERT: A 457 SER cc_start: 0.7856 (m) cc_final: 0.7348 (p) REVERT: A 491 LEU cc_start: 0.0989 (OUTLIER) cc_final: 0.0394 (tt) REVERT: A 532 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7043 (mt-10) REVERT: A 537 LYS cc_start: 0.6537 (tttp) cc_final: 0.6242 (tttm) REVERT: A 669 PHE cc_start: 0.5543 (OUTLIER) cc_final: 0.3960 (t80) REVERT: A 676 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.6110 (tmt170) REVERT: B 60 ARG cc_start: 0.3841 (OUTLIER) cc_final: 0.3467 (ptm160) REVERT: B 137 LYS cc_start: 0.5781 (mtmm) cc_final: 0.5542 (mtmt) REVERT: B 256 GLN cc_start: 0.5239 (tp40) cc_final: 0.4829 (tm-30) REVERT: B 260 ASP cc_start: 0.3758 (p0) cc_final: 0.3375 (p0) REVERT: B 294 HIS cc_start: 0.5167 (OUTLIER) cc_final: 0.4924 (m-70) REVERT: B 390 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.4899 (t80) REVERT: B 491 LEU cc_start: 0.1202 (OUTLIER) cc_final: 0.0660 (tt) REVERT: B 522 MET cc_start: 0.6421 (ttm) cc_final: 0.6202 (ttp) REVERT: B 532 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7061 (mt-10) REVERT: B 537 LYS cc_start: 0.6603 (tttp) cc_final: 0.6265 (tttm) REVERT: B 669 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.3974 (t80) REVERT: B 676 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.6107 (tmt170) outliers start: 65 outliers final: 38 residues processed: 185 average time/residue: 0.4477 time to fit residues: 90.6027 Evaluate side-chains 176 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 chunk 83 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 35 optimal weight: 0.0470 chunk 78 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.188920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137456 restraints weight = 13670.039| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.56 r_work: 0.3593 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11918 Z= 0.155 Angle : 0.756 14.017 16196 Z= 0.384 Chirality : 0.046 0.323 1818 Planarity : 0.006 0.064 2024 Dihedral : 8.969 68.563 1644 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.59 % Favored : 89.99 % Rotamer: Outliers : 4.45 % Allowed : 30.91 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.19 (0.24), residues: 1428 helix: 1.62 (0.18), residues: 906 sheet: -3.18 (0.55), residues: 46 loop : -3.49 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 556 TYR 0.016 0.001 TYR B 98 PHE 0.029 0.001 PHE A 396 TRP 0.019 0.001 TRP A 625 HIS 0.009 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00317 (11916) covalent geometry : angle 0.75577 (16196) hydrogen bonds : bond 0.05718 ( 638) hydrogen bonds : angle 4.67200 ( 1896) Misc. bond : bond 0.00639 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.3891 (OUTLIER) cc_final: 0.3354 (ptp-170) REVERT: A 212 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7093 (t70) REVERT: A 214 ASP cc_start: 0.6333 (p0) cc_final: 0.5847 (p0) REVERT: A 260 ASP cc_start: 0.4255 (p0) cc_final: 0.3779 (p0) REVERT: A 390 PHE cc_start: 0.5534 (OUTLIER) cc_final: 0.4881 (t80) REVERT: A 491 LEU cc_start: 0.1259 (OUTLIER) cc_final: 0.0791 (tt) REVERT: A 537 LYS cc_start: 0.6647 (tttp) cc_final: 0.6248 (tttm) REVERT: A 669 PHE cc_start: 0.5516 (OUTLIER) cc_final: 0.3921 (t80) REVERT: A 697 ARG cc_start: 0.7500 (tpt170) cc_final: 0.6115 (mtm110) REVERT: B 60 ARG cc_start: 0.3841 (OUTLIER) cc_final: 0.3316 (ptp-170) REVERT: B 212 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7094 (t70) REVERT: B 214 ASP cc_start: 0.6318 (p0) cc_final: 0.5815 (p0) REVERT: B 256 GLN cc_start: 0.5106 (tp40) cc_final: 0.4749 (tm-30) REVERT: B 294 HIS cc_start: 0.5036 (OUTLIER) cc_final: 0.4760 (m-70) REVERT: B 318 LYS cc_start: 0.7535 (tmtt) cc_final: 0.7119 (tmmt) REVERT: B 390 PHE cc_start: 0.5515 (OUTLIER) cc_final: 0.4871 (t80) REVERT: B 491 LEU cc_start: 0.1230 (OUTLIER) cc_final: 0.0744 (tt) REVERT: B 537 LYS cc_start: 0.6644 (tttp) cc_final: 0.6248 (tttm) REVERT: B 669 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.3940 (t80) REVERT: B 697 ARG cc_start: 0.7498 (tpt170) cc_final: 0.6111 (mtm110) outliers start: 55 outliers final: 26 residues processed: 192 average time/residue: 0.4494 time to fit residues: 94.2783 Evaluate side-chains 171 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 140 optimal weight: 0.0030 chunk 23 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.184983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.132692 restraints weight = 13614.544| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.56 r_work: 0.3543 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11918 Z= 0.166 Angle : 0.764 12.310 16196 Z= 0.390 Chirality : 0.046 0.300 1818 Planarity : 0.006 0.066 2024 Dihedral : 8.752 66.994 1640 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.38 % Favored : 90.34 % Rotamer: Outliers : 3.64 % Allowed : 32.69 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.14 (0.24), residues: 1428 helix: 1.61 (0.18), residues: 908 sheet: -3.21 (0.54), residues: 46 loop : -3.37 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 556 TYR 0.008 0.001 TYR A 98 PHE 0.027 0.001 PHE B 33 TRP 0.016 0.001 TRP A 625 HIS 0.004 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00345 (11916) covalent geometry : angle 0.76420 (16196) hydrogen bonds : bond 0.06352 ( 638) hydrogen bonds : angle 4.73198 ( 1896) Misc. bond : bond 0.00648 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.3944 (OUTLIER) cc_final: 0.3425 (ptp-170) REVERT: A 212 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7033 (t70) REVERT: A 214 ASP cc_start: 0.6361 (p0) cc_final: 0.5843 (p0) REVERT: A 247 ASP cc_start: 0.6529 (m-30) cc_final: 0.6324 (m-30) REVERT: A 260 ASP cc_start: 0.4209 (p0) cc_final: 0.3751 (p0) REVERT: A 304 LYS cc_start: 0.6400 (mtpp) cc_final: 0.6149 (mtmm) REVERT: A 390 PHE cc_start: 0.5570 (OUTLIER) cc_final: 0.4956 (t80) REVERT: A 396 PHE cc_start: 0.6187 (t80) cc_final: 0.5886 (t80) REVERT: A 457 SER cc_start: 0.7708 (m) cc_final: 0.7203 (p) REVERT: A 491 LEU cc_start: 0.1126 (OUTLIER) cc_final: 0.0631 (tt) REVERT: A 537 LYS cc_start: 0.6743 (tttp) cc_final: 0.6300 (tttt) REVERT: A 669 PHE cc_start: 0.5579 (OUTLIER) cc_final: 0.3991 (t80) REVERT: A 676 ARG cc_start: 0.6314 (tmt170) cc_final: 0.6102 (tmt170) REVERT: A 697 ARG cc_start: 0.7509 (tpt170) cc_final: 0.6077 (mtm110) REVERT: B 60 ARG cc_start: 0.3943 (OUTLIER) cc_final: 0.3423 (ptp-170) REVERT: B 212 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7073 (t70) REVERT: B 214 ASP cc_start: 0.6317 (p0) cc_final: 0.5777 (p0) REVERT: B 256 GLN cc_start: 0.5151 (tp40) cc_final: 0.4827 (tm-30) REVERT: B 295 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5079 (m-80) REVERT: B 318 LYS cc_start: 0.7583 (tmtt) cc_final: 0.7159 (tmmt) REVERT: B 390 PHE cc_start: 0.5524 (OUTLIER) cc_final: 0.4912 (t80) REVERT: B 491 LEU cc_start: 0.1203 (OUTLIER) cc_final: 0.0760 (tt) REVERT: B 532 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 537 LYS cc_start: 0.6731 (tttp) cc_final: 0.6281 (tttt) REVERT: B 669 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.4004 (t80) REVERT: B 676 ARG cc_start: 0.6314 (tmt170) cc_final: 0.6101 (tmt170) REVERT: B 697 ARG cc_start: 0.7503 (tpt170) cc_final: 0.6070 (mtm110) outliers start: 45 outliers final: 27 residues processed: 174 average time/residue: 0.4693 time to fit residues: 89.0391 Evaluate side-chains 169 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 89 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 0.0060 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 127 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.185211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132931 restraints weight = 13663.490| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.57 r_work: 0.3545 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11918 Z= 0.165 Angle : 0.759 11.487 16196 Z= 0.387 Chirality : 0.046 0.286 1818 Planarity : 0.006 0.067 2024 Dihedral : 8.374 66.572 1634 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.80 % Favored : 90.06 % Rotamer: Outliers : 3.56 % Allowed : 33.01 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.13 (0.24), residues: 1428 helix: 1.59 (0.18), residues: 916 sheet: -3.18 (0.54), residues: 46 loop : -3.39 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 556 TYR 0.008 0.001 TYR B 470 PHE 0.029 0.001 PHE A 33 TRP 0.017 0.001 TRP A 625 HIS 0.006 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00343 (11916) covalent geometry : angle 0.75913 (16196) hydrogen bonds : bond 0.06318 ( 638) hydrogen bonds : angle 4.73624 ( 1896) Misc. bond : bond 0.00597 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.3860 (OUTLIER) cc_final: 0.3458 (ptp-170) REVERT: A 212 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7024 (t70) REVERT: A 214 ASP cc_start: 0.6369 (p0) cc_final: 0.5871 (p0) REVERT: A 247 ASP cc_start: 0.6484 (m-30) cc_final: 0.6278 (m-30) REVERT: A 260 ASP cc_start: 0.4132 (p0) cc_final: 0.3709 (p0) REVERT: A 295 TYR cc_start: 0.5334 (OUTLIER) cc_final: 0.4478 (m-80) REVERT: A 304 LYS cc_start: 0.6401 (mtpp) cc_final: 0.6136 (mtmm) REVERT: A 318 LYS cc_start: 0.7118 (tmmt) cc_final: 0.6626 (ttmt) REVERT: A 390 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.5003 (t80) REVERT: A 396 PHE cc_start: 0.6281 (t80) cc_final: 0.5986 (t80) REVERT: A 457 SER cc_start: 0.7691 (m) cc_final: 0.7191 (p) REVERT: A 491 LEU cc_start: 0.1091 (OUTLIER) cc_final: 0.0592 (tt) REVERT: A 532 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7142 (mt-10) REVERT: A 537 LYS cc_start: 0.6761 (tttp) cc_final: 0.6344 (tttm) REVERT: A 669 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.3982 (t80) REVERT: A 697 ARG cc_start: 0.7495 (tpt170) cc_final: 0.6095 (mtm110) REVERT: B 60 ARG cc_start: 0.3861 (OUTLIER) cc_final: 0.3458 (ptp-170) REVERT: B 212 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7017 (t70) REVERT: B 214 ASP cc_start: 0.6321 (p0) cc_final: 0.5801 (p0) REVERT: B 256 GLN cc_start: 0.5155 (tp40) cc_final: 0.4864 (tm-30) REVERT: B 294 HIS cc_start: 0.4600 (OUTLIER) cc_final: 0.4175 (m-70) REVERT: B 318 LYS cc_start: 0.7550 (tmtt) cc_final: 0.7105 (tmmt) REVERT: B 390 PHE cc_start: 0.5504 (OUTLIER) cc_final: 0.4962 (t80) REVERT: B 491 LEU cc_start: 0.1159 (OUTLIER) cc_final: 0.0734 (tt) REVERT: B 532 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7131 (mt-10) REVERT: B 537 LYS cc_start: 0.6753 (tttp) cc_final: 0.6324 (tttm) REVERT: B 669 PHE cc_start: 0.5591 (OUTLIER) cc_final: 0.3992 (t80) REVERT: B 697 ARG cc_start: 0.7478 (tpt170) cc_final: 0.6076 (mtm110) outliers start: 44 outliers final: 26 residues processed: 172 average time/residue: 0.4974 time to fit residues: 92.9507 Evaluate side-chains 168 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 556 ARG Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 556 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 8 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 35 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.184410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131802 restraints weight = 13608.424| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.57 r_work: 0.3529 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11918 Z= 0.169 Angle : 0.755 10.841 16196 Z= 0.386 Chirality : 0.046 0.269 1818 Planarity : 0.006 0.068 2024 Dihedral : 8.292 68.789 1634 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.66 % Favored : 90.06 % Rotamer: Outliers : 3.32 % Allowed : 33.50 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.13 (0.24), residues: 1428 helix: 1.60 (0.18), residues: 916 sheet: -3.09 (0.54), residues: 46 loop : -3.43 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.008 0.001 TYR A 470 PHE 0.028 0.001 PHE B 33 TRP 0.017 0.001 TRP A 625 HIS 0.005 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00352 (11916) covalent geometry : angle 0.75520 (16196) hydrogen bonds : bond 0.06584 ( 638) hydrogen bonds : angle 4.77862 ( 1896) Misc. bond : bond 0.00568 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4633.19 seconds wall clock time: 79 minutes 22.75 seconds (4762.75 seconds total)