Starting phenix.real_space_refine on Mon Dec 30 00:29:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8grn_34209/12_2024/8grn_34209_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grn_34209/12_2024/8grn_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_34209/12_2024/8grn_34209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grn_34209/12_2024/8grn_34209.map" model { file = "/net/cci-nas-00/data/ceres_data/8grn_34209/12_2024/8grn_34209_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grn_34209/12_2024/8grn_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.03, per 1000 atoms: 0.69 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: 2.91 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: 1.04 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: 3.28 Time building geometry restraints manager: 3.32 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: 0.00 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: 3.580 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.350 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- 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 11916 Z= 2.108 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 *********************** 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 : 1.192 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: 1.0268 time to fit residues: 631.1254 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 : 1.393 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 11916 Z= 0.303 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 *********************** 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 : 1.459 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: 0.5106 (OUTLIER) cc_final: 0.4799 (tptp) REVERT: A 50 SER cc_start: 0.5208 (OUTLIER) cc_final: 0.4812 (m) REVERT: A 212 ASP cc_start: 0.5810 (OUTLIER) cc_final: 0.5534 (t70) REVERT: A 379 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6935 (mmp) REVERT: A 457 SER cc_start: 0.7415 (OUTLIER) cc_final: 0.7012 (p) REVERT: A 491 LEU cc_start: 0.3583 (OUTLIER) cc_final: 0.2275 (tt) REVERT: B 5 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4797 (tptp) REVERT: B 50 SER cc_start: 0.5206 (OUTLIER) cc_final: 0.4819 (m) REVERT: B 212 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5535 (t70) REVERT: B 379 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6941 (mmp) REVERT: B 457 SER cc_start: 0.7403 (OUTLIER) cc_final: 0.6996 (p) REVERT: B 491 LEU cc_start: 0.3593 (OUTLIER) cc_final: 0.2377 (tt) outliers start: 142 outliers final: 48 residues processed: 290 average time/residue: 1.0926 time to fit residues: 348.5926 Evaluate side-chains 212 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 50 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 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 250 SER Chi-restraints excluded: chain A residue 290 ASP 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 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 50 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 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 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 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 71 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 11916 Z= 0.292 Angle : 0.900 14.021 16196 Z= 0.469 Chirality : 0.050 0.225 1818 Planarity : 0.008 0.083 2024 Dihedral : 12.144 63.683 1698 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 1.05 % Allowed : 10.50 % Favored : 88.45 % Rotamer: Outliers : 8.82 % Allowed : 27.18 % Favored : 64.00 % 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: -1.62 (0.22), residues: 1428 helix: 0.48 (0.18), residues: 890 sheet: -3.33 (0.55), residues: 46 loop : -3.90 (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 A 33 TYR 0.019 0.002 TYR B 98 ARG 0.012 0.001 ARG A 556 *********************** 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 262 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 153 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.5294 (OUTLIER) cc_final: 0.4821 (m) REVERT: A 379 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6965 (mmp) REVERT: A 457 SER cc_start: 0.7351 (OUTLIER) cc_final: 0.6924 (p) REVERT: A 491 LEU cc_start: 0.3002 (OUTLIER) cc_final: 0.1551 (tt) REVERT: A 522 MET cc_start: 0.6223 (ttm) cc_final: 0.5942 (mtm) REVERT: A 582 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7457 (mt) REVERT: A 659 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7944 (mt) REVERT: B 50 SER cc_start: 0.5297 (OUTLIER) cc_final: 0.4831 (m) REVERT: B 294 HIS cc_start: 0.4139 (OUTLIER) cc_final: 0.3414 (m-70) REVERT: B 379 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6971 (mmp) REVERT: B 457 SER cc_start: 0.7348 (OUTLIER) cc_final: 0.6908 (p) REVERT: B 491 LEU cc_start: 0.3244 (OUTLIER) cc_final: 0.1979 (tt) REVERT: B 522 MET cc_start: 0.6216 (ttm) cc_final: 0.5931 (mtm) REVERT: B 582 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7456 (mt) REVERT: B 659 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7943 (mt) outliers start: 109 outliers final: 38 residues processed: 244 average time/residue: 1.1477 time to fit residues: 306.1598 Evaluate side-chains 195 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER 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 112 ILE 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 313 VAL Chi-restraints excluded: chain A residue 379 MET 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 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 50 SER 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 112 ILE Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 379 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 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 127 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 501 GLN B 74 HIS ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN B 501 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11916 Z= 0.260 Angle : 0.807 11.009 16196 Z= 0.419 Chirality : 0.047 0.195 1818 Planarity : 0.007 0.075 2024 Dihedral : 10.584 60.740 1664 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.29 % Favored : 88.94 % Rotamer: Outliers : 8.50 % Allowed : 27.18 % Favored : 64.32 % 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: -1.23 (0.23), residues: 1428 helix: 0.74 (0.18), residues: 900 sheet: -3.23 (0.55), residues: 46 loop : -3.74 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 625 HIS 0.005 0.001 HIS A 715 PHE 0.019 0.001 PHE B 624 TYR 0.016 0.001 TYR A 98 ARG 0.011 0.001 ARG A 556 *********************** 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 245 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 140 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.4768 (OUTLIER) cc_final: 0.4462 (m-80) REVERT: A 390 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6003 (t80) REVERT: A 457 SER cc_start: 0.7186 (OUTLIER) cc_final: 0.6805 (p) REVERT: A 491 LEU cc_start: 0.2711 (OUTLIER) cc_final: 0.1286 (tt) REVERT: A 508 MET cc_start: 0.5757 (mmt) cc_final: 0.4940 (mmt) REVERT: A 522 MET cc_start: 0.6212 (ttm) cc_final: 0.5888 (mtm) REVERT: A 535 MET cc_start: 0.7061 (mmm) cc_final: 0.5241 (mtm) REVERT: A 582 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7400 (mt) REVERT: A 642 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6191 (mp) REVERT: A 659 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7950 (mt) REVERT: A 669 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.3709 (t80) REVERT: B 294 HIS cc_start: 0.4027 (OUTLIER) cc_final: 0.3465 (m-70) REVERT: B 390 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5996 (t80) REVERT: B 491 LEU cc_start: 0.2665 (OUTLIER) cc_final: 0.1392 (tt) REVERT: B 508 MET cc_start: 0.5767 (mmt) cc_final: 0.4944 (mmt) REVERT: B 522 MET cc_start: 0.6207 (ttm) cc_final: 0.5890 (mtm) REVERT: B 535 MET cc_start: 0.7063 (mmm) cc_final: 0.5240 (mtm) REVERT: B 582 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7414 (mt) REVERT: B 642 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6189 (mp) REVERT: B 659 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7953 (mt) REVERT: B 669 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.3713 (t80) outliers start: 105 outliers final: 43 residues processed: 229 average time/residue: 1.0995 time to fit residues: 276.7948 Evaluate side-chains 187 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 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 369 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR 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 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 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 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 400 LEU 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 541 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 642 LEU Chi-restraints excluded: chain B residue 659 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 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11916 Z= 0.230 Angle : 0.772 10.825 16196 Z= 0.396 Chirality : 0.046 0.191 1818 Planarity : 0.007 0.073 2024 Dihedral : 10.070 59.519 1653 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.15 % Favored : 89.22 % Rotamer: Outliers : 6.80 % Allowed : 28.80 % Favored : 64.40 % 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: -0.83 (0.23), residues: 1428 helix: 1.06 (0.18), residues: 898 sheet: -3.23 (0.55), residues: 46 loop : -3.55 (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 33 TYR 0.016 0.001 TYR B 98 ARG 0.009 0.000 ARG A 556 *********************** 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 224 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 140 time to evaluate : 1.345 Fit side-chains REVERT: A 235 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.7110 (p) REVERT: A 391 ILE cc_start: 0.5089 (OUTLIER) cc_final: 0.4386 (tt) REVERT: A 491 LEU cc_start: 0.2311 (OUTLIER) cc_final: 0.0984 (tt) REVERT: A 535 MET cc_start: 0.7034 (mmm) cc_final: 0.6323 (mtm) REVERT: A 642 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6271 (mp) REVERT: A 659 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7929 (mt) REVERT: A 669 PHE cc_start: 0.5689 (OUTLIER) cc_final: 0.3673 (t80) REVERT: B 391 ILE cc_start: 0.5085 (OUTLIER) cc_final: 0.4379 (tt) REVERT: B 491 LEU cc_start: 0.2445 (OUTLIER) cc_final: 0.1215 (tt) REVERT: B 535 MET cc_start: 0.7033 (mmm) cc_final: 0.6319 (mtm) REVERT: B 642 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6275 (mp) REVERT: B 659 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7930 (mt) REVERT: B 669 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.3677 (t80) outliers start: 84 outliers final: 31 residues processed: 210 average time/residue: 1.1225 time to fit residues: 258.7569 Evaluate side-chains 174 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 642 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 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 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 ILE 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 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 659 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 123 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 609 GLN A 710 GLN B 14 ASN B 127 ASN B 609 GLN B 710 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11916 Z= 0.289 Angle : 0.800 10.561 16196 Z= 0.412 Chirality : 0.048 0.193 1818 Planarity : 0.007 0.088 2024 Dihedral : 8.971 59.849 1630 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.87 % Favored : 89.57 % Rotamer: Outliers : 6.23 % Allowed : 30.02 % Favored : 63.75 % 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: -0.72 (0.23), residues: 1428 helix: 1.17 (0.18), residues: 896 sheet: -3.20 (0.54), residues: 46 loop : -3.52 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.004 0.001 HIS A 715 PHE 0.026 0.002 PHE A 33 TYR 0.013 0.001 TYR A 98 ARG 0.027 0.001 ARG A 556 *********************** 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 213 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 390 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.5938 (t80) REVERT: A 491 LEU cc_start: 0.2219 (OUTLIER) cc_final: 0.0793 (tt) REVERT: A 642 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6136 (mp) REVERT: A 669 PHE cc_start: 0.5716 (OUTLIER) cc_final: 0.3657 (t80) REVERT: B 390 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5932 (t80) REVERT: B 491 LEU cc_start: 0.2289 (OUTLIER) cc_final: 0.1041 (tt) REVERT: B 642 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6135 (mp) REVERT: B 669 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.3665 (t80) outliers start: 77 outliers final: 40 residues processed: 203 average time/residue: 1.1031 time to fit residues: 245.3062 Evaluate side-chains 179 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 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 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 14 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11916 Z= 0.251 Angle : 0.774 9.977 16196 Z= 0.399 Chirality : 0.047 0.371 1818 Planarity : 0.007 0.072 2024 Dihedral : 10.488 177.133 1622 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.15 % Favored : 89.29 % Rotamer: Outliers : 5.26 % Allowed : 29.77 % 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: -0.60 (0.23), residues: 1428 helix: 1.24 (0.18), residues: 912 sheet: -3.24 (0.53), residues: 46 loop : -3.57 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 625 HIS 0.004 0.001 HIS A 715 PHE 0.027 0.001 PHE B 33 TYR 0.013 0.001 TYR B 98 ARG 0.009 0.000 ARG A 556 *********************** 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 201 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 136 time to evaluate : 1.234 Fit side-chains REVERT: A 390 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5903 (t80) REVERT: A 391 ILE cc_start: 0.5154 (OUTLIER) cc_final: 0.4536 (tt) REVERT: A 491 LEU cc_start: 0.2041 (OUTLIER) cc_final: 0.0665 (tt) REVERT: A 535 MET cc_start: 0.6977 (mmm) cc_final: 0.5213 (mtm) REVERT: A 642 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6207 (mp) REVERT: A 669 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.3626 (t80) REVERT: B 390 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5905 (t80) REVERT: B 391 ILE cc_start: 0.5130 (OUTLIER) cc_final: 0.4512 (tt) REVERT: B 491 LEU cc_start: 0.2272 (OUTLIER) cc_final: 0.1023 (tt) REVERT: B 535 MET cc_start: 0.6977 (mmm) cc_final: 0.5205 (mtm) REVERT: B 642 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6206 (mp) REVERT: B 669 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.3631 (t80) outliers start: 65 outliers final: 33 residues processed: 190 average time/residue: 1.0814 time to fit residues: 225.6214 Evaluate side-chains 173 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 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 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 391 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11916 Z= 0.246 Angle : 0.807 15.448 16196 Z= 0.416 Chirality : 0.048 0.378 1818 Planarity : 0.007 0.072 2024 Dihedral : 9.605 176.748 1622 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.29 % Favored : 89.29 % Rotamer: Outliers : 4.45 % Allowed : 30.10 % Favored : 65.45 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.46 (0.23), residues: 1428 helix: 1.37 (0.18), residues: 908 sheet: -3.22 (0.53), residues: 46 loop : -3.53 (0.24), residues: 474 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 0.013 0.001 TYR B 98 ARG 0.019 0.000 ARG A 556 *********************** 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 190 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 2.003 Fit side-chains revert: symmetry clash REVERT: A 390 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.5761 (t80) REVERT: A 391 ILE cc_start: 0.5092 (OUTLIER) cc_final: 0.4473 (tt) REVERT: A 491 LEU cc_start: 0.1967 (OUTLIER) cc_final: 0.0588 (tt) REVERT: A 535 MET cc_start: 0.6941 (mmm) cc_final: 0.5302 (mtm) REVERT: A 642 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6184 (mp) REVERT: A 669 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.3630 (t80) REVERT: B 390 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.5775 (t80) REVERT: B 391 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4468 (tt) REVERT: B 491 LEU cc_start: 0.2280 (OUTLIER) cc_final: 0.1029 (tt) REVERT: B 535 MET cc_start: 0.6945 (mmm) cc_final: 0.5301 (mtm) REVERT: B 642 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6183 (mp) REVERT: B 669 PHE cc_start: 0.5716 (OUTLIER) cc_final: 0.3634 (t80) outliers start: 55 outliers final: 33 residues processed: 181 average time/residue: 1.1856 time to fit residues: 238.9142 Evaluate side-chains 173 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 644 MET Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 717 VAL 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 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 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 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 294 HIS A 710 GLN B 127 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11916 Z= 0.268 Angle : 0.797 15.179 16196 Z= 0.412 Chirality : 0.048 0.383 1818 Planarity : 0.007 0.095 2024 Dihedral : 9.202 168.371 1620 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.80 % Favored : 89.92 % Rotamer: Outliers : 4.13 % Allowed : 30.26 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -0.42 (0.23), residues: 1428 helix: 1.37 (0.18), residues: 908 sheet: -3.13 (0.54), residues: 46 loop : -3.46 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 625 HIS 0.006 0.001 HIS B 294 PHE 0.029 0.002 PHE B 33 TYR 0.012 0.001 TYR B 98 ARG 0.005 0.000 ARG B 556 *********************** 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 182 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 131 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 390 PHE cc_start: 0.6586 (OUTLIER) cc_final: 0.5933 (t80) REVERT: A 391 ILE cc_start: 0.5212 (OUTLIER) cc_final: 0.4582 (tt) REVERT: A 491 LEU cc_start: 0.1956 (OUTLIER) cc_final: 0.0524 (tt) REVERT: A 537 LYS cc_start: 0.5358 (tttm) cc_final: 0.5080 (tttm) REVERT: A 642 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6145 (mp) REVERT: A 669 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.3609 (t80) REVERT: A 676 ARG cc_start: 0.5852 (tmt170) cc_final: 0.5642 (tpt90) REVERT: B 294 HIS cc_start: 0.3158 (OUTLIER) cc_final: 0.2297 (m-70) REVERT: B 390 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.5935 (t80) REVERT: B 391 ILE cc_start: 0.5173 (OUTLIER) cc_final: 0.4543 (tt) REVERT: B 491 LEU cc_start: 0.2277 (OUTLIER) cc_final: 0.1081 (tt) REVERT: B 537 LYS cc_start: 0.5361 (tttm) cc_final: 0.5086 (tttm) REVERT: B 642 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6156 (mp) REVERT: B 669 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.3614 (t80) REVERT: B 676 ARG cc_start: 0.5872 (tmt170) cc_final: 0.5646 (tpt90) outliers start: 51 outliers final: 31 residues processed: 175 average time/residue: 1.1478 time to fit residues: 220.0091 Evaluate side-chains 170 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 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 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU 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 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 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 642 LEU 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 82 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS A 710 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11916 Z= 0.262 Angle : 0.788 12.970 16196 Z= 0.406 Chirality : 0.047 0.340 1818 Planarity : 0.007 0.073 2024 Dihedral : 9.068 170.970 1618 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.94 % Favored : 89.92 % Rotamer: Outliers : 4.21 % Allowed : 30.74 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -0.34 (0.23), residues: 1428 helix: 1.42 (0.18), residues: 910 sheet: -3.10 (0.54), residues: 46 loop : -3.42 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.027 0.001 HIS A 294 PHE 0.029 0.002 PHE A 33 TYR 0.012 0.001 TYR B 98 ARG 0.008 0.000 ARG B 556 ********************** 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 185 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 390 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.5906 (t80) REVERT: A 391 ILE cc_start: 0.5119 (OUTLIER) cc_final: 0.4492 (tt) REVERT: A 491 LEU cc_start: 0.1977 (OUTLIER) cc_final: 0.0389 (tt) REVERT: A 537 LYS cc_start: 0.5443 (tttm) cc_final: 0.5172 (tttm) REVERT: A 642 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6182 (mp) REVERT: A 669 PHE cc_start: 0.5704 (OUTLIER) cc_final: 0.3603 (t80) REVERT: B 294 HIS cc_start: 0.2999 (OUTLIER) cc_final: 0.2321 (m-70) REVERT: B 390 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5906 (t80) REVERT: B 491 LEU cc_start: 0.2139 (OUTLIER) cc_final: 0.0931 (tt) REVERT: B 537 LYS cc_start: 0.5444 (tttm) cc_final: 0.5175 (tttm) REVERT: B 642 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6196 (mp) REVERT: B 669 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.3609 (t80) outliers start: 52 outliers final: 31 residues processed: 177 average time/residue: 1.1893 time to fit residues: 230.7235 Evaluate side-chains 169 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 248 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 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 580 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU 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 235 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 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 642 LEU 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 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 115 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 294 HIS A 710 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.186250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134482 restraints weight = 13607.649| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.58 r_work: 0.3561 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11916 Z= 0.216 Angle : 0.738 11.614 16196 Z= 0.378 Chirality : 0.045 0.293 1818 Planarity : 0.007 0.067 2024 Dihedral : 8.853 171.704 1618 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.87 % Favored : 89.99 % Rotamer: Outliers : 3.16 % Allowed : 32.12 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.21 (0.23), residues: 1428 helix: 1.53 (0.18), residues: 916 sheet: -3.11 (0.54), residues: 46 loop : -3.44 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.007 0.001 HIS B 294 PHE 0.030 0.001 PHE B 33 TYR 0.015 0.001 TYR A 98 ARG 0.009 0.000 ARG B 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5154.37 seconds wall clock time: 93 minutes 18.06 seconds (5598.06 seconds total)