Starting phenix.real_space_refine on Thu Oct 22 19:54:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4k_48883/10_2026/9n4k_48883_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4k_48883/10_2026/9n4k_48883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n4k_48883/10_2026/9n4k_48883_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4k_48883/10_2026/9n4k_48883_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n4k_48883/10_2026/9n4k_48883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4k_48883/10_2026/9n4k_48883.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 2834 2.51 5 N 774 2.21 5 O 906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4578 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 772 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "B" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 822 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 97} Chain: "C" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 603 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: F, E, D, H Time building chain proxies: 1.28, per 1000 atoms: 0.28 Number of scatterers: 4578 At special positions: 0 Unit cell: (119.138, 76.349, 69.637, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 906 8.00 N 774 7.00 C 2834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 445 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS E 412 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 441 " - pdb=" SG CYS E 510 " distance=2.03 Simple disulfide: pdb=" SG CYS E 445 " - pdb=" SG CYS E 512 " distance=2.03 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 59 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 103 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 102 " distance=2.03 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 53 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 42 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 70 " distance=2.04 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 53 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 70 " distance=2.04 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS D 99 " distance=2.03 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 Links applied BETA1-4 " NAG B 601 " - " NAG B 602 " " NAG B 602 " - " BMA B 603 " " NAG E 601 " - " NAG E 602 " " NAG E 602 " - " BMA E 603 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 201 " - " ASN A 42 " " NAG B 601 " - " ASN B 454 " " NAG E 601 " - " ASN E 454 " " NAG F 201 " - " ASN F 42 " " NAG G 1 " - " ASN A 65 " " NAG H 1 " - " ASN F 65 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 138.8 milliseconds 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 14 sheets defined 10.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'E' and resid 456 through 469 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 73 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.383A pdb=" N LEU A 72 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG A 64 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 413 through 414 removed outlier: 3.514A pdb=" N ASP B 442 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA5, first strand: chain 'B' and resid 430 through 432 removed outlier: 6.029A pdb=" N ILE B 430 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE B 491 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ARG B 508 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 482 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 506 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASN B 484 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 413 through 414 removed outlier: 3.514A pdb=" N ASP E 442 " --> pdb=" O ARG E 413 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 419 through 420 Processing sheet with id=AA8, first strand: chain 'E' and resid 430 through 432 removed outlier: 6.029A pdb=" N ILE E 430 " --> pdb=" O PHE E 491 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE E 491 " --> pdb=" O ILE E 430 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ARG E 508 " --> pdb=" O PRO E 480 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS E 482 " --> pdb=" O VAL E 506 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL E 506 " --> pdb=" O LYS E 482 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN E 484 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AB1, first strand: chain 'F' and resid 32 through 33 removed outlier: 5.383A pdb=" N LEU F 72 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG F 64 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 71 Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 35 Processing sheet with id=AB5, first strand: chain 'D' and resid 66 through 71 120 hydrogen bonds defined for protein. 294 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: 0.59 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1485 1.35 - 1.47: 1203 1.47 - 1.59: 1924 1.59 - 1.72: 0 1.72 - 1.84: 74 Bond restraints: 4686 Sorted by residual: bond pdb=" CB VAL B 473 " pdb=" CG1 VAL B 473 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB VAL E 473 " pdb=" CG1 VAL E 473 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" CB CYS D 48 " pdb=" SG CYS D 48 " ideal model delta sigma weight residual 1.808 1.842 -0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB CYS C 48 " pdb=" SG CYS C 48 " ideal model delta sigma weight residual 1.808 1.842 -0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CG PRO E 480 " pdb=" CD PRO E 480 " ideal model delta sigma weight residual 1.503 1.473 0.030 3.40e-02 8.65e+02 7.69e-01 ... (remaining 4681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 6121 1.94 - 3.89: 209 3.89 - 5.83: 16 5.83 - 7.77: 0 7.77 - 9.71: 2 Bond angle restraints: 6348 Sorted by residual: angle pdb=" CA LEU B 464 " pdb=" CB LEU B 464 " pdb=" CG LEU B 464 " ideal model delta sigma weight residual 116.30 106.59 9.71 3.50e+00 8.16e-02 7.70e+00 angle pdb=" CA LEU E 464 " pdb=" CB LEU E 464 " pdb=" CG LEU E 464 " ideal model delta sigma weight residual 116.30 106.61 9.69 3.50e+00 8.16e-02 7.66e+00 angle pdb=" C ASN E 469 " pdb=" CA ASN E 469 " pdb=" CB ASN E 469 " ideal model delta sigma weight residual 110.17 115.03 -4.86 1.97e+00 2.58e-01 6.09e+00 angle pdb=" C ASN B 469 " pdb=" CA ASN B 469 " pdb=" CB ASN B 469 " ideal model delta sigma weight residual 110.17 114.99 -4.82 1.97e+00 2.58e-01 5.98e+00 angle pdb=" CG1 VAL B 473 " pdb=" CB VAL B 473 " pdb=" CG2 VAL B 473 " ideal model delta sigma weight residual 110.80 105.49 5.31 2.20e+00 2.07e-01 5.82e+00 ... (remaining 6343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 2563 11.82 - 23.63: 323 23.63 - 35.45: 98 35.45 - 47.27: 38 47.27 - 59.09: 16 Dihedral angle restraints: 3038 sinusoidal: 1428 harmonic: 1610 Sorted by residual: dihedral pdb=" CA PHE E 447 " pdb=" C PHE E 447 " pdb=" N PRO E 448 " pdb=" CA PRO E 448 " ideal model delta harmonic sigma weight residual 0.00 -29.48 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PHE B 447 " pdb=" C PHE B 447 " pdb=" N PRO B 448 " pdb=" CA PRO B 448 " ideal model delta harmonic sigma weight residual 0.00 -29.43 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CB CYS D 94 " pdb=" SG CYS D 94 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 54.48 38.52 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 3035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 421 0.035 - 0.070: 182 0.070 - 0.105: 61 0.105 - 0.140: 21 0.140 - 0.175: 13 Chirality restraints: 698 Sorted by residual: chirality pdb=" CA LYS E 475 " pdb=" N LYS E 475 " pdb=" C LYS E 475 " pdb=" CB LYS E 475 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CB VAL E 465 " pdb=" CA VAL E 465 " pdb=" CG1 VAL E 465 " pdb=" CG2 VAL E 465 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA LYS B 475 " pdb=" N LYS B 475 " pdb=" C LYS B 475 " pdb=" CB LYS B 475 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 695 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 447 " -0.022 2.00e-02 2.50e+03 4.41e-02 3.41e+01 pdb=" CG PHE E 447 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE E 447 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE E 447 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE E 447 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE E 447 " 0.042 2.00e-02 2.50e+03 pdb=" CZ PHE E 447 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 447 " 0.022 2.00e-02 2.50e+03 4.40e-02 3.39e+01 pdb=" CG PHE B 447 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 447 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 447 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 447 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE B 447 " -0.042 2.00e-02 2.50e+03 pdb=" CZ PHE B 447 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 470 " -0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C PRO E 470 " 0.087 2.00e-02 2.50e+03 pdb=" O PRO E 470 " -0.032 2.00e-02 2.50e+03 pdb=" N GLU E 471 " -0.030 2.00e-02 2.50e+03 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 2767 3.04 - 3.50: 4237 3.50 - 3.97: 6973 3.97 - 4.43: 7943 4.43 - 4.90: 12945 Nonbonded interactions: 34865 Sorted by model distance: nonbonded pdb=" O2 BMA E 603 " pdb=" O3 BMA E 603 " model vdw 2.573 2.432 nonbonded pdb=" O2 BMA B 603 " pdb=" O3 BMA B 603 " model vdw 2.573 2.432 nonbonded pdb=" N ILE C 59 " pdb=" N ASN C 60 " model vdw 2.578 2.560 nonbonded pdb=" N ILE D 59 " pdb=" N ASN D 60 " model vdw 2.578 2.560 nonbonded pdb=" O2 BMA G 3 " pdb=" O3 BMA G 3 " model vdw 2.581 2.432 ... (remaining 34860 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 3.690 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.003 0.035 4726 Z= 0.142 Angle : 0.778 9.713 6442 Z= 0.418 Chirality : 0.050 0.175 698 Planarity : 0.007 0.059 818 Dihedral : 11.857 59.087 1924 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.34), residues: 540 helix: -0.88 (0.68), residues: 58 sheet: -2.54 (0.37), residues: 174 loop : -2.21 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 503 TYR 0.054 0.004 TYR B 472 PHE 0.087 0.004 PHE E 447 TRP 0.035 0.004 TRP E 429 HIS 0.028 0.004 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4686) covalent geometry : angle 0.75872 / 0.41 ( 6348) SS BOND : bond 0.00322 / 0.21 ( 26) SS BOND : angle 1.50684 / 0.82 ( 52) hydrogen bonds : bond 0.12113 / 8.28 ( 120) hydrogen bonds : angle 7.50094 / 5.01 ( 294) link_BETA1-4 : bond 0.00466 / 0.26 ( 8) link_BETA1-4 : angle 1.32005 / 0.87 ( 24) link_NAG-ASN : bond 0.00305 / 0.19 ( 6) link_NAG-ASN : angle 2.12953 / 1.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 THR cc_start: 0.9030 (p) cc_final: 0.8749 (p) REVERT: B 446 SER cc_start: 0.8173 (p) cc_final: 0.7972 (m) REVERT: B 493 ASP cc_start: 0.8238 (p0) cc_final: 0.7990 (p0) REVERT: E 446 SER cc_start: 0.8333 (p) cc_final: 0.8045 (m) REVERT: F 54 ASP cc_start: 0.7890 (t0) cc_final: 0.7574 (t0) REVERT: C 60 ASN cc_start: 0.8382 (t0) cc_final: 0.7866 (t0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0820 time to fit residues: 21.3677 Evaluate side-chains 136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 50, 19, 30] chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 HIS C 72 GLN C 95 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.066716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053811 restraints weight = 18189.442| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.99 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4726 Z= 0.148 Angle : 0.718 9.124 6442 Z= 0.367 Chirality : 0.044 0.180 698 Planarity : 0.005 0.034 818 Dihedral : 5.160 38.456 882 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.30 % Allowed : 14.96 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.33), residues: 540 helix: -0.29 (0.67), residues: 60 sheet: -2.11 (0.37), residues: 158 loop : -1.64 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 40 TYR 0.018 0.002 TYR B 436 PHE 0.019 0.002 PHE B 447 TRP 0.021 0.001 TRP A 36 HIS 0.004 0.001 HIS E 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 4686) covalent geometry : angle 0.69839 / 0.36 ( 6348) SS BOND : bond 0.00361 / 0.21 ( 26) SS BOND : angle 1.48174 / 0.83 ( 52) hydrogen bonds : bond 0.04210 / 2.77 ( 120) hydrogen bonds : angle 6.15575 / 4.21 ( 294) link_BETA1-4 : bond 0.00419 / 0.23 ( 8) link_BETA1-4 : angle 1.34523 / 0.90 ( 24) link_NAG-ASN : bond 0.00198 / 0.12 ( 6) link_NAG-ASN : angle 1.98585 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 446 SER cc_start: 0.8641 (p) cc_final: 0.8129 (m) REVERT: B 450 ASN cc_start: 0.7844 (p0) cc_final: 0.7425 (p0) REVERT: E 436 TYR cc_start: 0.8614 (p90) cc_final: 0.8318 (p90) REVERT: E 444 GLU cc_start: 0.8747 (pt0) cc_final: 0.8401 (pm20) REVERT: E 453 MET cc_start: 0.8462 (mmm) cc_final: 0.8036 (mtt) REVERT: F 81 ASP cc_start: 0.9020 (t0) cc_final: 0.8773 (t0) REVERT: C 47 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.8011 (t-170) REVERT: C 60 ASN cc_start: 0.8660 (t0) cc_final: 0.8172 (t0) REVERT: C 63 PHE cc_start: 0.8914 (m-80) cc_final: 0.8580 (m-10) REVERT: C 74 TYR cc_start: 0.8844 (t80) cc_final: 0.8504 (t80) REVERT: C 78 LYS cc_start: 0.9182 (ttmm) cc_final: 0.8810 (ttmt) REVERT: C 92 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7251 (mt-10) REVERT: D 60 ASN cc_start: 0.8904 (t0) cc_final: 0.8622 (t0) REVERT: D 63 PHE cc_start: 0.8469 (m-10) cc_final: 0.8173 (m-10) REVERT: D 67 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6359 (tm-30) REVERT: D 74 TYR cc_start: 0.9022 (t80) cc_final: 0.8545 (t80) REVERT: D 75 GLU cc_start: 0.8592 (pt0) cc_final: 0.8337 (pt0) REVERT: D 78 LYS cc_start: 0.9310 (ttmm) cc_final: 0.8992 (tppp) REVERT: D 92 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7280 (mt-10) outliers start: 21 outliers final: 13 residues processed: 164 average time/residue: 0.0782 time to fit residues: 15.9748 Evaluate side-chains 144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [27, 51, 13, 48, 40, 49, 12, 17, 4, 8, 29] chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 HIS ** E 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.063514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.050793 restraints weight = 18696.810| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 5.00 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4726 Z= 0.187 Angle : 0.661 5.131 6442 Z= 0.340 Chirality : 0.042 0.148 698 Planarity : 0.004 0.028 818 Dihedral : 5.190 39.263 882 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.71 % Allowed : 15.57 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.34), residues: 540 helix: 0.12 (0.72), residues: 60 sheet: -2.15 (0.35), residues: 170 loop : -1.43 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 508 TYR 0.019 0.002 TYR B 472 PHE 0.012 0.002 PHE B 447 TRP 0.017 0.001 TRP A 36 HIS 0.008 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 4686) covalent geometry : angle 0.64232 / 0.34 ( 6348) SS BOND : bond 0.00329 / 0.22 ( 26) SS BOND : angle 1.16289 / 0.68 ( 52) hydrogen bonds : bond 0.03539 / 2.30 ( 120) hydrogen bonds : angle 5.84069 / 4.03 ( 294) link_BETA1-4 : bond 0.00327 / 0.19 ( 8) link_BETA1-4 : angle 1.45381 / 0.96 ( 24) link_NAG-ASN : bond 0.00223 / 0.10 ( 6) link_NAG-ASN : angle 2.01536 / 1.23 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.9256 (t) cc_final: 0.9036 (m) REVERT: B 444 GLU cc_start: 0.8615 (pt0) cc_final: 0.8402 (pm20) REVERT: B 446 SER cc_start: 0.8836 (p) cc_final: 0.8495 (m) REVERT: E 444 GLU cc_start: 0.8697 (pt0) cc_final: 0.8300 (pm20) REVERT: E 453 MET cc_start: 0.8547 (mmm) cc_final: 0.8183 (mtt) REVERT: F 31 TYR cc_start: 0.9450 (t80) cc_final: 0.9143 (t80) REVERT: F 54 ASP cc_start: 0.8766 (t0) cc_final: 0.8384 (t0) REVERT: F 81 ASP cc_start: 0.9186 (t0) cc_final: 0.8754 (t0) REVERT: C 60 ASN cc_start: 0.8807 (t0) cc_final: 0.8294 (t0) REVERT: C 63 PHE cc_start: 0.8991 (m-80) cc_final: 0.8563 (m-10) REVERT: C 92 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7476 (mt-10) REVERT: D 60 ASN cc_start: 0.8777 (t0) cc_final: 0.8563 (t0) REVERT: D 67 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6730 (tm-30) REVERT: D 75 GLU cc_start: 0.8673 (pt0) cc_final: 0.8355 (pt0) REVERT: D 92 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7480 (mt-10) outliers start: 23 outliers final: 19 residues processed: 148 average time/residue: 0.0704 time to fit residues: 13.2749 Evaluate side-chains 139 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [3, 0, 12, 6, 46, 43, 31, 5, 19, 32, 22] chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN E 415 HIS ** C 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 100 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.063196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.050327 restraints weight = 18715.517| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.90 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4726 Z= 0.166 Angle : 0.653 7.312 6442 Z= 0.334 Chirality : 0.042 0.150 698 Planarity : 0.004 0.039 818 Dihedral : 5.308 38.314 882 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.71 % Allowed : 16.19 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.36), residues: 540 helix: 0.20 (0.72), residues: 60 sheet: -1.85 (0.34), residues: 188 loop : -1.19 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 503 TYR 0.020 0.002 TYR C 74 PHE 0.013 0.002 PHE D 71 TRP 0.007 0.001 TRP F 78 HIS 0.006 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 4686) covalent geometry : angle 0.63047 / 0.33 ( 6348) SS BOND : bond 0.00340 / 0.20 ( 26) SS BOND : angle 1.40661 / 0.77 ( 52) hydrogen bonds : bond 0.03359 / 2.22 ( 120) hydrogen bonds : angle 5.74793 / 3.97 ( 294) link_BETA1-4 : bond 0.00354 / 0.20 ( 8) link_BETA1-4 : angle 1.39387 / 0.92 ( 24) link_NAG-ASN : bond 0.00169 / 0.08 ( 6) link_NAG-ASN : angle 1.98722 / 1.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 444 GLU cc_start: 0.8665 (pt0) cc_final: 0.8319 (pm20) REVERT: B 446 SER cc_start: 0.8891 (p) cc_final: 0.8564 (m) REVERT: E 444 GLU cc_start: 0.8660 (pt0) cc_final: 0.8234 (pm20) REVERT: E 453 MET cc_start: 0.8465 (mmm) cc_final: 0.8218 (mtt) REVERT: F 54 ASP cc_start: 0.8861 (t0) cc_final: 0.8616 (t0) REVERT: F 55 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8708 (mmmt) REVERT: F 81 ASP cc_start: 0.9252 (t0) cc_final: 0.8776 (t0) REVERT: F 93 THR cc_start: 0.9382 (p) cc_final: 0.9073 (t) REVERT: C 60 ASN cc_start: 0.8778 (t0) cc_final: 0.8238 (t0) REVERT: C 63 PHE cc_start: 0.8997 (m-80) cc_final: 0.8549 (m-10) REVERT: C 74 TYR cc_start: 0.9067 (t80) cc_final: 0.8812 (t80) REVERT: C 78 LYS cc_start: 0.9284 (ttmm) cc_final: 0.8965 (ttmt) REVERT: C 92 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7252 (mt-10) REVERT: D 60 ASN cc_start: 0.8926 (t0) cc_final: 0.8582 (t0) REVERT: D 61 ASP cc_start: 0.8683 (p0) cc_final: 0.8446 (p0) REVERT: D 67 GLN cc_start: 0.7146 (tm-30) cc_final: 0.6802 (tm-30) REVERT: D 75 GLU cc_start: 0.8688 (pt0) cc_final: 0.8255 (pt0) REVERT: D 92 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7408 (mt-10) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 0.0659 time to fit residues: 12.2707 Evaluate side-chains 140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [11, 12, 33, 20, 18, 1, 43, 39, 26, 51, 13] chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 20 optimal weight: 0.0970 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN D 67 GLN D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.051649 restraints weight = 18401.068| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.91 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4726 Z= 0.110 Angle : 0.614 6.018 6442 Z= 0.313 Chirality : 0.042 0.161 698 Planarity : 0.004 0.028 818 Dihedral : 5.182 36.032 882 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.10 % Allowed : 18.24 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.35), residues: 540 helix: 0.22 (0.71), residues: 60 sheet: -1.87 (0.33), residues: 192 loop : -1.07 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 508 TYR 0.017 0.002 TYR E 436 PHE 0.016 0.002 PHE D 71 TRP 0.006 0.001 TRP F 78 HIS 0.003 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 4686) covalent geometry : angle 0.59912 / 0.31 ( 6348) SS BOND : bond 0.00220 / 0.15 ( 26) SS BOND : angle 0.96645 / 0.55 ( 52) hydrogen bonds : bond 0.03284 / 2.17 ( 120) hydrogen bonds : angle 5.44419 / 3.79 ( 294) link_BETA1-4 : bond 0.00417 / 0.23 ( 8) link_BETA1-4 : angle 1.29523 / 0.87 ( 24) link_NAG-ASN : bond 0.00155 / 0.07 ( 6) link_NAG-ASN : angle 1.83337 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TRP cc_start: 0.9068 (t-100) cc_final: 0.8445 (t-100) REVERT: B 444 GLU cc_start: 0.8548 (pt0) cc_final: 0.8275 (pm20) REVERT: B 446 SER cc_start: 0.8865 (p) cc_final: 0.8544 (m) REVERT: E 444 GLU cc_start: 0.8579 (pt0) cc_final: 0.8160 (pm20) REVERT: F 31 TYR cc_start: 0.9464 (t80) cc_final: 0.9211 (t80) REVERT: F 54 ASP cc_start: 0.9049 (t0) cc_final: 0.8599 (t0) REVERT: F 55 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8392 (mmmt) REVERT: F 81 ASP cc_start: 0.9268 (t0) cc_final: 0.8758 (t0) REVERT: F 93 THR cc_start: 0.9346 (p) cc_final: 0.9034 (t) REVERT: C 38 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8314 (pp20) REVERT: C 45 GLU cc_start: 0.8488 (tp30) cc_final: 0.8255 (tp30) REVERT: C 60 ASN cc_start: 0.8758 (t0) cc_final: 0.8190 (t0) REVERT: C 63 PHE cc_start: 0.8995 (m-80) cc_final: 0.8546 (m-10) REVERT: C 92 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 60 ASN cc_start: 0.8902 (t0) cc_final: 0.8559 (t0) REVERT: D 67 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: D 75 GLU cc_start: 0.8689 (pt0) cc_final: 0.8285 (pt0) REVERT: D 80 THR cc_start: 0.9307 (t) cc_final: 0.9072 (t) REVERT: D 92 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7295 (mt-10) outliers start: 20 outliers final: 12 residues processed: 153 average time/residue: 0.0669 time to fit residues: 13.0311 Evaluate side-chains 139 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 67 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [16, 30, 20, 38, 49, 10, 45, 39, 13, 42, 50] chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN D 67 GLN D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.050664 restraints weight = 19154.504| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 5.01 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4726 Z= 0.159 Angle : 0.638 6.390 6442 Z= 0.330 Chirality : 0.042 0.167 698 Planarity : 0.004 0.029 818 Dihedral : 5.210 37.461 882 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.30 % Allowed : 19.06 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.35), residues: 540 helix: 0.20 (0.71), residues: 60 sheet: -1.86 (0.33), residues: 192 loop : -1.03 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 508 TYR 0.019 0.002 TYR B 472 PHE 0.019 0.002 PHE C 71 TRP 0.005 0.001 TRP F 78 HIS 0.003 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4686) covalent geometry : angle 0.62281 / 0.33 ( 6348) SS BOND : bond 0.00287 / 0.21 ( 26) SS BOND : angle 0.91906 / 0.55 ( 52) hydrogen bonds : bond 0.03151 / 2.09 ( 120) hydrogen bonds : angle 5.60203 / 3.93 ( 294) link_BETA1-4 : bond 0.00343 / 0.20 ( 8) link_BETA1-4 : angle 1.39228 / 0.92 ( 24) link_NAG-ASN : bond 0.00171 / 0.08 ( 6) link_NAG-ASN : angle 1.91264 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8634 (tp40) cc_final: 0.8373 (tp-100) REVERT: B 444 GLU cc_start: 0.8643 (pt0) cc_final: 0.8234 (pm20) REVERT: B 446 SER cc_start: 0.8927 (p) cc_final: 0.8650 (m) REVERT: E 444 GLU cc_start: 0.8626 (pt0) cc_final: 0.8115 (pm20) REVERT: F 54 ASP cc_start: 0.9064 (t0) cc_final: 0.8646 (t0) REVERT: F 55 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8738 (mmmt) REVERT: F 81 ASP cc_start: 0.9305 (t0) cc_final: 0.8783 (t0) REVERT: F 93 THR cc_start: 0.9371 (p) cc_final: 0.9058 (t) REVERT: C 38 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8419 (pp20) REVERT: C 45 GLU cc_start: 0.8294 (tp30) cc_final: 0.8067 (tp30) REVERT: C 60 ASN cc_start: 0.8772 (t0) cc_final: 0.8243 (t0) REVERT: C 63 PHE cc_start: 0.8985 (m-80) cc_final: 0.8516 (m-10) REVERT: C 92 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7338 (mt-10) REVERT: D 75 GLU cc_start: 0.8696 (pt0) cc_final: 0.8268 (pt0) REVERT: D 92 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 21 outliers final: 17 residues processed: 133 average time/residue: 0.0712 time to fit residues: 12.0085 Evaluate side-chains 135 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 469 ASN Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [33, 48, 1, 32, 20, 7, 11, 14, 31, 23, 44] chunk 33 optimal weight: 0.0370 chunk 48 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.064345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.051577 restraints weight = 18818.018| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 5.01 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4726 Z= 0.117 Angle : 0.631 6.797 6442 Z= 0.327 Chirality : 0.042 0.195 698 Planarity : 0.003 0.029 818 Dihedral : 5.139 36.399 882 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.69 % Allowed : 19.67 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.35), residues: 540 helix: 0.35 (0.71), residues: 58 sheet: -1.69 (0.36), residues: 176 loop : -1.09 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 503 TYR 0.013 0.001 TYR E 436 PHE 0.021 0.002 PHE C 71 TRP 0.006 0.001 TRP F 78 HIS 0.002 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4686) covalent geometry : angle 0.61808 / 0.32 ( 6348) SS BOND : bond 0.00248 / 0.18 ( 26) SS BOND : angle 0.86648 / 0.51 ( 52) hydrogen bonds : bond 0.03141 / 2.06 ( 120) hydrogen bonds : angle 5.48769 / 3.87 ( 294) link_BETA1-4 : bond 0.00404 / 0.23 ( 8) link_BETA1-4 : angle 1.31240 / 0.88 ( 24) link_NAG-ASN : bond 0.00106 / 0.05 ( 6) link_NAG-ASN : angle 1.83308 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TRP cc_start: 0.9121 (t-100) cc_final: 0.8455 (t-100) REVERT: A 98 GLN cc_start: 0.8659 (tp40) cc_final: 0.8387 (tp-100) REVERT: B 444 GLU cc_start: 0.8560 (pt0) cc_final: 0.8236 (pm20) REVERT: B 446 SER cc_start: 0.8879 (p) cc_final: 0.8545 (m) REVERT: B 488 VAL cc_start: 0.9721 (t) cc_final: 0.9336 (p) REVERT: E 444 GLU cc_start: 0.8587 (pt0) cc_final: 0.8105 (pm20) REVERT: F 46 LEU cc_start: 0.9135 (mp) cc_final: 0.8919 (mp) REVERT: F 54 ASP cc_start: 0.9069 (t0) cc_final: 0.8826 (t0) REVERT: F 81 ASP cc_start: 0.9299 (t0) cc_final: 0.8767 (t0) REVERT: F 93 THR cc_start: 0.9361 (p) cc_final: 0.9051 (t) REVERT: C 38 GLU cc_start: 0.9062 (pt0) cc_final: 0.8554 (pp20) REVERT: C 60 ASN cc_start: 0.8764 (t0) cc_final: 0.8250 (t0) REVERT: C 63 PHE cc_start: 0.8978 (m-80) cc_final: 0.8517 (m-10) REVERT: C 78 LYS cc_start: 0.9285 (ttmm) cc_final: 0.9061 (ttmm) REVERT: C 92 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7320 (mt-10) REVERT: D 63 PHE cc_start: 0.8881 (m-80) cc_final: 0.8646 (m-80) REVERT: D 75 GLU cc_start: 0.8682 (pt0) cc_final: 0.8270 (pt0) REVERT: D 92 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7152 (mt-10) outliers start: 18 outliers final: 14 residues processed: 142 average time/residue: 0.0645 time to fit residues: 11.8482 Evaluate side-chains 137 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [33, 26, 37, 45, 48, 25, 29, 32, 35, 2, 43] chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN D 52 GLN D 72 GLN D 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.063097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050514 restraints weight = 19004.007| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 5.03 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4726 Z= 0.144 Angle : 0.652 6.962 6442 Z= 0.335 Chirality : 0.042 0.167 698 Planarity : 0.003 0.031 818 Dihedral : 5.199 37.879 882 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.69 % Allowed : 20.49 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.36), residues: 540 helix: 0.40 (0.72), residues: 58 sheet: -1.61 (0.36), residues: 176 loop : -1.03 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 503 TYR 0.017 0.001 TYR B 436 PHE 0.029 0.002 PHE C 71 TRP 0.004 0.001 TRP F 78 HIS 0.002 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4686) covalent geometry : angle 0.63893 / 0.33 ( 6348) SS BOND : bond 0.00264 / 0.19 ( 26) SS BOND : angle 0.87953 / 0.54 ( 52) hydrogen bonds : bond 0.03088 / 2.02 ( 120) hydrogen bonds : angle 5.52621 / 3.88 ( 294) link_BETA1-4 : bond 0.00345 / 0.20 ( 8) link_BETA1-4 : angle 1.39755 / 0.93 ( 24) link_NAG-ASN : bond 0.00117 / 0.06 ( 6) link_NAG-ASN : angle 1.86247 / 1.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8688 (tp40) cc_final: 0.8406 (tp-100) REVERT: B 444 GLU cc_start: 0.8618 (pt0) cc_final: 0.8181 (pm20) REVERT: B 446 SER cc_start: 0.8894 (p) cc_final: 0.8568 (m) REVERT: B 488 VAL cc_start: 0.9738 (t) cc_final: 0.9360 (p) REVERT: E 444 GLU cc_start: 0.8600 (pt0) cc_final: 0.8081 (pm20) REVERT: F 46 LEU cc_start: 0.9144 (mp) cc_final: 0.8922 (mp) REVERT: F 81 ASP cc_start: 0.9324 (t0) cc_final: 0.8774 (t0) REVERT: F 93 THR cc_start: 0.9376 (p) cc_final: 0.9074 (t) REVERT: C 38 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8511 (pp20) REVERT: C 60 ASN cc_start: 0.8818 (t0) cc_final: 0.8344 (t0) REVERT: C 63 PHE cc_start: 0.8979 (m-80) cc_final: 0.8516 (m-10) REVERT: C 78 LYS cc_start: 0.9335 (ttmm) cc_final: 0.9100 (ttmm) REVERT: C 92 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7324 (mt-10) REVERT: D 63 PHE cc_start: 0.8833 (m-80) cc_final: 0.8632 (m-80) REVERT: D 75 GLU cc_start: 0.8699 (pt0) cc_final: 0.8274 (pt0) REVERT: D 92 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7196 (mt-10) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.0693 time to fit residues: 11.8662 Evaluate side-chains 133 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [17, 6, 3, 34, 40, 25, 49, 22, 19, 23, 39] chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN D 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.063686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051022 restraints weight = 18446.402| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 5.00 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4726 Z= 0.130 Angle : 0.665 7.552 6442 Z= 0.344 Chirality : 0.043 0.167 698 Planarity : 0.003 0.031 818 Dihedral : 5.303 37.413 882 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.48 % Allowed : 20.70 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.35), residues: 540 helix: 0.44 (0.72), residues: 58 sheet: -1.46 (0.42), residues: 136 loop : -1.32 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 503 TYR 0.017 0.001 TYR E 436 PHE 0.030 0.002 PHE C 71 TRP 0.006 0.001 TRP A 78 HIS 0.002 0.001 HIS B 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 4686) covalent geometry : angle 0.65335 / 0.34 ( 6348) SS BOND : bond 0.00240 / 0.17 ( 26) SS BOND : angle 0.84449 / 0.51 ( 52) hydrogen bonds : bond 0.03036 / 1.98 ( 120) hydrogen bonds : angle 5.47939 / 3.84 ( 294) link_BETA1-4 : bond 0.00375 / 0.21 ( 8) link_BETA1-4 : angle 1.32745 / 0.89 ( 24) link_NAG-ASN : bond 0.00073 / 0.04 ( 6) link_NAG-ASN : angle 1.81844 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8692 (tp40) cc_final: 0.8424 (tp-100) REVERT: B 444 GLU cc_start: 0.8563 (pt0) cc_final: 0.8156 (pm20) REVERT: B 446 SER cc_start: 0.8895 (p) cc_final: 0.8589 (m) REVERT: B 488 VAL cc_start: 0.9764 (t) cc_final: 0.9420 (p) REVERT: B 505 MET cc_start: 0.9493 (mmm) cc_final: 0.9248 (mmm) REVERT: E 444 GLU cc_start: 0.8629 (pt0) cc_final: 0.8127 (pm20) REVERT: E 500 LYS cc_start: 0.8578 (tppp) cc_final: 0.8352 (mmmm) REVERT: F 46 LEU cc_start: 0.9147 (mp) cc_final: 0.8920 (mp) REVERT: F 55 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8660 (mtmm) REVERT: F 81 ASP cc_start: 0.9324 (t0) cc_final: 0.8775 (t0) REVERT: F 93 THR cc_start: 0.9371 (p) cc_final: 0.9072 (t) REVERT: C 38 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8498 (pp20) REVERT: C 60 ASN cc_start: 0.8765 (t0) cc_final: 0.8293 (t0) REVERT: C 63 PHE cc_start: 0.8978 (m-80) cc_final: 0.8511 (m-10) REVERT: C 78 LYS cc_start: 0.9328 (ttmm) cc_final: 0.9067 (ttmm) REVERT: C 92 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7329 (mt-10) REVERT: D 75 GLU cc_start: 0.8698 (pt0) cc_final: 0.8265 (pt0) REVERT: D 92 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7237 (mt-10) outliers start: 17 outliers final: 15 residues processed: 140 average time/residue: 0.0706 time to fit residues: 12.5520 Evaluate side-chains 137 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [40, 45, 18, 24, 31, 5, 15, 22, 44, 39, 43] chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 0.0010 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.063787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.050950 restraints weight = 18850.696| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 5.04 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4726 Z= 0.131 Angle : 0.661 7.580 6442 Z= 0.342 Chirality : 0.042 0.169 698 Planarity : 0.003 0.028 818 Dihedral : 5.268 38.150 882 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.28 % Allowed : 21.11 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.35), residues: 540 helix: 0.34 (0.71), residues: 58 sheet: -1.51 (0.42), residues: 136 loop : -1.28 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 503 TYR 0.022 0.002 TYR C 74 PHE 0.027 0.002 PHE C 71 TRP 0.005 0.001 TRP E 429 HIS 0.002 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 4686) covalent geometry : angle 0.64927 / 0.34 ( 6348) SS BOND : bond 0.00216 / 0.16 ( 26) SS BOND : angle 0.83438 / 0.51 ( 52) hydrogen bonds : bond 0.03046 / 2.00 ( 120) hydrogen bonds : angle 5.56239 / 3.88 ( 294) link_BETA1-4 : bond 0.00363 / 0.21 ( 8) link_BETA1-4 : angle 1.35539 / 0.90 ( 24) link_NAG-ASN : bond 0.00055 / 0.03 ( 6) link_NAG-ASN : angle 1.82962 / 1.12 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1080 Ramachandran restraints generated. 540 Oldfield, 0 Emsley, 540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8717 (tp40) cc_final: 0.8451 (tp-100) REVERT: B 444 GLU cc_start: 0.8572 (pt0) cc_final: 0.8280 (pm20) REVERT: B 446 SER cc_start: 0.8872 (p) cc_final: 0.8566 (m) REVERT: B 488 VAL cc_start: 0.9777 (t) cc_final: 0.9440 (p) REVERT: B 505 MET cc_start: 0.9496 (mmm) cc_final: 0.9243 (mmm) REVERT: E 444 GLU cc_start: 0.8484 (pt0) cc_final: 0.8056 (pm20) REVERT: E 472 TYR cc_start: 0.8769 (m-80) cc_final: 0.8545 (m-80) REVERT: E 500 LYS cc_start: 0.8641 (tppp) cc_final: 0.8384 (mmmm) REVERT: F 46 LEU cc_start: 0.9165 (mp) cc_final: 0.8938 (mp) REVERT: F 55 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8680 (mtmm) REVERT: F 81 ASP cc_start: 0.9335 (t0) cc_final: 0.8799 (t0) REVERT: F 93 THR cc_start: 0.9379 (p) cc_final: 0.9083 (t) REVERT: C 38 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8492 (pp20) REVERT: C 60 ASN cc_start: 0.8752 (t0) cc_final: 0.8354 (t0) REVERT: C 63 PHE cc_start: 0.8983 (m-80) cc_final: 0.8695 (m-80) REVERT: C 92 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7310 (mt-10) REVERT: D 75 GLU cc_start: 0.8705 (pt0) cc_final: 0.8268 (pt0) REVERT: D 92 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7267 (mt-10) outliers start: 16 outliers final: 15 residues processed: 135 average time/residue: 0.0669 time to fit residues: 11.5921 Evaluate side-chains 137 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 85 TYR Chi-restraints excluded: chain F residue 90 CYS Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [20, 21, 43, 11, 26, 33, 1, 13, 47, 2, 36] chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 95 GLN D 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.050439 restraints weight = 18382.798| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 5.00 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4726 Z= 0.122 Angle : 0.665 7.844 6442 Z= 0.344 Chirality : 0.043 0.172 698 Planarity : 0.003 0.025 818 Dihedral : 5.222 38.079 882 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.48 % Allowed : 20.90 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.35), residues: 540 helix: 0.30 (0.71), residues: 58 sheet: -1.52 (0.42), residues: 136 loop : -1.25 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 503 TYR 0.018 0.001 TYR D 74 PHE 0.037 0.002 PHE D 71 TRP 0.006 0.001 TRP F 78 HIS 0.002 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4686) covalent geometry : angle 0.65428 / 0.34 ( 6348) SS BOND : bond 0.00195 / 0.15 ( 26) SS BOND : angle 0.82392 / 0.50 ( 52) hydrogen bonds : bond 0.03025 / 1.98 ( 120) hydrogen bonds : angle 5.54825 / 3.88 ( 294) link_BETA1-4 : bond 0.00382 / 0.22 ( 8) link_BETA1-4 : angle 1.32019 / 0.88 ( 24) link_NAG-ASN : bond 0.00103 / 0.05 ( 6) link_NAG-ASN : angle 1.78055 / 1.09 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.88 seconds wall clock time: 19 minutes 39.15 seconds (1179.15 seconds total)