Starting phenix.real_space_refine on Thu Sep 26 01:40:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/09_2024/8grn_34209_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/09_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/09_2024/8grn_34209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/09_2024/8grn_34209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/09_2024/8grn_34209_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grn_34209/09_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.04, per 1000 atoms: 0.78 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=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.3 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: 1.16 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: 3.21 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 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: 1.57 - 2.23: 22 2.23 - 2.90: 5488 2.90 - 3.57: 15804 3.57 - 4.23: 27381 4.23 - 4.90: 45980 Nonbonded interactions: 94675 Sorted by model distance: nonbonded pdb=" CD LYS B 554 " pdb=" NH1 ARG B 556 " model vdw 1.568 3.520 nonbonded pdb=" CD LYS A 554 " pdb=" NH1 ARG A 556 " model vdw 1.568 3.520 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 ... (remaining 94670 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: 3.940 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 30.350 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: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.520 ------------------------------------------------------------------------------- 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= 2.111 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 : 1.568 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 fitting. rotamer outliers: 452 poor density : 183 time to evaluate : 1.894 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: 1.0037 time to fit residues: 616.7833 Evaluate side-chains 325 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 153 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN A 476 ASN A 490 GLN A 497 GLN A 500 ASN A 543 HIS A 568 ASN A 573 GLN A 575 GLN A 616 GLN A 687 GLN B 63 ASN B 90 HIS B 124 ASN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 476 ASN B 490 GLN B 497 GLN B 500 ASN B 543 HIS B 568 ASN B 573 GLN B 575 GLN B 687 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.3845 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= 0.311 Angle : 0.992 15.046 16196 Z= 0.527 Chirality : 0.056 0.325 1818 Planarity : 0.009 0.103 2024 Dihedral : 15.759 73.987 1980 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 1.19 % Allowed : 12.18 % Favored : 86.62 % Rotamer: Outliers : 12.22 % Allowed : 25.24 % Favored : 62.54 % 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: -2.83 (0.21), residues: 1428 helix: -0.52 (0.17), residues: 876 sheet: -3.52 (0.53), residues: 46 loop : -4.24 (0.22), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 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 B 98 ARG 0.011 0.001 ARG B 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 320 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 169 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.5107 (OUTLIER) cc_final: 0.4799 (tptp) REVERT: A 50 SER cc_start: 0.5302 (OUTLIER) cc_final: 0.4843 (m) REVERT: A 178 MET cc_start: 0.5855 (ttp) cc_final: 0.5648 (ttp) REVERT: A 212 ASP cc_start: 0.5814 (OUTLIER) cc_final: 0.5532 (t70) REVERT: A 376 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.4914 (mtt180) REVERT: A 379 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6948 (mmp) REVERT: A 457 SER cc_start: 0.7409 (OUTLIER) cc_final: 0.7017 (p) REVERT: A 491 LEU cc_start: 0.3780 (OUTLIER) cc_final: 0.2317 (tt) REVERT: A 590 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5938 (ttp) REVERT: B 5 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4800 (tptp) REVERT: B 50 SER cc_start: 0.5306 (OUTLIER) cc_final: 0.4851 (m) REVERT: B 178 MET cc_start: 0.5855 (ttp) cc_final: 0.5643 (ttp) REVERT: B 212 ASP cc_start: 0.5804 (OUTLIER) cc_final: 0.5522 (t70) REVERT: B 376 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.4912 (mtt180) REVERT: B 379 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6955 (mmp) REVERT: B 457 SER cc_start: 0.7413 (OUTLIER) cc_final: 0.7016 (p) REVERT: B 491 LEU cc_start: 0.3751 (OUTLIER) cc_final: 0.2403 (tt) REVERT: B 590 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5942 (ttp) outliers start: 151 outliers final: 50 residues processed: 294 average time/residue: 1.0865 time to fit residues: 349.0559 Evaluate side-chains 217 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 151 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 68 SER Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 THR 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 376 ARG Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 ILE 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 267 THR Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 376 ARG 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 565 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 0.0370 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 190 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11916 Z= 0.257 Angle : 0.840 12.955 16196 Z= 0.439 Chirality : 0.049 0.237 1818 Planarity : 0.008 0.085 2024 Dihedral : 12.170 64.580 1718 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.85 % Favored : 88.17 % Rotamer: Outliers : 8.98 % Allowed : 27.43 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.51 (0.22), residues: 1428 helix: 0.56 (0.18), residues: 890 sheet: -3.37 (0.55), residues: 46 loop : -3.84 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 75 HIS 0.006 0.001 HIS A 715 PHE 0.019 0.002 PHE A 33 TYR 0.022 0.001 TYR B 98 ARG 0.006 0.000 ARG A 274 *********************** 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 276 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 165 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7034 (ttt) REVERT: A 178 MET cc_start: 0.6089 (ttp) cc_final: 0.5849 (ttp) REVERT: A 400 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6986 (tp) REVERT: A 457 SER cc_start: 0.7336 (OUTLIER) cc_final: 0.6916 (p) REVERT: A 491 LEU cc_start: 0.3014 (OUTLIER) cc_final: 0.1640 (tt) REVERT: A 582 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7422 (mt) REVERT: A 659 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7893 (mt) REVERT: A 669 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.4089 (t80) REVERT: A 691 MET cc_start: 0.5460 (mtm) cc_final: 0.5189 (mtp) REVERT: B 82 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7034 (ttt) REVERT: B 178 MET cc_start: 0.6083 (ttp) cc_final: 0.5836 (ttp) REVERT: B 284 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.2975 (mp) REVERT: B 294 HIS cc_start: 0.4267 (OUTLIER) cc_final: 0.3497 (m-70) REVERT: B 457 SER cc_start: 0.7315 (OUTLIER) cc_final: 0.6895 (p) REVERT: B 491 LEU cc_start: 0.3040 (OUTLIER) cc_final: 0.1826 (tt) REVERT: B 582 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7431 (mt) REVERT: B 659 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7898 (mt) REVERT: B 669 PHE cc_start: 0.5638 (OUTLIER) cc_final: 0.4088 (t80) REVERT: B 691 MET cc_start: 0.5460 (mtm) cc_final: 0.5190 (mtp) outliers start: 111 outliers final: 39 residues processed: 251 average time/residue: 1.0277 time to fit residues: 283.8777 Evaluate side-chains 198 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 144 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 82 MET 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 294 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 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 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 82 MET 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 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 669 PHE 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: 1.9990 chunk 97 optimal weight: 0.0870 chunk 67 optimal weight: 0.0170 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 263 GLN A 427 GLN A 501 GLN B 74 HIS ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN B 270 ASN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN B 501 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5029 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= 0.252 Angle : 0.788 10.956 16196 Z= 0.411 Chirality : 0.047 0.187 1818 Planarity : 0.007 0.075 2024 Dihedral : 10.496 60.422 1664 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.43 % Favored : 88.80 % Rotamer: Outliers : 8.90 % Allowed : 28.40 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1428 helix: 0.82 (0.18), residues: 896 sheet: -3.27 (0.55), residues: 46 loop : -3.71 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.005 0.001 HIS A 715 PHE 0.019 0.002 PHE B 624 TYR 0.016 0.001 TYR A 98 ARG 0.002 0.000 ARG A 274 *********************** 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 249 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 139 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6945 (ttt) REVERT: A 390 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6029 (t80) REVERT: A 491 LEU cc_start: 0.2763 (OUTLIER) cc_final: 0.1373 (tt) REVERT: A 582 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7438 (mt) REVERT: A 642 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6239 (mp) REVERT: A 669 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.3802 (t80) REVERT: B 82 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6940 (ttt) REVERT: B 294 HIS cc_start: 0.4070 (OUTLIER) cc_final: 0.3726 (m-70) REVERT: B 390 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5991 (t80) REVERT: B 457 SER cc_start: 0.7157 (OUTLIER) cc_final: 0.6770 (p) REVERT: B 491 LEU cc_start: 0.2616 (OUTLIER) cc_final: 0.1274 (tt) REVERT: B 508 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.5384 (mmt) REVERT: B 582 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7439 (mt) REVERT: B 642 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6234 (mp) REVERT: B 669 PHE cc_start: 0.5581 (OUTLIER) cc_final: 0.3803 (t80) outliers start: 110 outliers final: 48 residues processed: 227 average time/residue: 0.7642 time to fit residues: 192.1648 Evaluate side-chains 187 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 124 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 MET 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 248 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 313 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 568 ASN 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 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 MET 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 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 442 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 568 ASN 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 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: 4.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 710 GLN B 127 ASN B 263 GLN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 11916 Z= 0.321 Angle : 0.821 10.831 16196 Z= 0.426 Chirality : 0.049 0.202 1818 Planarity : 0.007 0.077 2024 Dihedral : 9.988 59.372 1654 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.34 % Favored : 88.10 % Rotamer: Outliers : 7.20 % Allowed : 29.29 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.02 (0.23), residues: 1428 helix: 0.91 (0.18), residues: 896 sheet: -3.19 (0.55), residues: 46 loop : -3.63 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 625 HIS 0.005 0.001 HIS A 715 PHE 0.023 0.002 PHE B 33 TYR 0.014 0.001 TYR A 98 ARG 0.006 0.001 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 136 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6945 (ttt) REVERT: A 390 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6156 (t80) REVERT: A 391 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.4698 (tt) REVERT: A 491 LEU cc_start: 0.2489 (OUTLIER) cc_final: 0.1102 (tt) REVERT: A 582 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 642 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6203 (mp) REVERT: A 669 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.3941 (t80) REVERT: B 82 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6934 (ttt) REVERT: B 294 HIS cc_start: 0.4196 (OUTLIER) cc_final: 0.3578 (m-70) REVERT: B 390 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.6151 (t80) REVERT: B 391 ILE cc_start: 0.5400 (OUTLIER) cc_final: 0.4669 (tt) REVERT: B 491 LEU cc_start: 0.2400 (OUTLIER) cc_final: 0.1129 (tt) REVERT: B 582 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7499 (mt) REVERT: B 642 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6199 (mp) REVERT: B 669 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.3942 (t80) outliers start: 89 outliers final: 46 residues processed: 209 average time/residue: 0.9090 time to fit residues: 207.7456 Evaluate side-chains 192 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 131 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 82 MET 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 248 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 498 SER 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 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 MET 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 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 498 SER 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 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 676 ARG Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11916 Z= 0.249 Angle : 0.757 10.309 16196 Z= 0.390 Chirality : 0.046 0.191 1818 Planarity : 0.007 0.071 2024 Dihedral : 9.528 59.706 1652 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.73 % Favored : 89.71 % Rotamer: Outliers : 6.63 % Allowed : 30.02 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.75 (0.23), residues: 1428 helix: 1.13 (0.18), residues: 896 sheet: -3.21 (0.54), residues: 46 loop : -3.52 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 625 HIS 0.004 0.001 HIS A 715 PHE 0.027 0.002 PHE B 33 TYR 0.014 0.001 TYR B 98 ARG 0.007 0.000 ARG B 85 *********************** 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 216 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 134 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7010 (ttt) REVERT: A 491 LEU cc_start: 0.2236 (OUTLIER) cc_final: 0.0921 (tt) REVERT: A 582 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7454 (mt) REVERT: A 642 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6170 (mp) REVERT: A 669 PHE cc_start: 0.5696 (OUTLIER) cc_final: 0.3891 (t80) REVERT: B 82 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6880 (ttt) REVERT: B 491 LEU cc_start: 0.2201 (OUTLIER) cc_final: 0.0994 (tt) REVERT: B 582 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7455 (mt) REVERT: B 642 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6169 (mp) REVERT: B 669 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.3894 (t80) outliers start: 82 outliers final: 38 residues processed: 204 average time/residue: 1.0339 time to fit residues: 231.4362 Evaluate side-chains 175 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 82 MET 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 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 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 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain 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 82 MET 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 311 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 498 SER 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 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 676 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 76 optimal weight: 0.0010 chunk 136 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 127 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: 0.6608 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11916 Z= 0.234 Angle : 0.748 9.969 16196 Z= 0.382 Chirality : 0.045 0.182 1818 Planarity : 0.007 0.070 2024 Dihedral : 8.939 59.862 1644 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.01 % Favored : 89.43 % Rotamer: Outliers : 5.74 % Allowed : 31.80 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.58 (0.23), residues: 1428 helix: 1.26 (0.18), residues: 906 sheet: -3.19 (0.53), residues: 46 loop : -3.54 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 625 HIS 0.003 0.001 HIS A 715 PHE 0.027 0.001 PHE B 33 TYR 0.014 0.001 TYR A 98 ARG 0.004 0.000 ARG A 85 *********************** 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 207 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 136 time to evaluate : 1.346 Fit side-chains REVERT: A 313 VAL cc_start: 0.6680 (t) cc_final: 0.6466 (p) REVERT: A 390 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5918 (t80) REVERT: A 491 LEU cc_start: 0.2143 (OUTLIER) cc_final: 0.0911 (tt) REVERT: A 642 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6224 (mp) REVERT: A 669 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.3886 (t80) REVERT: B 390 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.5920 (t80) REVERT: B 491 LEU cc_start: 0.2071 (OUTLIER) cc_final: 0.0870 (tt) REVERT: B 642 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6209 (mp) REVERT: B 669 PHE cc_start: 0.5679 (OUTLIER) cc_final: 0.3889 (t80) outliers start: 71 outliers final: 35 residues processed: 192 average time/residue: 1.1452 time to fit residues: 240.1745 Evaluate side-chains 176 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 133 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU 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 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 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 676 ARG Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 16 LEU 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 390 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 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: 6.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.0070 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.0470 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 31 GLN B 127 ASN B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11916 Z= 0.213 Angle : 0.731 9.910 16196 Z= 0.371 Chirality : 0.045 0.329 1818 Planarity : 0.006 0.068 2024 Dihedral : 8.119 58.457 1629 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.59 % Favored : 89.99 % Rotamer: Outliers : 4.13 % Allowed : 33.58 % Favored : 62.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1428 helix: 1.42 (0.18), residues: 906 sheet: -3.10 (0.53), residues: 46 loop : -3.47 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.019 0.001 HIS A 294 PHE 0.026 0.001 PHE A 396 TYR 0.024 0.001 TYR B 542 ARG 0.003 0.000 ARG A 60 *********************** 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 194 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 143 time to evaluate : 1.337 Fit side-chains REVERT: A 248 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5891 (mt) REVERT: A 457 SER cc_start: 0.6826 (m) cc_final: 0.6613 (p) REVERT: A 491 LEU cc_start: 0.2207 (OUTLIER) cc_final: 0.1022 (tt) REVERT: A 642 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6304 (mp) REVERT: A 669 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.3945 (t80) REVERT: B 491 LEU cc_start: 0.2141 (OUTLIER) cc_final: 0.0930 (tt) REVERT: B 642 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6301 (mp) REVERT: B 669 PHE cc_start: 0.5679 (OUTLIER) cc_final: 0.3945 (t80) outliers start: 51 outliers final: 22 residues processed: 181 average time/residue: 1.1350 time to fit residues: 227.7487 Evaluate side-chains 172 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 248 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 TYR 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 717 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 717 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 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 31 GLN A 127 ASN A 294 HIS ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 31 GLN B 710 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11916 Z= 0.270 Angle : 0.768 9.581 16196 Z= 0.396 Chirality : 0.047 0.345 1818 Planarity : 0.007 0.072 2024 Dihedral : 7.692 59.646 1619 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.08 % Favored : 89.50 % Rotamer: Outliers : 4.13 % Allowed : 33.41 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.44 (0.23), residues: 1428 helix: 1.36 (0.18), residues: 906 sheet: -3.09 (0.53), residues: 46 loop : -3.45 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.021 0.001 HIS A 294 PHE 0.030 0.002 PHE A 33 TYR 0.021 0.001 TYR B 542 ARG 0.004 0.000 ARG B 85 *********************** 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 192 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 141 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5887 (t80) REVERT: A 391 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4583 (tt) REVERT: A 491 LEU cc_start: 0.2188 (OUTLIER) cc_final: 0.0915 (tt) REVERT: A 642 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6218 (mp) REVERT: A 669 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.3842 (t80) REVERT: B 294 HIS cc_start: 0.2904 (OUTLIER) cc_final: 0.2680 (m-70) REVERT: B 390 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.5728 (t80) REVERT: B 394 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6147 (mp) REVERT: B 491 LEU cc_start: 0.2050 (OUTLIER) cc_final: 0.0759 (tt) REVERT: B 642 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6216 (mp) REVERT: B 669 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.3842 (t80) outliers start: 51 outliers final: 30 residues processed: 186 average time/residue: 1.1095 time to fit residues: 225.8396 Evaluate side-chains 176 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 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 498 SER 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 394 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 498 SER 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 717 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 0.2980 chunk 130 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 31 GLN B 127 ASN B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11916 Z= 0.235 Angle : 0.752 9.670 16196 Z= 0.384 Chirality : 0.046 0.366 1818 Planarity : 0.007 0.071 2024 Dihedral : 7.590 59.990 1618 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.66 % Favored : 90.06 % Rotamer: Outliers : 3.56 % Allowed : 33.74 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1428 helix: 1.38 (0.18), residues: 914 sheet: -3.08 (0.54), residues: 46 loop : -3.42 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.007 0.001 HIS B 294 PHE 0.031 0.001 PHE B 33 TYR 0.021 0.001 TYR A 542 ARG 0.015 0.001 ARG B 36 ********************** 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 178 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 134 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5793 (t80) REVERT: A 491 LEU cc_start: 0.2039 (OUTLIER) cc_final: 0.0709 (tt) REVERT: A 642 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6267 (mp) REVERT: A 669 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.3887 (t80) REVERT: B 390 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5588 (t80) REVERT: B 394 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6003 (mp) REVERT: B 491 LEU cc_start: 0.2045 (OUTLIER) cc_final: 0.0699 (tt) REVERT: B 642 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6265 (mp) REVERT: B 669 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.3891 (t80) outliers start: 44 outliers final: 29 residues processed: 172 average time/residue: 1.2126 time to fit residues: 227.8023 Evaluate side-chains 173 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 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 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 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 394 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 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: 0.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 6 optimal weight: 0.0070 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN B 31 GLN B 256 GLN ** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.183441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131514 restraints weight = 13583.140| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.58 r_work: 0.3516 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11916 Z= 0.223 Angle : 0.722 9.764 16196 Z= 0.370 Chirality : 0.046 0.392 1818 Planarity : 0.006 0.069 2024 Dihedral : 7.470 59.796 1618 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.94 % Favored : 89.78 % Rotamer: Outliers : 3.40 % Allowed : 33.82 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.26 (0.23), residues: 1428 helix: 1.48 (0.18), residues: 914 sheet: -3.10 (0.54), residues: 46 loop : -3.41 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 625 HIS 0.008 0.001 HIS B 294 PHE 0.029 0.001 PHE B 33 TYR 0.014 0.001 TYR A 98 ARG 0.004 0.000 ARG A 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5069.67 seconds wall clock time: 95 minutes 48.68 seconds (5748.68 seconds total)