Starting phenix.real_space_refine on Tue Jul 29 22:37:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grn_34209/07_2025/8grn_34209_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grn_34209/07_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_34209/07_2025/8grn_34209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grn_34209/07_2025/8grn_34209.map" model { file = "/net/cci-nas-00/data/ceres_data/8grn_34209/07_2025/8grn_34209_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grn_34209/07_2025/8grn_34209_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.33, per 1000 atoms: 0.72 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.99 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: 3.16 Time building geometry restraints manager: 3.56 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.090 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.005 TRP B 75 HIS 0.015 0.004 HIS B 236 PHE 0.047 0.005 PHE B 624 TYR 0.035 0.004 TYR B 618 ARG 0.006 0.001 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.16807 ( 638) hydrogen bonds : angle 9.43256 ( 1896) covalent geometry : bond 0.03261 (11916) covalent geometry : angle 3.21901 (16196) 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 : 1.320 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: 0.9507 time to fit residues: 585.0724 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 : 1.159 ------------------------------------------------------------------------------- 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 119 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 90 HIS ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 490 GLN A 500 ASN A 543 HIS A 546 ASN 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 476 ASN B 490 GLN B 500 ASN B 543 HIS B 546 ASN 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 = 0.4210 r_free = 0.4210 target = 0.189567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140259 restraints weight = 13253.812| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.51 r_work: 0.3579 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11918 Z= 0.238 Angle : 0.977 14.814 16196 Z= 0.514 Chirality : 0.055 0.337 1818 Planarity : 0.009 0.100 2024 Dihedral : 15.730 71.861 1980 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.98 % Allowed : 11.97 % Favored : 87.04 % Rotamer: Outliers : 11.49 % Allowed : 25.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.21), residues: 1428 helix: -0.48 (0.17), residues: 876 sheet: -3.56 (0.53), residues: 46 loop : -4.31 (0.22), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 625 HIS 0.006 0.001 HIS B 715 PHE 0.023 0.002 PHE B 136 TYR 0.023 0.002 TYR A 98 ARG 0.015 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.09168 ( 638) hydrogen bonds : angle 5.86567 ( 1896) covalent geometry : bond 0.00476 (11916) covalent geometry : angle 0.97713 (16196) Misc. bond : bond 0.00237 ( 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 317 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 175 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5657 (tptp) REVERT: A 137 LYS cc_start: 0.5446 (mtmm) cc_final: 0.5151 (mtmt) REVERT: A 212 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7380 (t70) REVERT: A 214 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6161 (p0) REVERT: A 273 ILE cc_start: 0.5192 (OUTLIER) cc_final: 0.4914 (pp) REVERT: A 292 ILE cc_start: 0.1090 (OUTLIER) cc_final: 0.0779 (tt) REVERT: A 318 LYS cc_start: 0.7028 (tmtt) cc_final: 0.6692 (tmmt) REVERT: A 379 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6320 (mmp) REVERT: A 457 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7650 (p) REVERT: A 491 LEU cc_start: 0.2128 (OUTLIER) cc_final: 0.1472 (tt) REVERT: A 532 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7127 (mt-10) REVERT: A 590 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7403 (ttp) REVERT: B 5 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5659 (tptp) REVERT: B 137 LYS cc_start: 0.5463 (mtmm) cc_final: 0.5222 (mtmt) REVERT: B 212 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7309 (t70) REVERT: B 214 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6147 (p0) REVERT: B 256 GLN cc_start: 0.5196 (tp40) cc_final: 0.4751 (tm-30) REVERT: B 304 LYS cc_start: 0.6252 (mmmm) cc_final: 0.5973 (mtmm) REVERT: B 379 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6307 (mmp) REVERT: B 457 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7644 (p) REVERT: B 491 LEU cc_start: 0.2217 (OUTLIER) cc_final: 0.1626 (tt) REVERT: B 532 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7105 (mt-10) REVERT: B 590 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7424 (ttp) outliers start: 142 outliers final: 48 residues processed: 290 average time/residue: 1.5717 time to fit residues: 501.1748 Evaluate side-chains 216 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 152 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 68 SER 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 214 ASP Chi-restraints excluded: chain A residue 250 SER 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 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 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 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 68 SER 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 214 ASP Chi-restraints excluded: chain B residue 258 TRP 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 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 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 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** B 74 HIS ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 398 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.173899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120771 restraints weight = 12912.741| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.46 r_work: 0.3340 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 11918 Z= 0.256 Angle : 0.931 14.198 16196 Z= 0.488 Chirality : 0.052 0.242 1818 Planarity : 0.008 0.084 2024 Dihedral : 12.384 63.983 1706 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.84 % Allowed : 11.34 % Favored : 87.82 % Rotamer: Outliers : 9.39 % Allowed : 26.46 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.22), residues: 1428 helix: 0.35 (0.18), residues: 890 sheet: -3.31 (0.55), residues: 46 loop : -3.96 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 75 HIS 0.006 0.001 HIS A 715 PHE 0.019 0.002 PHE B 624 TYR 0.019 0.002 TYR B 98 ARG 0.015 0.001 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.09823 ( 638) hydrogen bonds : angle 5.56893 ( 1896) covalent geometry : bond 0.00547 (11916) covalent geometry : angle 0.93108 (16196) Misc. bond : bond 0.00298 ( 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 264 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 148 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5769 (tptp) REVERT: A 71 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6720 (pptt) REVERT: A 137 LYS cc_start: 0.5268 (mtmm) cc_final: 0.5037 (mtmt) REVERT: A 212 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7136 (t70) REVERT: A 214 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6088 (p0) REVERT: A 292 ILE cc_start: 0.1038 (OUTLIER) cc_final: 0.0792 (tt) REVERT: A 318 LYS cc_start: 0.6956 (tmtt) cc_final: 0.6559 (tmmt) REVERT: A 376 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5647 (mtt180) REVERT: A 379 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.6103 (mmp) REVERT: A 439 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5783 (mt) REVERT: A 457 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7372 (p) REVERT: A 491 LEU cc_start: 0.1546 (OUTLIER) cc_final: 0.0851 (tt) REVERT: A 522 MET cc_start: 0.6216 (ttm) cc_final: 0.5995 (mtm) REVERT: A 532 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7056 (mt-10) REVERT: A 590 MET cc_start: 0.7650 (ttt) cc_final: 0.7269 (ttp) REVERT: A 697 ARG cc_start: 0.7718 (tpt170) cc_final: 0.6632 (mtm110) REVERT: B 5 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5756 (tptp) REVERT: B 71 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6713 (pptt) REVERT: B 137 LYS cc_start: 0.5343 (mtmm) cc_final: 0.5108 (mtmt) REVERT: B 212 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7022 (t70) REVERT: B 214 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.6062 (p0) REVERT: B 256 GLN cc_start: 0.5046 (tp40) cc_final: 0.4620 (tm-30) REVERT: B 294 HIS cc_start: 0.5378 (OUTLIER) cc_final: 0.4907 (m-70) REVERT: B 304 LYS cc_start: 0.6141 (mmmm) cc_final: 0.5819 (mtmm) REVERT: B 376 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5631 (mtt180) REVERT: B 379 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.6079 (mmp) REVERT: B 439 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5771 (mt) REVERT: B 457 SER cc_start: 0.8019 (OUTLIER) cc_final: 0.7348 (p) REVERT: B 491 LEU cc_start: 0.1760 (OUTLIER) cc_final: 0.1158 (tt) REVERT: B 522 MET cc_start: 0.6224 (ttm) cc_final: 0.6002 (mtm) REVERT: B 532 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7065 (mt-10) REVERT: B 590 MET cc_start: 0.7645 (ttt) cc_final: 0.7263 (ttp) REVERT: B 697 ARG cc_start: 0.7714 (tpt170) cc_final: 0.6629 (mtm110) outliers start: 116 outliers final: 50 residues processed: 244 average time/residue: 1.2541 time to fit residues: 333.6717 Evaluate side-chains 209 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 139 time to evaluate : 2.187 ------------------------------------------------------------------------------- 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 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 235 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 284 LEU 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 313 VAL Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 422 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 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 550 VAL 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 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 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE 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 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 301 LYS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 422 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 491 LEU Chi-restraints excluded: chain B residue 492 ASN 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 582 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 20 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.187211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137030 restraints weight = 13389.485| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.44 r_work: 0.3584 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11918 Z= 0.197 Angle : 0.812 11.043 16196 Z= 0.423 Chirality : 0.047 0.219 1818 Planarity : 0.008 0.074 2024 Dihedral : 11.234 61.976 1680 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.43 % Favored : 88.80 % Rotamer: Outliers : 9.71 % Allowed : 25.89 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1428 helix: 0.72 (0.18), residues: 896 sheet: -3.23 (0.55), residues: 46 loop : -3.77 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 625 HIS 0.005 0.001 HIS A 715 PHE 0.020 0.001 PHE A 136 TYR 0.018 0.001 TYR B 542 ARG 0.009 0.001 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.08074 ( 638) hydrogen bonds : angle 5.25561 ( 1896) covalent geometry : bond 0.00400 (11916) covalent geometry : angle 0.81157 (16196) Misc. bond : bond 0.00287 ( 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 262 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 142 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5904 (tptp) REVERT: A 33 PHE cc_start: 0.6796 (p90) cc_final: 0.6483 (p90) REVERT: A 36 ARG cc_start: 0.5713 (OUTLIER) cc_final: 0.5269 (ptp-110) REVERT: A 137 LYS cc_start: 0.5541 (mtmm) cc_final: 0.5324 (mtmt) REVERT: A 212 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7268 (t70) REVERT: A 214 ASP cc_start: 0.6553 (m-30) cc_final: 0.6279 (p0) REVERT: A 318 LYS cc_start: 0.6987 (tmtt) cc_final: 0.6572 (ttmt) REVERT: A 390 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4918 (t80) REVERT: A 457 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7481 (p) REVERT: A 491 LEU cc_start: 0.1605 (OUTLIER) cc_final: 0.0948 (tt) REVERT: A 522 MET cc_start: 0.6526 (ttm) cc_final: 0.6274 (mtm) REVERT: A 535 MET cc_start: 0.7322 (mmm) cc_final: 0.6295 (mtm) REVERT: A 669 PHE cc_start: 0.5485 (OUTLIER) cc_final: 0.4002 (t80) REVERT: A 697 ARG cc_start: 0.7808 (tpt170) cc_final: 0.6704 (mtm110) REVERT: B 5 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5920 (tptp) REVERT: B 33 PHE cc_start: 0.6792 (p90) cc_final: 0.6482 (p90) REVERT: B 36 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.5260 (ptp-110) REVERT: B 137 LYS cc_start: 0.5608 (mtmm) cc_final: 0.5388 (mtmt) REVERT: B 212 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7227 (t70) REVERT: B 214 ASP cc_start: 0.6793 (m-30) cc_final: 0.6585 (p0) REVERT: B 256 GLN cc_start: 0.5247 (tp40) cc_final: 0.4818 (tm-30) REVERT: B 294 HIS cc_start: 0.5368 (OUTLIER) cc_final: 0.4948 (m-70) REVERT: B 304 LYS cc_start: 0.6378 (mmmm) cc_final: 0.6023 (mtmm) REVERT: B 311 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: B 369 TYR cc_start: 0.4461 (OUTLIER) cc_final: 0.4248 (m-80) REVERT: B 390 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.4892 (t80) REVERT: B 491 LEU cc_start: 0.1661 (OUTLIER) cc_final: 0.1078 (tt) REVERT: B 522 MET cc_start: 0.6514 (ttm) cc_final: 0.6261 (mtm) REVERT: B 535 MET cc_start: 0.7325 (mmm) cc_final: 0.6286 (mtm) REVERT: B 642 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5705 (mp) REVERT: B 669 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.4001 (t80) REVERT: B 697 ARG cc_start: 0.7829 (tpt170) cc_final: 0.6720 (mtm110) outliers start: 120 outliers final: 45 residues processed: 243 average time/residue: 1.2012 time to fit residues: 319.9876 Evaluate side-chains 194 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 132 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 36 ARG 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 212 ASP Chi-restraints excluded: chain A residue 235 THR 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 422 ILE 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 519 THR Chi-restraints excluded: chain A residue 541 ILE 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 5 LYS Chi-restraints excluded: chain B residue 36 ARG 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 311 GLU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 422 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 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 541 ILE 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 95 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 263 GLN B 127 ASN B 263 GLN ** B 294 HIS ** 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 = 0.4135 r_free = 0.4135 target = 0.184648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134154 restraints weight = 13298.105| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.55 r_work: 0.3528 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11918 Z= 0.175 Angle : 0.771 10.784 16196 Z= 0.394 Chirality : 0.046 0.199 1818 Planarity : 0.007 0.074 2024 Dihedral : 10.118 59.610 1659 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.87 % Favored : 89.50 % Rotamer: Outliers : 6.47 % Allowed : 28.48 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1428 helix: 1.09 (0.18), residues: 898 sheet: -3.27 (0.54), residues: 46 loop : -3.57 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 625 HIS 0.005 0.001 HIS A 715 PHE 0.022 0.001 PHE A 136 TYR 0.016 0.001 TYR B 98 ARG 0.017 0.001 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.07037 ( 638) hydrogen bonds : angle 5.02702 ( 1896) covalent geometry : bond 0.00352 (11916) covalent geometry : angle 0.77061 (16196) Misc. bond : bond 0.00013 ( 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 223 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 143 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 60 ARG cc_start: 0.3853 (OUTLIER) cc_final: 0.3343 (ptm160) REVERT: A 85 ARG cc_start: 0.7315 (mmm160) cc_final: 0.6671 (tpt90) REVERT: A 137 LYS cc_start: 0.5679 (mtmm) cc_final: 0.5422 (mtmt) REVERT: A 212 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7121 (t70) REVERT: A 214 ASP cc_start: 0.6601 (m-30) cc_final: 0.6305 (p0) REVERT: A 247 ASP cc_start: 0.6581 (m-30) cc_final: 0.6358 (m-30) REVERT: A 318 LYS cc_start: 0.6987 (tmtt) cc_final: 0.6558 (ttmt) REVERT: A 391 ILE cc_start: 0.4748 (OUTLIER) cc_final: 0.4540 (tt) REVERT: A 457 SER cc_start: 0.7842 (m) cc_final: 0.7337 (p) REVERT: A 491 LEU cc_start: 0.1349 (OUTLIER) cc_final: 0.0707 (tt) REVERT: A 535 MET cc_start: 0.7303 (mmm) cc_final: 0.6974 (mtm) REVERT: A 669 PHE cc_start: 0.5609 (OUTLIER) cc_final: 0.4027 (t80) REVERT: A 697 ARG cc_start: 0.7569 (tpt170) cc_final: 0.6449 (mtm110) REVERT: B 60 ARG cc_start: 0.3857 (OUTLIER) cc_final: 0.3347 (ptm160) REVERT: B 85 ARG cc_start: 0.7313 (mmm160) cc_final: 0.6674 (tpt90) REVERT: B 137 LYS cc_start: 0.5758 (mtmm) cc_final: 0.5492 (mtmt) REVERT: B 256 GLN cc_start: 0.5134 (tp40) cc_final: 0.4722 (tm-30) REVERT: B 304 LYS cc_start: 0.6235 (mmmm) cc_final: 0.5881 (mtmm) REVERT: B 391 ILE cc_start: 0.4723 (OUTLIER) cc_final: 0.4515 (tt) REVERT: B 457 SER cc_start: 0.7833 (m) cc_final: 0.7356 (p) REVERT: B 491 LEU cc_start: 0.1406 (OUTLIER) cc_final: 0.0840 (tt) REVERT: B 535 MET cc_start: 0.7326 (mmm) cc_final: 0.7046 (mtm) REVERT: B 642 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5820 (mp) REVERT: B 669 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.4034 (t80) REVERT: B 697 ARG cc_start: 0.7581 (tpt170) cc_final: 0.6459 (mtm110) outliers start: 80 outliers final: 33 residues processed: 210 average time/residue: 1.4029 time to fit residues: 323.4691 Evaluate side-chains 172 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 267 THR Chi-restraints excluded: chain A residue 274 ARG 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 391 ILE Chi-restraints excluded: chain A residue 425 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 669 PHE Chi-restraints excluded: chain A residue 676 ARG 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 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 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 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 17 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 127 ASN A 710 GLN B 14 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.181307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129671 restraints weight = 13666.360| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.55 r_work: 0.3495 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11918 Z= 0.186 Angle : 0.782 12.549 16196 Z= 0.400 Chirality : 0.046 0.188 1818 Planarity : 0.007 0.092 2024 Dihedral : 9.243 59.358 1640 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.66 % Favored : 89.78 % Rotamer: Outliers : 6.80 % Allowed : 28.48 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.23), residues: 1428 helix: 1.22 (0.18), residues: 898 sheet: -3.31 (0.52), residues: 46 loop : -3.48 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.004 0.001 HIS A 715 PHE 0.022 0.001 PHE B 33 TYR 0.014 0.001 TYR B 98 ARG 0.015 0.000 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.07364 ( 638) hydrogen bonds : angle 5.04153 ( 1896) covalent geometry : bond 0.00392 (11916) covalent geometry : angle 0.78200 (16196) Misc. bond : bond 0.00559 ( 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 219 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 135 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.3847 (OUTLIER) cc_final: 0.3394 (ptm160) REVERT: A 137 LYS cc_start: 0.5680 (mtmm) cc_final: 0.5460 (mtmt) REVERT: A 212 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7241 (t70) REVERT: A 239 VAL cc_start: 0.5841 (t) cc_final: 0.5557 (t) REVERT: A 247 ASP cc_start: 0.6648 (m-30) cc_final: 0.6429 (m-30) REVERT: A 318 LYS cc_start: 0.7052 (tmtt) cc_final: 0.6580 (tmmt) REVERT: A 390 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.4868 (t80) REVERT: A 457 SER cc_start: 0.7846 (m) cc_final: 0.7337 (p) REVERT: A 491 LEU cc_start: 0.1181 (OUTLIER) cc_final: 0.0524 (tt) REVERT: A 542 TYR cc_start: 0.6060 (t80) cc_final: 0.5856 (t80) REVERT: A 669 PHE cc_start: 0.5550 (OUTLIER) cc_final: 0.3913 (t80) REVERT: A 697 ARG cc_start: 0.7521 (tpt170) cc_final: 0.6357 (mtm110) REVERT: B 60 ARG cc_start: 0.3849 (OUTLIER) cc_final: 0.3396 (ptm160) REVERT: B 137 LYS cc_start: 0.5729 (mtmm) cc_final: 0.5507 (mtmt) REVERT: B 256 GLN cc_start: 0.5172 (tp40) cc_final: 0.4760 (tm-30) REVERT: B 304 LYS cc_start: 0.6236 (mmmm) cc_final: 0.5882 (mtmm) REVERT: B 311 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: B 390 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.5012 (t80) REVERT: B 457 SER cc_start: 0.7851 (m) cc_final: 0.7360 (p) REVERT: B 491 LEU cc_start: 0.1236 (OUTLIER) cc_final: 0.0675 (tt) REVERT: B 542 TYR cc_start: 0.6036 (t80) cc_final: 0.5827 (t80) REVERT: B 642 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5784 (mp) REVERT: B 669 PHE cc_start: 0.5544 (OUTLIER) cc_final: 0.3913 (t80) REVERT: B 697 ARG cc_start: 0.7517 (tpt170) cc_final: 0.6353 (mtm110) outliers start: 84 outliers final: 44 residues processed: 205 average time/residue: 1.4285 time to fit residues: 323.9629 Evaluate side-chains 183 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 289 VAL 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 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 580 LEU 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 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 284 LEU 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 311 GLU 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 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 126 optimal weight: 0.2980 chunk 133 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 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 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** 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 = 0.4080 r_free = 0.4080 target = 0.181521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129729 restraints weight = 13778.578| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.57 r_work: 0.3499 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11918 Z= 0.176 Angle : 0.751 9.959 16196 Z= 0.385 Chirality : 0.047 0.363 1818 Planarity : 0.007 0.070 2024 Dihedral : 8.970 59.972 1640 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.73 % Favored : 89.71 % Rotamer: Outliers : 5.42 % Allowed : 29.61 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.23), residues: 1428 helix: 1.32 (0.18), residues: 910 sheet: -3.23 (0.53), residues: 46 loop : -3.54 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.004 0.001 HIS A 715 PHE 0.028 0.001 PHE A 33 TYR 0.014 0.001 TYR B 98 ARG 0.007 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.07096 ( 638) hydrogen bonds : angle 4.98201 ( 1896) covalent geometry : bond 0.00368 (11916) covalent geometry : angle 0.75101 (16196) Misc. bond : bond 0.00362 ( 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 211 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 144 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 60 ARG cc_start: 0.3847 (OUTLIER) cc_final: 0.3303 (ptp-170) REVERT: A 85 ARG cc_start: 0.7302 (tpt90) cc_final: 0.6926 (tpp-160) REVERT: A 137 LYS cc_start: 0.5668 (mtmm) cc_final: 0.5457 (mtmt) REVERT: A 239 VAL cc_start: 0.5770 (t) cc_final: 0.5406 (t) REVERT: A 247 ASP cc_start: 0.6640 (m-30) cc_final: 0.6437 (m-30) REVERT: A 260 ASP cc_start: 0.3693 (p0) cc_final: 0.3285 (p0) REVERT: A 318 LYS cc_start: 0.7097 (tmtt) cc_final: 0.6625 (tmmt) REVERT: A 390 PHE cc_start: 0.5612 (OUTLIER) cc_final: 0.4930 (t80) REVERT: A 457 SER cc_start: 0.7812 (m) cc_final: 0.7323 (p) REVERT: A 491 LEU cc_start: 0.0944 (OUTLIER) cc_final: 0.0315 (tt) REVERT: A 537 LYS cc_start: 0.6473 (tttp) cc_final: 0.5945 (tppt) REVERT: A 669 PHE cc_start: 0.5477 (OUTLIER) cc_final: 0.3831 (t80) REVERT: A 676 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.6148 (tmt170) REVERT: B 60 ARG cc_start: 0.3846 (OUTLIER) cc_final: 0.3302 (ptp-170) REVERT: B 85 ARG cc_start: 0.7286 (tpt90) cc_final: 0.6931 (tpp-160) REVERT: B 137 LYS cc_start: 0.5741 (mtmm) cc_final: 0.5524 (mtmt) REVERT: B 256 GLN cc_start: 0.5230 (tp40) cc_final: 0.4813 (tm-30) REVERT: B 260 ASP cc_start: 0.3668 (p0) cc_final: 0.3284 (p0) REVERT: B 304 LYS cc_start: 0.6322 (mmmm) cc_final: 0.5957 (mtmm) REVERT: B 390 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.4951 (t80) REVERT: B 457 SER cc_start: 0.7813 (m) cc_final: 0.7341 (p) REVERT: B 491 LEU cc_start: 0.1189 (OUTLIER) cc_final: 0.0640 (tt) REVERT: B 642 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5773 (mp) REVERT: B 669 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.3842 (t80) REVERT: B 676 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.6137 (tmt170) outliers start: 67 outliers final: 41 residues processed: 200 average time/residue: 1.0619 time to fit residues: 232.8783 Evaluate side-chains 186 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 267 THR 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 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 580 LEU 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 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 284 LEU 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 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 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 710 GLN ** 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 = 0.4087 r_free = 0.4087 target = 0.182290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130217 restraints weight = 13679.117| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.57 r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11918 Z= 0.176 Angle : 0.791 19.905 16196 Z= 0.404 Chirality : 0.046 0.366 1818 Planarity : 0.008 0.207 2024 Dihedral : 8.844 59.074 1638 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.80 % Favored : 89.78 % Rotamer: Outliers : 5.42 % Allowed : 29.45 % Favored : 65.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1428 helix: 1.43 (0.18), residues: 908 sheet: -3.21 (0.53), residues: 46 loop : -3.50 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.004 0.001 HIS A 715 PHE 0.028 0.001 PHE A 33 TYR 0.014 0.001 TYR B 98 ARG 0.033 0.001 ARG B 556 Details of bonding type rmsd hydrogen bonds : bond 0.06896 ( 638) hydrogen bonds : angle 4.94064 ( 1896) covalent geometry : bond 0.00357 (11916) covalent geometry : angle 0.79050 (16196) Misc. bond : bond 0.00849 ( 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 206 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 139 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.3948 (OUTLIER) cc_final: 0.3463 (ptp-170) REVERT: A 85 ARG cc_start: 0.7285 (tpt90) cc_final: 0.6928 (tpp-160) REVERT: A 247 ASP cc_start: 0.6628 (m-30) cc_final: 0.6424 (m-30) REVERT: A 260 ASP cc_start: 0.3678 (p0) cc_final: 0.3284 (p0) REVERT: A 390 PHE cc_start: 0.5580 (OUTLIER) cc_final: 0.4914 (t80) REVERT: A 457 SER cc_start: 0.7740 (m) cc_final: 0.7242 (p) REVERT: A 491 LEU cc_start: 0.0958 (OUTLIER) cc_final: 0.0349 (tt) REVERT: A 537 LYS cc_start: 0.6657 (tttp) cc_final: 0.6250 (tttm) REVERT: A 669 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.3838 (t80) REVERT: A 676 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.6155 (tmt170) REVERT: A 697 ARG cc_start: 0.7458 (tpt170) cc_final: 0.6162 (mtm110) REVERT: B 60 ARG cc_start: 0.3949 (OUTLIER) cc_final: 0.3462 (ptp-170) REVERT: B 85 ARG cc_start: 0.7295 (tpt90) cc_final: 0.6942 (tpp-160) REVERT: B 256 GLN cc_start: 0.5196 (tp40) cc_final: 0.4794 (tm-30) REVERT: B 260 ASP cc_start: 0.3736 (p0) cc_final: 0.3360 (p0) REVERT: B 390 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.4950 (t80) REVERT: B 457 SER cc_start: 0.7719 (m) cc_final: 0.7244 (p) REVERT: B 491 LEU cc_start: 0.1303 (OUTLIER) cc_final: 0.0785 (tt) REVERT: B 537 LYS cc_start: 0.6640 (tttp) cc_final: 0.6238 (tttm) REVERT: B 669 PHE cc_start: 0.5442 (OUTLIER) cc_final: 0.3809 (t80) REVERT: B 676 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.6156 (tmt170) REVERT: B 697 ARG cc_start: 0.7464 (tpt170) cc_final: 0.6165 (mtm110) outliers start: 67 outliers final: 38 residues processed: 193 average time/residue: 1.0704 time to fit residues: 226.4139 Evaluate side-chains 182 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 294 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 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 554 LYS Chi-restraints excluded: chain A residue 580 LEU 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 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 284 LEU 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 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 580 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 135 optimal weight: 0.3980 chunk 74 optimal weight: 0.2980 chunk 118 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 609 GLN A 710 GLN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.183147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131051 restraints weight = 13689.200| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.57 r_work: 0.3518 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11918 Z= 0.171 Angle : 0.771 17.856 16196 Z= 0.393 Chirality : 0.046 0.315 1818 Planarity : 0.007 0.160 2024 Dihedral : 8.641 59.518 1638 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.52 % Favored : 90.20 % Rotamer: Outliers : 4.21 % Allowed : 30.99 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1428 helix: 1.49 (0.18), residues: 908 sheet: -3.18 (0.53), residues: 46 loop : -3.41 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 625 HIS 0.004 0.001 HIS A 715 PHE 0.031 0.001 PHE A 33 TYR 0.014 0.001 TYR B 98 ARG 0.030 0.001 ARG B 556 Details of bonding type rmsd hydrogen bonds : bond 0.06678 ( 638) hydrogen bonds : angle 4.87049 ( 1896) covalent geometry : bond 0.00352 (11916) covalent geometry : angle 0.77118 (16196) Misc. bond : bond 0.00946 ( 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 193 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 60 ARG cc_start: 0.4015 (OUTLIER) cc_final: 0.3500 (ptp-170) REVERT: A 260 ASP cc_start: 0.3718 (p0) cc_final: 0.3336 (p0) REVERT: A 390 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.4950 (t80) REVERT: A 457 SER cc_start: 0.7713 (m) cc_final: 0.7239 (p) REVERT: A 491 LEU cc_start: 0.0924 (OUTLIER) cc_final: 0.0349 (tt) REVERT: A 537 LYS cc_start: 0.6778 (tttp) cc_final: 0.6352 (tttm) REVERT: A 669 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.3879 (t80) REVERT: A 697 ARG cc_start: 0.7460 (tpt170) cc_final: 0.6097 (mtm110) REVERT: B 60 ARG cc_start: 0.4038 (OUTLIER) cc_final: 0.3526 (ptp-170) REVERT: B 256 GLN cc_start: 0.5185 (tp40) cc_final: 0.4786 (tm-30) REVERT: B 260 ASP cc_start: 0.3623 (p0) cc_final: 0.3204 (p0) REVERT: B 318 LYS cc_start: 0.7591 (tmtt) cc_final: 0.7233 (tmmt) REVERT: B 390 PHE cc_start: 0.5570 (OUTLIER) cc_final: 0.4974 (t80) REVERT: B 457 SER cc_start: 0.7733 (m) cc_final: 0.7260 (p) REVERT: B 491 LEU cc_start: 0.1393 (OUTLIER) cc_final: 0.0926 (tt) REVERT: B 537 LYS cc_start: 0.6743 (tttp) cc_final: 0.6325 (tttm) REVERT: B 669 PHE cc_start: 0.5497 (OUTLIER) cc_final: 0.3831 (t80) REVERT: B 697 ARG cc_start: 0.7468 (tpt170) cc_final: 0.6101 (mtm110) outliers start: 52 outliers final: 35 residues processed: 183 average time/residue: 1.1430 time to fit residues: 228.4235 Evaluate side-chains 178 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 112 ILE 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 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 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 580 LEU 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 112 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 235 THR 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 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 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 580 LEU 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 136 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 294 HIS ** 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 = 0.4051 r_free = 0.4051 target = 0.178247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125806 restraints weight = 13535.950| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.55 r_work: 0.3451 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.5757 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= 0.207 Angle : 0.809 16.074 16196 Z= 0.415 Chirality : 0.048 0.320 1818 Planarity : 0.007 0.131 2024 Dihedral : 8.514 58.940 1634 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.15 % Favored : 89.71 % Rotamer: Outliers : 3.96 % Allowed : 31.31 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1428 helix: 1.42 (0.18), residues: 908 sheet: -2.79 (0.54), residues: 42 loop : -3.35 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.005 0.001 HIS A 715 PHE 0.030 0.002 PHE B 33 TYR 0.012 0.001 TYR A 98 ARG 0.027 0.001 ARG B 556 Details of bonding type rmsd hydrogen bonds : bond 0.08133 ( 638) hydrogen bonds : angle 5.08574 ( 1896) covalent geometry : bond 0.00446 (11916) covalent geometry : angle 0.80875 (16196) Misc. bond : bond 0.00605 ( 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 187 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 60 ARG cc_start: 0.4015 (OUTLIER) cc_final: 0.3492 (ptp-170) REVERT: A 260 ASP cc_start: 0.3819 (p0) cc_final: 0.3459 (p0) REVERT: A 318 LYS cc_start: 0.7088 (tmmt) cc_final: 0.6656 (tmmt) REVERT: A 390 PHE cc_start: 0.5611 (OUTLIER) cc_final: 0.4992 (t80) REVERT: A 457 SER cc_start: 0.7864 (m) cc_final: 0.7387 (p) REVERT: A 491 LEU cc_start: 0.0923 (OUTLIER) cc_final: 0.0301 (tt) REVERT: A 537 LYS cc_start: 0.6601 (tttp) cc_final: 0.6171 (tttm) REVERT: A 669 PHE cc_start: 0.5472 (OUTLIER) cc_final: 0.3850 (t80) REVERT: A 676 ARG cc_start: 0.6464 (tmt170) cc_final: 0.6056 (tpt90) REVERT: A 697 ARG cc_start: 0.7426 (tpt170) cc_final: 0.6043 (mtm110) REVERT: B 60 ARG cc_start: 0.4017 (OUTLIER) cc_final: 0.3515 (ptp-170) REVERT: B 256 GLN cc_start: 0.5217 (tp40) cc_final: 0.4828 (tm-30) REVERT: B 318 LYS cc_start: 0.7661 (tmtt) cc_final: 0.7241 (tmmt) REVERT: B 390 PHE cc_start: 0.5559 (OUTLIER) cc_final: 0.4995 (t80) REVERT: B 457 SER cc_start: 0.7878 (m) cc_final: 0.7417 (p) REVERT: B 491 LEU cc_start: 0.1172 (OUTLIER) cc_final: 0.0674 (tt) REVERT: B 537 LYS cc_start: 0.6576 (tttp) cc_final: 0.6153 (tttm) REVERT: B 669 PHE cc_start: 0.5472 (OUTLIER) cc_final: 0.3864 (t80) REVERT: B 676 ARG cc_start: 0.6490 (tmt170) cc_final: 0.6073 (tpt90) REVERT: B 697 ARG cc_start: 0.7417 (tpt170) cc_final: 0.6021 (mtm110) outliers start: 49 outliers final: 34 residues processed: 178 average time/residue: 1.1332 time to fit residues: 220.7798 Evaluate side-chains 176 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 264 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 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 554 LYS 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 717 VAL 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 212 ASP Chi-restraints excluded: chain B residue 235 THR 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 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 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR 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 717 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 127 ASN ** B 294 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.177656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125118 restraints weight = 13657.080| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.56 r_work: 0.3447 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.5772 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= 0.207 Angle : 0.799 14.051 16196 Z= 0.410 Chirality : 0.048 0.327 1818 Planarity : 0.007 0.113 2024 Dihedral : 8.376 58.510 1634 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.73 % Favored : 90.13 % Rotamer: Outliers : 4.05 % Allowed : 31.31 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1428 helix: 1.35 (0.18), residues: 910 sheet: -3.05 (0.54), residues: 46 loop : -3.36 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 625 HIS 0.004 0.001 HIS A 715 PHE 0.030 0.002 PHE B 33 TYR 0.012 0.001 TYR B 98 ARG 0.023 0.001 ARG B 556 Details of bonding type rmsd hydrogen bonds : bond 0.08172 ( 638) hydrogen bonds : angle 5.11508 ( 1896) covalent geometry : bond 0.00449 (11916) covalent geometry : angle 0.79917 (16196) Misc. bond : bond 0.00527 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12542.56 seconds wall clock time: 224 minutes 10.31 seconds (13450.31 seconds total)