Starting phenix.real_space_refine on Sun Dec 29 13:30:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6m_36008/12_2024/8j6m_36008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6m_36008/12_2024/8j6m_36008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6m_36008/12_2024/8j6m_36008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6m_36008/12_2024/8j6m_36008.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6m_36008/12_2024/8j6m_36008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6m_36008/12_2024/8j6m_36008.cif" } resolution = 2.77 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= 0.000 sd= 0.153 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 56 5.16 5 Na 1 4.78 5 C 7084 2.51 5 N 1644 2.21 5 O 1812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10599 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 5284 Chain: "A" Number of atoms: 5165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 641, 5156 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 5284 Chain: "B" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 134 Unusual residues: {' NA': 1, ' ZN': 1, 'CLR': 4, 'OLA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Unusual residues: {' ZN': 1, 'CLR': 4, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.35, per 1000 atoms: 1.07 Number of scatterers: 10599 At special positions: 0 Unit cell: (113.36, 86.32, 126.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 56 16.00 Na 1 11.00 O 1812 8.00 N 1644 7.00 C 7084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.04 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.07 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: 2.77 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 905 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 795 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 905 " - pdb=" NE2 HIS B 791 " 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 50.5% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 251 through 255 Proline residue: B 254 - end of helix No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 302 through 338 removed outlier: 3.833A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 474 removed outlier: 4.509A pdb=" N TRP B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) Proline residue: B 458 - end of helix removed outlier: 3.605A pdb=" N THR B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.727A pdb=" N ALA B 486 " --> pdb=" O PHE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.934A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.891A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 536 Processing helix chain 'B' and resid 542 through 563 Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.808A pdb=" N ASP B 574 " --> pdb=" O PHE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.851A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 622 removed outlier: 3.555A pdb=" N ALA B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 648 removed outlier: 3.583A pdb=" N THR B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 3.970A pdb=" N ASN B 694 " --> pdb=" O GLY B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 735 Processing helix chain 'B' and resid 740 through 762 Processing helix chain 'B' and resid 771 through 777 removed outlier: 3.514A pdb=" N GLU B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 812 removed outlier: 3.537A pdb=" N ALA B 799 " --> pdb=" O HIS B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 818 removed outlier: 3.693A pdb=" N ASP B 817 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 818 " --> pdb=" O ASP B 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Proline residue: A 254 - end of helix No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 302 through 338 removed outlier: 3.834A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 474 removed outlier: 4.504A pdb=" N TRP A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.603A pdb=" N THR A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.909A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 529 removed outlier: 3.777A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 542 through 565 removed outlier: 4.139A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.803A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 622 removed outlier: 3.553A pdb=" N ALA A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 648 Processing helix chain 'A' and resid 683 through 705 removed outlier: 3.503A pdb=" N ASN A 694 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 735 Processing helix chain 'A' and resid 740 through 762 Processing helix chain 'A' and resid 771 through 777 removed outlier: 3.568A pdb=" N GLU A 777 " --> pdb=" O ALA A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 812 removed outlier: 3.537A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.502A pdb=" N ASP A 817 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 818 " --> pdb=" O ASP A 815 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 50 through 56 removed outlier: 4.390A pdb=" N HIS B 50 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 163 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 77 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA4, first strand: chain 'B' and resid 170 through 171 removed outlier: 4.793A pdb=" N LYS B 192 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 181 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 56 removed outlier: 4.390A pdb=" N HIS A 50 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 163 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA9, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.794A pdb=" N LYS A 192 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 176 through 181 634 hydrogen bonds defined for protein. 1822 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: 3.72 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1967 1.32 - 1.45: 3197 1.45 - 1.59: 5648 1.59 - 1.72: 0 1.72 - 1.85: 86 Bond restraints: 10898 Sorted by residual: bond pdb=" C TYR A 81 " pdb=" CA BTYR A 81 " ideal model delta sigma weight residual 1.521 1.422 0.099 1.19e-02 7.06e+03 6.96e+01 bond pdb=" C10 OLA A 906 " pdb=" C9 OLA A 906 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C10 OLA B 907 " pdb=" C9 OLA B 907 " ideal model delta sigma weight residual 1.332 1.469 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" N TYR B 81 " pdb=" CA BTYR B 81 " ideal model delta sigma weight residual 1.456 1.409 0.048 1.21e-02 6.83e+03 1.55e+01 bond pdb=" CA VAL A 108 " pdb=" C VAL A 108 " ideal model delta sigma weight residual 1.525 1.557 -0.033 9.10e-03 1.21e+04 1.29e+01 ... (remaining 10893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 14191 2.39 - 4.79: 547 4.79 - 7.18: 96 7.18 - 9.58: 28 9.58 - 11.97: 6 Bond angle restraints: 14868 Sorted by residual: angle pdb=" N VAL A 534 " pdb=" CA VAL A 534 " pdb=" C VAL A 534 " ideal model delta sigma weight residual 110.53 119.47 -8.94 9.40e-01 1.13e+00 9.04e+01 angle pdb=" N SER A 274 " pdb=" CA SER A 274 " pdb=" C SER A 274 " ideal model delta sigma weight residual 111.28 121.07 -9.79 1.09e+00 8.42e-01 8.06e+01 angle pdb=" N VAL B 534 " pdb=" CA VAL B 534 " pdb=" C VAL B 534 " ideal model delta sigma weight residual 110.53 118.91 -8.38 9.40e-01 1.13e+00 7.95e+01 angle pdb=" N PHE B 275 " pdb=" CA PHE B 275 " pdb=" C PHE B 275 " ideal model delta sigma weight residual 110.19 119.77 -9.58 1.24e+00 6.50e-01 5.97e+01 angle pdb=" N LEU A 155 " pdb=" CA LEU A 155 " pdb=" C LEU A 155 " ideal model delta sigma weight residual 110.17 98.20 11.97 1.61e+00 3.86e-01 5.53e+01 ... (remaining 14863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.91: 6274 24.91 - 49.82: 410 49.82 - 74.73: 46 74.73 - 99.64: 17 99.64 - 124.55: 3 Dihedral angle restraints: 6750 sinusoidal: 2932 harmonic: 3818 Sorted by residual: dihedral pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " pdb=" SG CYS A 782 " pdb=" CB CYS A 782 " ideal model delta sinusoidal sigma weight residual 93.00 34.75 58.25 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS B 485 " pdb=" SG CYS B 485 " pdb=" SG CYS B 782 " pdb=" CB CYS B 782 " ideal model delta sinusoidal sigma weight residual 93.00 37.35 55.65 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA CYS A 782 " pdb=" C CYS A 782 " pdb=" N ILE A 783 " pdb=" CA ILE A 783 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 6747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1445 0.101 - 0.202: 196 0.202 - 0.303: 52 0.303 - 0.404: 12 0.404 - 0.506: 5 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CA PHE B 317 " pdb=" N PHE B 317 " pdb=" C PHE B 317 " pdb=" CB PHE B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.39e+00 chirality pdb=" CA PHE A 317 " pdb=" N PHE A 317 " pdb=" C PHE A 317 " pdb=" CB PHE A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CA ASN B 83 " pdb=" N ASN B 83 " pdb=" C ASN B 83 " pdb=" CB ASN B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1707 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA A 906 " -0.279 2.00e-02 2.50e+03 2.13e-01 4.54e+02 pdb=" C11 OLA A 906 " 0.114 2.00e-02 2.50e+03 pdb=" C8 OLA A 906 " -0.115 2.00e-02 2.50e+03 pdb=" C9 OLA A 906 " 0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA B 907 " 0.279 2.00e-02 2.50e+03 2.13e-01 4.54e+02 pdb=" C11 OLA B 907 " -0.114 2.00e-02 2.50e+03 pdb=" C8 OLA B 907 " 0.114 2.00e-02 2.50e+03 pdb=" C9 OLA B 907 " -0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 525 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ALA B 525 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA B 525 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 526 " 0.020 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 28 2.47 - 3.07: 7058 3.07 - 3.68: 15994 3.68 - 4.29: 26004 4.29 - 4.90: 42374 Nonbonded interactions: 91458 Sorted by model distance: nonbonded pdb=" OD1 ASP B 574 " pdb="ZN ZN B 905 " model vdw 1.857 2.230 nonbonded pdb=" NE2 GLN B 100 " pdb=" O ASN A 90 " model vdw 2.291 3.120 nonbonded pdb=" OD1 ASP A 574 " pdb="ZN ZN A 901 " model vdw 2.292 2.230 nonbonded pdb=" NZ LYS B 732 " pdb=" OD1 ASP B 813 " model vdw 2.302 3.120 nonbonded pdb=" NZ LYS A 732 " pdb=" OD1 ASP A 813 " model vdw 2.302 3.120 ... (remaining 91453 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' and (resid 44 through 80 or resid 82 through 827 or resid 902 through \ 904)) selection = (chain 'B' and (resid 44 through 80 or resid 82 through 827 or resid 902 through \ 904)) } 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=0.50 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: 1.720 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.450 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.008 0.138 10898 Z= 0.522 Angle : 1.104 11.972 14868 Z= 0.699 Chirality : 0.083 0.506 1710 Planarity : 0.009 0.213 1806 Dihedral : 16.073 124.552 4262 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 1.59 % Allowed : 16.96 % Favored : 81.45 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 12.50 % 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: 0.97 (0.22), residues: 1268 helix: 1.31 (0.20), residues: 580 sheet: 1.50 (0.27), residues: 284 loop : -0.95 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 106 HIS 0.004 0.001 HIS A 636 PHE 0.023 0.002 PHE A 317 TYR 0.021 0.002 TYR B 605 ARG 0.007 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.136 Fit side-chains REVERT: B 61 GLU cc_start: 0.8596 (tt0) cc_final: 0.8376 (tt0) REVERT: B 118 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6760 (mtp180) REVERT: B 123 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8288 (mm110) REVERT: B 302 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7401 (mmtt) REVERT: B 586 MET cc_start: 0.8307 (mtm) cc_final: 0.8098 (mtp) REVERT: B 684 MET cc_start: 0.5846 (tmt) cc_final: 0.5295 (mpp) REVERT: B 702 LEU cc_start: 0.7717 (tp) cc_final: 0.7302 (tt) REVERT: B 707 ARG cc_start: 0.7243 (tpp80) cc_final: 0.6898 (mmm160) REVERT: B 738 LYS cc_start: 0.7521 (mttt) cc_final: 0.7302 (mtpm) REVERT: A 61 GLU cc_start: 0.8588 (tt0) cc_final: 0.8357 (tt0) REVERT: A 118 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6685 (mtp180) REVERT: A 302 LYS cc_start: 0.8036 (mptm) cc_final: 0.7561 (mmtt) REVERT: A 505 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8235 (m) REVERT: A 684 MET cc_start: 0.5580 (tmt) cc_final: 0.5113 (mpp) REVERT: A 707 ARG cc_start: 0.7280 (tpp80) cc_final: 0.6963 (mmm160) REVERT: A 774 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7634 (mt-10) outliers start: 18 outliers final: 9 residues processed: 203 average time/residue: 1.0650 time to fit residues: 236.2212 Evaluate side-chains 168 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN B 720 ASN A 461 GLN A 475 ASN A 541 HIS A 646 GLN A 694 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10898 Z= 0.255 Angle : 0.606 7.245 14868 Z= 0.310 Chirality : 0.045 0.190 1710 Planarity : 0.004 0.035 1806 Dihedral : 8.469 55.936 1964 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.00 % Allowed : 18.29 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.65 (0.22), residues: 1268 helix: 2.23 (0.19), residues: 584 sheet: 1.33 (0.28), residues: 284 loop : -0.83 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.005 0.001 HIS B 563 PHE 0.023 0.002 PHE A 317 TYR 0.015 0.002 TYR A 605 ARG 0.006 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.115 Fit side-chains REVERT: B 61 GLU cc_start: 0.8335 (tt0) cc_final: 0.8118 (tt0) REVERT: B 90 ASN cc_start: 0.7893 (m-40) cc_final: 0.7669 (m-40) REVERT: B 118 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.6718 (mtp180) REVERT: B 158 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: B 274 SER cc_start: 0.7460 (m) cc_final: 0.7204 (t) REVERT: B 576 SER cc_start: 0.8313 (m) cc_final: 0.7987 (p) REVERT: B 684 MET cc_start: 0.5613 (tmt) cc_final: 0.5050 (mpm) REVERT: B 702 LEU cc_start: 0.7742 (tp) cc_final: 0.7337 (tt) REVERT: B 707 ARG cc_start: 0.7136 (tpp80) cc_final: 0.6841 (mmm160) REVERT: B 738 LYS cc_start: 0.7574 (mttt) cc_final: 0.7117 (mtpm) REVERT: A 90 ASN cc_start: 0.7763 (m-40) cc_final: 0.7554 (m-40) REVERT: A 118 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.6649 (mtp180) REVERT: A 158 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: A 302 LYS cc_start: 0.7868 (mptm) cc_final: 0.7549 (mmtm) REVERT: A 536 TYR cc_start: 0.7656 (m-80) cc_final: 0.7374 (m-80) REVERT: A 576 SER cc_start: 0.8230 (m) cc_final: 0.7897 (p) REVERT: A 684 MET cc_start: 0.5385 (tmt) cc_final: 0.4900 (mpp) REVERT: A 692 LEU cc_start: 0.7587 (mp) cc_final: 0.7355 (mp) REVERT: A 707 ARG cc_start: 0.7143 (tpp80) cc_final: 0.6821 (mmm160) REVERT: A 738 LYS cc_start: 0.6906 (mtpm) cc_final: 0.5709 (mmtp) REVERT: A 774 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7627 (mt-10) outliers start: 34 outliers final: 18 residues processed: 192 average time/residue: 0.9680 time to fit residues: 204.6906 Evaluate side-chains 179 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 713 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN B 475 ASN B 720 ASN B 779 ASN A 646 GLN A 764 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10898 Z= 0.355 Angle : 0.613 8.127 14868 Z= 0.315 Chirality : 0.046 0.160 1710 Planarity : 0.004 0.039 1806 Dihedral : 7.535 58.242 1956 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.53 % Allowed : 18.90 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.53 (0.22), residues: 1268 helix: 2.19 (0.20), residues: 584 sheet: 1.16 (0.29), residues: 284 loop : -0.91 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 629 HIS 0.006 0.001 HIS A 563 PHE 0.016 0.002 PHE A 317 TYR 0.019 0.002 TYR A 605 ARG 0.005 0.001 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.194 Fit side-chains REVERT: B 118 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6632 (mtp180) REVERT: B 158 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: B 207 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: B 274 SER cc_start: 0.7372 (OUTLIER) cc_final: 0.7091 (t) REVERT: B 297 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 576 SER cc_start: 0.8491 (m) cc_final: 0.8116 (p) REVERT: B 702 LEU cc_start: 0.7795 (tp) cc_final: 0.7412 (tt) REVERT: B 707 ARG cc_start: 0.7170 (tpp80) cc_final: 0.6906 (mmm160) REVERT: B 738 LYS cc_start: 0.7675 (mttt) cc_final: 0.7199 (mtpm) REVERT: A 90 ASN cc_start: 0.7841 (m-40) cc_final: 0.7568 (m-40) REVERT: A 118 ARG cc_start: 0.7252 (ttm-80) cc_final: 0.6590 (mtp180) REVERT: A 158 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: A 207 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: A 297 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8366 (mm) REVERT: A 302 LYS cc_start: 0.7956 (mptm) cc_final: 0.7656 (mmmm) REVERT: A 536 TYR cc_start: 0.7614 (m-80) cc_final: 0.7329 (m-80) REVERT: A 576 SER cc_start: 0.8324 (m) cc_final: 0.7922 (p) REVERT: A 692 LEU cc_start: 0.7621 (mp) cc_final: 0.7386 (mp) REVERT: A 707 ARG cc_start: 0.7215 (tpp80) cc_final: 0.6930 (mmm160) REVERT: A 774 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7565 (mt-10) outliers start: 40 outliers final: 22 residues processed: 187 average time/residue: 0.9745 time to fit residues: 201.0472 Evaluate side-chains 191 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 0.0570 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 ASN B 646 GLN B 720 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10898 Z= 0.219 Angle : 0.524 7.497 14868 Z= 0.270 Chirality : 0.043 0.142 1710 Planarity : 0.003 0.038 1806 Dihedral : 7.239 59.377 1956 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.71 % Allowed : 19.26 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.78 (0.23), residues: 1268 helix: 2.50 (0.20), residues: 584 sheet: 1.10 (0.29), residues: 284 loop : -0.80 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 PHE 0.013 0.001 PHE A 317 TYR 0.021 0.002 TYR A 605 ARG 0.004 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 1.175 Fit side-chains REVERT: B 118 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6565 (mtp180) REVERT: B 207 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 274 SER cc_start: 0.7331 (OUTLIER) cc_final: 0.7099 (t) REVERT: B 297 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8444 (mm) REVERT: B 576 SER cc_start: 0.8441 (m) cc_final: 0.8039 (p) REVERT: B 702 LEU cc_start: 0.7805 (tp) cc_final: 0.7448 (tt) REVERT: B 707 ARG cc_start: 0.7231 (tpp80) cc_final: 0.6882 (mmm160) REVERT: B 738 LYS cc_start: 0.7626 (mttt) cc_final: 0.7148 (mtmm) REVERT: B 753 MET cc_start: 0.8702 (mmt) cc_final: 0.8063 (mmt) REVERT: A 61 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: A 90 ASN cc_start: 0.7864 (m-40) cc_final: 0.7602 (m-40) REVERT: A 118 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6508 (mtp180) REVERT: A 207 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: A 297 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 454 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6608 (t80) REVERT: A 524 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6361 (mtt180) REVERT: A 536 TYR cc_start: 0.7695 (m-80) cc_final: 0.7454 (m-80) REVERT: A 576 SER cc_start: 0.8280 (m) cc_final: 0.7842 (p) REVERT: A 692 LEU cc_start: 0.7566 (mp) cc_final: 0.7302 (mm) REVERT: A 707 ARG cc_start: 0.7215 (tpp80) cc_final: 0.6881 (mmm160) REVERT: A 753 MET cc_start: 0.8664 (mmt) cc_final: 0.7916 (mmt) REVERT: A 774 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7609 (mt-10) outliers start: 42 outliers final: 21 residues processed: 184 average time/residue: 0.9561 time to fit residues: 193.9527 Evaluate side-chains 182 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 1 optimal weight: 0.0270 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS B 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10898 Z= 0.190 Angle : 0.490 6.500 14868 Z= 0.254 Chirality : 0.041 0.141 1710 Planarity : 0.003 0.036 1806 Dihedral : 6.980 59.936 1952 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.36 % Allowed : 19.79 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.93 (0.23), residues: 1268 helix: 2.67 (0.20), residues: 584 sheet: 1.06 (0.29), residues: 284 loop : -0.72 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.004 0.001 HIS A 563 PHE 0.012 0.001 PHE A 317 TYR 0.019 0.001 TYR A 605 ARG 0.007 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.070 Fit side-chains REVERT: B 118 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6500 (mtp180) REVERT: B 158 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: B 207 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: B 297 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8432 (mm) REVERT: B 576 SER cc_start: 0.8422 (m) cc_final: 0.8008 (p) REVERT: B 707 ARG cc_start: 0.7241 (tpp80) cc_final: 0.6877 (mmm160) REVERT: B 738 LYS cc_start: 0.7451 (mttt) cc_final: 0.6688 (mtmm) REVERT: B 815 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6835 (p0) REVERT: A 61 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: A 83 ASN cc_start: 0.8164 (p0) cc_final: 0.7886 (p0) REVERT: A 90 ASN cc_start: 0.7842 (m-40) cc_final: 0.7497 (m-40) REVERT: A 118 ARG cc_start: 0.7178 (ttm-80) cc_final: 0.6423 (mtp180) REVERT: A 158 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: A 207 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: A 297 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 536 TYR cc_start: 0.7761 (m-80) cc_final: 0.7539 (m-80) REVERT: A 576 SER cc_start: 0.8478 (m) cc_final: 0.8034 (p) REVERT: A 692 LEU cc_start: 0.7610 (mp) cc_final: 0.7369 (mm) REVERT: A 707 ARG cc_start: 0.7226 (tpp80) cc_final: 0.6860 (mmm160) REVERT: A 713 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8150 (mmm) REVERT: A 738 LYS cc_start: 0.7021 (mtpm) cc_final: 0.6189 (mtmm) REVERT: A 753 MET cc_start: 0.8643 (mmt) cc_final: 0.7904 (mmt) REVERT: A 774 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7582 (mt-10) outliers start: 38 outliers final: 22 residues processed: 179 average time/residue: 0.9496 time to fit residues: 187.8326 Evaluate side-chains 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 815 ASP Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10898 Z= 0.249 Angle : 0.525 7.242 14868 Z= 0.269 Chirality : 0.042 0.142 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.975 59.945 1951 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.15 % Allowed : 19.43 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.89 (0.23), residues: 1268 helix: 2.64 (0.20), residues: 584 sheet: 1.16 (0.30), residues: 272 loop : -0.80 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.005 0.001 HIS A 563 PHE 0.011 0.001 PHE B 632 TYR 0.023 0.002 TYR A 605 ARG 0.005 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.193 Fit side-chains REVERT: B 118 ARG cc_start: 0.7261 (ttm-80) cc_final: 0.6587 (mtp180) REVERT: B 158 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: B 207 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: B 297 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 519 ASP cc_start: 0.6922 (t0) cc_final: 0.6618 (t70) REVERT: B 576 SER cc_start: 0.8446 (m) cc_final: 0.8003 (p) REVERT: B 702 LEU cc_start: 0.7752 (tp) cc_final: 0.7366 (tt) REVERT: B 707 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6885 (mmm160) REVERT: B 738 LYS cc_start: 0.7465 (mttt) cc_final: 0.6718 (mtmm) REVERT: B 753 MET cc_start: 0.8700 (mmt) cc_final: 0.8134 (mmt) REVERT: B 815 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6794 (p0) REVERT: A 83 ASN cc_start: 0.8261 (p0) cc_final: 0.8059 (p0) REVERT: A 90 ASN cc_start: 0.7821 (m-40) cc_final: 0.7528 (m-40) REVERT: A 118 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6522 (mtp180) REVERT: A 158 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: A 207 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 297 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8415 (mm) REVERT: A 454 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6437 (t80) REVERT: A 524 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6464 (mtt180) REVERT: A 536 TYR cc_start: 0.7780 (m-80) cc_final: 0.7535 (m-80) REVERT: A 576 SER cc_start: 0.8505 (m) cc_final: 0.8022 (p) REVERT: A 692 LEU cc_start: 0.7590 (mp) cc_final: 0.7354 (mm) REVERT: A 707 ARG cc_start: 0.7238 (tpp80) cc_final: 0.6868 (mmm160) REVERT: A 713 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: A 738 LYS cc_start: 0.7155 (mtpm) cc_final: 0.6318 (mtmm) REVERT: A 753 MET cc_start: 0.8716 (mmt) cc_final: 0.7981 (mmt) REVERT: A 774 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7598 (mt-10) outliers start: 47 outliers final: 27 residues processed: 182 average time/residue: 1.0121 time to fit residues: 202.3196 Evaluate side-chains 190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 815 ASP Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN A 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10898 Z= 0.171 Angle : 0.477 7.038 14868 Z= 0.246 Chirality : 0.041 0.141 1710 Planarity : 0.003 0.037 1806 Dihedral : 6.797 59.415 1951 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.36 % Allowed : 20.14 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.05 (0.23), residues: 1268 helix: 2.78 (0.20), residues: 584 sheet: 1.17 (0.30), residues: 272 loop : -0.67 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS A 563 PHE 0.011 0.001 PHE B 317 TYR 0.022 0.001 TYR A 605 ARG 0.006 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.385 Fit side-chains REVERT: B 100 GLN cc_start: 0.8326 (tt0) cc_final: 0.7872 (tm-30) REVERT: B 101 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7405 (mppt) REVERT: B 118 ARG cc_start: 0.7226 (ttm-80) cc_final: 0.6519 (mtp180) REVERT: B 152 MET cc_start: 0.8511 (mtt) cc_final: 0.8220 (mtt) REVERT: B 158 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: B 207 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 576 SER cc_start: 0.8465 (m) cc_final: 0.8004 (p) REVERT: B 577 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: B 702 LEU cc_start: 0.7709 (tp) cc_final: 0.7318 (tt) REVERT: B 707 ARG cc_start: 0.7242 (tpp80) cc_final: 0.6875 (mmm160) REVERT: B 713 MET cc_start: 0.8104 (mmm) cc_final: 0.7857 (mtp) REVERT: B 738 LYS cc_start: 0.7407 (mttt) cc_final: 0.6675 (mtmm) REVERT: B 753 MET cc_start: 0.8700 (mmt) cc_final: 0.8132 (mmt) REVERT: B 815 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6777 (p0) REVERT: A 83 ASN cc_start: 0.8077 (p0) cc_final: 0.7841 (p0) REVERT: A 90 ASN cc_start: 0.7712 (m-40) cc_final: 0.7437 (m-40) REVERT: A 118 ARG cc_start: 0.7183 (ttm-80) cc_final: 0.6481 (mtp180) REVERT: A 158 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: A 207 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: A 297 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 454 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6404 (t80) REVERT: A 536 TYR cc_start: 0.7775 (m-80) cc_final: 0.7531 (m-80) REVERT: A 576 SER cc_start: 0.8483 (m) cc_final: 0.8003 (p) REVERT: A 692 LEU cc_start: 0.7574 (mp) cc_final: 0.7343 (mm) REVERT: A 707 ARG cc_start: 0.7252 (tpp80) cc_final: 0.6883 (mmm160) REVERT: A 713 MET cc_start: 0.8362 (mmt) cc_final: 0.8151 (mmm) REVERT: A 738 LYS cc_start: 0.6992 (mtpm) cc_final: 0.6178 (mtmm) REVERT: A 753 MET cc_start: 0.8630 (mmt) cc_final: 0.7972 (mmt) outliers start: 38 outliers final: 22 residues processed: 183 average time/residue: 0.9934 time to fit residues: 200.5166 Evaluate side-chains 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 815 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 ASN B 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10898 Z= 0.230 Angle : 0.506 6.664 14868 Z= 0.260 Chirality : 0.042 0.142 1710 Planarity : 0.003 0.036 1806 Dihedral : 6.826 59.440 1951 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.36 % Allowed : 19.88 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.00 (0.23), residues: 1268 helix: 2.73 (0.20), residues: 584 sheet: 1.28 (0.30), residues: 268 loop : -0.75 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 563 PHE 0.011 0.001 PHE B 632 TYR 0.018 0.002 TYR A 605 ARG 0.005 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.227 Fit side-chains REVERT: B 101 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7438 (mppt) REVERT: B 118 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6477 (mtp180) REVERT: B 152 MET cc_start: 0.8502 (mtt) cc_final: 0.8168 (mtt) REVERT: B 158 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: B 207 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: B 519 ASP cc_start: 0.6880 (t0) cc_final: 0.6621 (t70) REVERT: B 576 SER cc_start: 0.8427 (m) cc_final: 0.7963 (p) REVERT: B 577 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: B 702 LEU cc_start: 0.7762 (tp) cc_final: 0.7369 (tt) REVERT: B 707 ARG cc_start: 0.7250 (tpp80) cc_final: 0.6876 (mmm160) REVERT: B 738 LYS cc_start: 0.7405 (mttt) cc_final: 0.6681 (mtmm) REVERT: B 753 MET cc_start: 0.8702 (mmt) cc_final: 0.8155 (mmt) REVERT: B 815 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6819 (p0) REVERT: A 83 ASN cc_start: 0.8181 (p0) cc_final: 0.7952 (p0) REVERT: A 90 ASN cc_start: 0.7734 (m-40) cc_final: 0.7448 (m-40) REVERT: A 118 ARG cc_start: 0.7191 (ttm-80) cc_final: 0.6419 (mtp180) REVERT: A 158 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: A 207 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 297 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 454 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.6482 (t80) REVERT: A 536 TYR cc_start: 0.7784 (m-80) cc_final: 0.7530 (m-80) REVERT: A 576 SER cc_start: 0.8492 (m) cc_final: 0.7993 (p) REVERT: A 692 LEU cc_start: 0.7554 (mp) cc_final: 0.7325 (mm) REVERT: A 707 ARG cc_start: 0.7257 (tpp80) cc_final: 0.6881 (mmm160) REVERT: A 713 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8148 (mmm) REVERT: A 738 LYS cc_start: 0.7127 (mtpm) cc_final: 0.6315 (mtmm) REVERT: A 753 MET cc_start: 0.8693 (mmt) cc_final: 0.8040 (mmt) outliers start: 38 outliers final: 24 residues processed: 178 average time/residue: 0.9743 time to fit residues: 191.1518 Evaluate side-chains 187 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 815 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 10898 Z= 0.442 Angle : 0.644 9.386 14868 Z= 0.328 Chirality : 0.047 0.174 1710 Planarity : 0.004 0.043 1806 Dihedral : 7.347 58.708 1951 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.98 % Allowed : 19.35 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.52 (0.23), residues: 1268 helix: 2.27 (0.20), residues: 584 sheet: 1.10 (0.31), residues: 272 loop : -0.95 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 629 HIS 0.006 0.002 HIS A 563 PHE 0.015 0.002 PHE B 632 TYR 0.032 0.003 TYR A 605 ARG 0.006 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.199 Fit side-chains REVERT: B 101 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7333 (mppt) REVERT: B 118 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6626 (mtp180) REVERT: B 158 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: B 207 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 274 SER cc_start: 0.7313 (OUTLIER) cc_final: 0.7084 (t) REVERT: B 297 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 576 SER cc_start: 0.8555 (m) cc_final: 0.8083 (p) REVERT: B 577 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: B 702 LEU cc_start: 0.7800 (tp) cc_final: 0.7441 (tt) REVERT: B 707 ARG cc_start: 0.7297 (tpp80) cc_final: 0.6900 (mmm160) REVERT: B 738 LYS cc_start: 0.7544 (mttt) cc_final: 0.7033 (mtmm) REVERT: A 83 ASN cc_start: 0.8604 (p0) cc_final: 0.8294 (p0) REVERT: A 90 ASN cc_start: 0.7789 (m-40) cc_final: 0.7551 (m-40) REVERT: A 118 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.6492 (mtp180) REVERT: A 158 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: A 207 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 454 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6624 (t80) REVERT: A 519 ASP cc_start: 0.7079 (t0) cc_final: 0.6769 (t70) REVERT: A 536 TYR cc_start: 0.7784 (m-80) cc_final: 0.7580 (m-80) REVERT: A 576 SER cc_start: 0.8352 (m) cc_final: 0.7864 (p) REVERT: A 692 LEU cc_start: 0.7540 (mp) cc_final: 0.7247 (mm) REVERT: A 702 LEU cc_start: 0.7792 (tp) cc_final: 0.7404 (tt) REVERT: A 707 ARG cc_start: 0.7284 (tpp80) cc_final: 0.6886 (mmm160) REVERT: A 713 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8148 (mmm) outliers start: 45 outliers final: 25 residues processed: 175 average time/residue: 0.9685 time to fit residues: 186.8982 Evaluate side-chains 180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 454 PHE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 646 GLN A 764 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10898 Z= 0.240 Angle : 0.529 7.154 14868 Z= 0.273 Chirality : 0.042 0.145 1710 Planarity : 0.003 0.039 1806 Dihedral : 7.072 57.380 1951 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.18 % Allowed : 20.23 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.76 (0.23), residues: 1268 helix: 2.49 (0.20), residues: 584 sheet: 1.12 (0.31), residues: 272 loop : -0.80 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.005 0.001 HIS A 563 PHE 0.011 0.001 PHE B 632 TYR 0.032 0.002 TYR A 605 ARG 0.005 0.000 ARG B 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.213 Fit side-chains REVERT: B 101 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7573 (mppt) REVERT: B 118 ARG cc_start: 0.7254 (ttm-80) cc_final: 0.6608 (mtp180) REVERT: B 158 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: B 207 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: B 274 SER cc_start: 0.7108 (OUTLIER) cc_final: 0.6861 (t) REVERT: B 297 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8360 (mm) REVERT: B 576 SER cc_start: 0.8474 (m) cc_final: 0.8025 (p) REVERT: B 577 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: B 702 LEU cc_start: 0.7751 (tp) cc_final: 0.7369 (tt) REVERT: B 707 ARG cc_start: 0.7284 (tpp80) cc_final: 0.6898 (mmm160) REVERT: B 738 LYS cc_start: 0.7460 (mttt) cc_final: 0.6959 (mtmm) REVERT: B 753 MET cc_start: 0.8696 (mmt) cc_final: 0.8088 (mmt) REVERT: A 90 ASN cc_start: 0.7746 (m-40) cc_final: 0.7530 (m-40) REVERT: A 118 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6487 (mtp180) REVERT: A 158 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: A 207 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 524 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6337 (mtt180) REVERT: A 576 SER cc_start: 0.8298 (m) cc_final: 0.7831 (p) REVERT: A 692 LEU cc_start: 0.7454 (mp) cc_final: 0.7237 (mm) REVERT: A 707 ARG cc_start: 0.7290 (tpp80) cc_final: 0.6893 (mmm160) REVERT: A 713 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8121 (mmm) REVERT: A 753 MET cc_start: 0.8723 (mmt) cc_final: 0.8018 (mmt) outliers start: 36 outliers final: 24 residues processed: 168 average time/residue: 1.0495 time to fit residues: 194.3441 Evaluate side-chains 180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 524 ARG Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 764 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 ASN B 646 GLN A 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116895 restraints weight = 18169.269| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.56 r_work: 0.3104 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10898 Z= 0.273 Angle : 0.541 7.316 14868 Z= 0.279 Chirality : 0.043 0.142 1710 Planarity : 0.003 0.037 1806 Dihedral : 7.071 57.446 1951 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.18 % Allowed : 19.96 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.75 (0.23), residues: 1268 helix: 2.49 (0.20), residues: 584 sheet: 1.11 (0.31), residues: 272 loop : -0.80 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 629 HIS 0.005 0.001 HIS A 563 PHE 0.012 0.002 PHE B 632 TYR 0.031 0.002 TYR A 605 ARG 0.005 0.001 ARG A 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.57 seconds wall clock time: 71 minutes 32.94 seconds (4292.94 seconds total)