Starting phenix.real_space_refine on Mon Apr 28 05:27:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk0_19254/04_2025/8rk0_19254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk0_19254/04_2025/8rk0_19254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rk0_19254/04_2025/8rk0_19254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk0_19254/04_2025/8rk0_19254.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk0_19254/04_2025/8rk0_19254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk0_19254/04_2025/8rk0_19254.cif" } resolution = 3.38 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= 0.004 sd= 0.031 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 58 5.16 5 C 4344 2.51 5 N 1136 2.21 5 O 1402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6940 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 637 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2523 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 26, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 637 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2523 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 26, 'TRANS': 295} Chain breaks: 1 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "D" 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: 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 Time building chain proxies: 5.60, per 1000 atoms: 0.81 Number of scatterers: 6940 At special positions: 0 Unit cell: (102.176, 88.168, 77.456, 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 58 16.00 O 1402 8.00 N 1136 7.00 C 4344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 229 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 504 " distance=2.03 Simple disulfide: pdb=" SG CYS D 452 " - pdb=" SG CYS D 626 " distance=2.03 Simple disulfide: pdb=" SG CYS D 459 " - pdb=" SG CYS D 487 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 565 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 553 " distance=2.03 Simple disulfide: pdb=" SG CYS D 570 " - pdb=" SG CYS D 603 " distance=2.03 Simple disulfide: pdb=" SG CYS D 587 " - pdb=" SG CYS D 591 " distance=2.03 Simple disulfide: pdb=" SG CYS D 613 " - pdb=" SG CYS D 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 452 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 459 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 591 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 650 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG F 1 " - " ASN C 305 " " NAG I 1 " - " ASN B 448 " " NAG K 1 " - " ASN A 305 " " NAG L 1 " - " ASN D 448 " " NAG N 1 " - " ASN B 423 " " NAG O 1 " - " ASN D 557 " " NAG P 1 " - " ASN D 629 " " NAG Q 1 " - " ASN D 651 " " NAG S 1 " - " ASN B 557 " " NAG T 1 " - " ASN B 629 " " NAG U 1 " - " ASN B 651 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 930.1 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 18 sheets defined 11.8% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'D' and resid 405 through 409 Processing helix chain 'D' and resid 432 through 442 removed outlier: 3.661A pdb=" N PHE D 442 " --> pdb=" O ILE D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 457 Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.621A pdb=" N PHE D 465 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.709A pdb=" N SER D 502 " --> pdb=" O PRO D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 432 through 442 removed outlier: 3.645A pdb=" N PHE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.609A pdb=" N PHE B 465 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 removed outlier: 3.729A pdb=" N SER B 502 " --> pdb=" O PRO B 499 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 503 " --> pdb=" O ALA B 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 503' Processing helix chain 'B' and resid 599 through 604 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.524A pdb=" N ASN B 629 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AA2, first strand: chain 'C' and resid 212 through 215 removed outlier: 4.141A pdb=" N VAL C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 229 through 231 Processing sheet with id=AA4, first strand: chain 'D' and resid 413 through 416 Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AA6, first strand: chain 'D' and resid 514 through 516 removed outlier: 5.460A pdb=" N MET D 556 " --> pdb=" O PRO D 506 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY D 552 " --> pdb=" O PHE D 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 613 through 615 Processing sheet with id=AA8, first strand: chain 'D' and resid 664 through 665 removed outlier: 6.114A pdb=" N ASP D 664 " --> pdb=" O PHE D 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 677 through 679 removed outlier: 4.643A pdb=" N HIS D 697 " --> pdb=" O TYR D 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AB2, first strand: chain 'A' and resid 212 through 215 Processing sheet with id=AB3, first strand: chain 'A' and resid 229 through 231 Processing sheet with id=AB4, first strand: chain 'B' and resid 413 through 416 Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'B' and resid 514 through 517 removed outlier: 4.765A pdb=" N VAL B 507 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET B 556 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B 552 " --> pdb=" O PHE B 510 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 613 through 615 Processing sheet with id=AB8, first strand: chain 'B' and resid 664 through 665 removed outlier: 6.261A pdb=" N ASP B 664 " --> pdb=" O PHE B 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 677 through 679 108 hydrogen bonds defined for protein. 273 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: 1.69 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2119 1.34 - 1.46: 1904 1.46 - 1.58: 3047 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 7138 Sorted by residual: bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 5.95e+00 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.567 -0.048 2.00e-02 2.50e+03 5.76e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C1 BMA S 3 " pdb=" O5 BMA S 3 " ideal model delta sigma weight residual 1.410 1.449 -0.039 2.00e-02 2.50e+03 3.86e+00 ... (remaining 7133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 9413 2.32 - 4.64: 279 4.64 - 6.96: 58 6.96 - 9.28: 5 9.28 - 11.59: 1 Bond angle restraints: 9756 Sorted by residual: angle pdb=" C CYS C 306 " pdb=" N SER C 307 " pdb=" CA SER C 307 " ideal model delta sigma weight residual 121.54 129.71 -8.17 1.91e+00 2.74e-01 1.83e+01 angle pdb=" N THR B 511 " pdb=" CA THR B 511 " pdb=" C THR B 511 " ideal model delta sigma weight residual 108.47 101.44 7.03 1.79e+00 3.12e-01 1.54e+01 angle pdb=" N THR D 511 " pdb=" CA THR D 511 " pdb=" C THR D 511 " ideal model delta sigma weight residual 108.47 101.74 6.73 1.79e+00 3.12e-01 1.41e+01 angle pdb=" CA LEU A 308 " pdb=" CB LEU A 308 " pdb=" CG LEU A 308 " ideal model delta sigma weight residual 116.30 127.89 -11.59 3.50e+00 8.16e-02 1.10e+01 angle pdb=" C ASP C 233 " pdb=" CA ASP C 233 " pdb=" CB ASP C 233 " ideal model delta sigma weight residual 110.34 114.94 -4.60 1.40e+00 5.10e-01 1.08e+01 ... (remaining 9751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 4349 25.77 - 51.55: 291 51.55 - 77.32: 73 77.32 - 103.09: 54 103.09 - 128.86: 33 Dihedral angle restraints: 4800 sinusoidal: 2468 harmonic: 2332 Sorted by residual: dihedral pdb=" CA THR D 511 " pdb=" C THR D 511 " pdb=" N PRO D 512 " pdb=" CA PRO D 512 " ideal model delta harmonic sigma weight residual -180.00 -115.21 -64.79 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" CA THR B 511 " pdb=" C THR B 511 " pdb=" N PRO B 512 " pdb=" CA PRO B 512 " ideal model delta harmonic sigma weight residual -180.00 -115.46 -64.54 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CB CYS A 229 " pdb=" SG CYS A 229 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 21.29 71.71 1 1.00e+01 1.00e-02 6.59e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 929 0.062 - 0.125: 219 0.125 - 0.187: 24 0.187 - 0.250: 1 0.250 - 0.312: 12 Chirality restraints: 1185 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 305 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 423 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1182 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 511 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C THR D 511 " -0.055 2.00e-02 2.50e+03 pdb=" O THR D 511 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO D 512 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 233 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASP C 233 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP C 233 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN C 234 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 511 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C THR B 511 " 0.055 2.00e-02 2.50e+03 pdb=" O THR B 511 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO B 512 " -0.019 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 283 2.67 - 3.23: 7271 3.23 - 3.78: 11473 3.78 - 4.34: 14495 4.34 - 4.90: 22187 Nonbonded interactions: 55709 Sorted by model distance: nonbonded pdb=" OH TYR A 309 " pdb=" O ASN B 659 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP A 232 " pdb=" OG1 THR A 235 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASP C 232 " pdb=" OG1 THR C 235 " model vdw 2.187 3.040 nonbonded pdb=" O ASP B 521 " pdb=" NZ LYS B 525 " model vdw 2.188 3.120 nonbonded pdb=" OH TYR C 309 " pdb=" O ASN D 659 " model vdw 2.202 3.040 ... (remaining 55704 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.420 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.005 0.049 7199 Z= 0.243 Angle : 0.942 11.595 9911 Z= 0.434 Chirality : 0.058 0.312 1185 Planarity : 0.006 0.052 1192 Dihedral : 23.310 128.865 3242 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 0.14 % Allowed : 30.03 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.41 (0.30), residues: 796 helix: -0.68 (0.66), residues: 68 sheet: -0.43 (0.57), residues: 90 loop : -2.08 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 622 HIS 0.003 0.001 HIS B 673 PHE 0.009 0.001 PHE D 538 TYR 0.021 0.002 TYR D 709 ARG 0.002 0.000 ARG C 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 11) link_NAG-ASN : angle 2.35814 ( 33) link_BETA1-4 : bond 0.00554 ( 26) link_BETA1-4 : angle 2.12385 ( 78) hydrogen bonds : bond 0.22450 ( 108) hydrogen bonds : angle 8.03004 ( 273) SS BOND : bond 0.00262 ( 22) SS BOND : angle 1.21276 ( 44) covalent geometry : bond 0.00493 ( 7138) covalent geometry : angle 0.91611 ( 9756) Misc. bond : bond 0.00126 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.757 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1754 time to fit residues: 17.4003 Evaluate side-chains 66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 556 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 HIS C 299 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 ASN B 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060122 restraints weight = 24837.228| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 6.39 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7199 Z= 0.187 Angle : 0.851 8.029 9911 Z= 0.397 Chirality : 0.052 0.239 1185 Planarity : 0.006 0.053 1192 Dihedral : 18.963 115.262 1835 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 4.53 % Allowed : 24.79 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.44 (0.29), residues: 796 helix: -0.97 (0.70), residues: 58 sheet: -0.57 (0.57), residues: 90 loop : -2.03 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 622 HIS 0.003 0.001 HIS A 222 PHE 0.011 0.001 PHE D 538 TYR 0.021 0.001 TYR D 709 ARG 0.005 0.001 ARG B 636 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 11) link_NAG-ASN : angle 2.18859 ( 33) link_BETA1-4 : bond 0.00536 ( 26) link_BETA1-4 : angle 2.22235 ( 78) hydrogen bonds : bond 0.04498 ( 108) hydrogen bonds : angle 6.76886 ( 273) SS BOND : bond 0.00488 ( 22) SS BOND : angle 1.13644 ( 44) covalent geometry : bond 0.00403 ( 7138) covalent geometry : angle 0.82091 ( 9756) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.810 Fit side-chains REVERT: D 415 ASN cc_start: 0.9287 (t0) cc_final: 0.9048 (t0) REVERT: D 536 ASP cc_start: 0.7283 (t0) cc_final: 0.6969 (t0) REVERT: D 673 HIS cc_start: 0.7635 (t-90) cc_final: 0.7253 (t-90) REVERT: D 706 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8756 (tp40) outliers start: 32 outliers final: 13 residues processed: 92 average time/residue: 0.1584 time to fit residues: 20.9457 Evaluate side-chains 76 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 48 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.080282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058806 restraints weight = 25140.882| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 6.36 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7199 Z= 0.236 Angle : 0.853 8.094 9911 Z= 0.398 Chirality : 0.051 0.252 1185 Planarity : 0.006 0.054 1192 Dihedral : 15.833 115.092 1832 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 5.24 % Allowed : 22.80 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.46 (0.30), residues: 796 helix: -1.04 (0.70), residues: 58 sheet: -0.53 (0.54), residues: 100 loop : -2.06 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 622 HIS 0.007 0.001 HIS C 222 PHE 0.012 0.002 PHE B 442 TYR 0.032 0.002 TYR C 250 ARG 0.005 0.001 ARG A 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 11) link_NAG-ASN : angle 2.50429 ( 33) link_BETA1-4 : bond 0.00594 ( 26) link_BETA1-4 : angle 2.05761 ( 78) hydrogen bonds : bond 0.04397 ( 108) hydrogen bonds : angle 6.64823 ( 273) SS BOND : bond 0.00519 ( 22) SS BOND : angle 1.13315 ( 44) covalent geometry : bond 0.00502 ( 7138) covalent geometry : angle 0.82405 ( 9756) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.766 Fit side-chains REVERT: D 536 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7169 (t0) REVERT: D 673 HIS cc_start: 0.7711 (t-90) cc_final: 0.7294 (t-90) outliers start: 37 outliers final: 19 residues processed: 91 average time/residue: 0.1488 time to fit residues: 19.6050 Evaluate side-chains 81 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059853 restraints weight = 25111.443| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 6.51 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7199 Z= 0.173 Angle : 0.818 9.246 9911 Z= 0.384 Chirality : 0.050 0.275 1185 Planarity : 0.006 0.049 1192 Dihedral : 13.679 113.045 1832 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.82 % Favored : 86.06 % Rotamer: Outliers : 4.67 % Allowed : 23.09 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.43 (0.29), residues: 796 helix: -1.04 (0.69), residues: 58 sheet: -0.84 (0.55), residues: 90 loop : -1.97 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 622 HIS 0.007 0.001 HIS D 595 PHE 0.010 0.001 PHE B 538 TYR 0.018 0.001 TYR D 709 ARG 0.003 0.000 ARG A 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 11) link_NAG-ASN : angle 2.39335 ( 33) link_BETA1-4 : bond 0.00583 ( 26) link_BETA1-4 : angle 2.02268 ( 78) hydrogen bonds : bond 0.03616 ( 108) hydrogen bonds : angle 6.52665 ( 273) SS BOND : bond 0.00363 ( 22) SS BOND : angle 1.11430 ( 44) covalent geometry : bond 0.00374 ( 7138) covalent geometry : angle 0.78878 ( 9756) Misc. bond : bond 0.00060 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1997 (OUTLIER) cc_final: -0.0310 (mpt180) REVERT: D 536 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7096 (t0) REVERT: D 673 HIS cc_start: 0.7815 (t-90) cc_final: 0.7221 (t-90) REVERT: D 706 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8851 (tp40) REVERT: A 294 ARG cc_start: 0.1900 (OUTLIER) cc_final: -0.0399 (mpt180) REVERT: B 523 LYS cc_start: 0.8438 (mtmm) cc_final: 0.7951 (mmtt) REVERT: B 536 ASP cc_start: 0.7794 (m-30) cc_final: 0.7349 (t0) outliers start: 33 outliers final: 18 residues processed: 89 average time/residue: 0.1829 time to fit residues: 22.4280 Evaluate side-chains 83 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.083178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061299 restraints weight = 24397.124| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 6.49 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7199 Z= 0.137 Angle : 0.792 9.568 9911 Z= 0.373 Chirality : 0.049 0.263 1185 Planarity : 0.005 0.045 1192 Dihedral : 12.253 110.046 1832 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 4.39 % Allowed : 24.93 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.27 % 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: -2.36 (0.29), residues: 796 helix: -1.05 (0.69), residues: 58 sheet: -0.86 (0.53), residues: 90 loop : -1.90 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 622 HIS 0.006 0.001 HIS B 595 PHE 0.011 0.001 PHE B 538 TYR 0.016 0.001 TYR D 709 ARG 0.002 0.000 ARG C 195 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 11) link_NAG-ASN : angle 2.16689 ( 33) link_BETA1-4 : bond 0.00634 ( 26) link_BETA1-4 : angle 1.83706 ( 78) hydrogen bonds : bond 0.03333 ( 108) hydrogen bonds : angle 6.44690 ( 273) SS BOND : bond 0.00321 ( 22) SS BOND : angle 1.13347 ( 44) covalent geometry : bond 0.00296 ( 7138) covalent geometry : angle 0.76752 ( 9756) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2036 (OUTLIER) cc_final: -0.0309 (mpt180) REVERT: D 536 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.7024 (t0) REVERT: D 617 TYR cc_start: 0.9461 (p90) cc_final: 0.9240 (p90) REVERT: D 673 HIS cc_start: 0.7746 (t-90) cc_final: 0.7099 (t-90) REVERT: D 706 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8819 (tp40) REVERT: A 294 ARG cc_start: 0.2028 (OUTLIER) cc_final: -0.0409 (mpt180) REVERT: B 523 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7881 (mmtt) REVERT: B 536 ASP cc_start: 0.7747 (m-30) cc_final: 0.7316 (t0) outliers start: 31 outliers final: 17 residues processed: 92 average time/residue: 0.1810 time to fit residues: 22.9380 Evaluate side-chains 87 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.081011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.059123 restraints weight = 25150.582| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 6.48 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7199 Z= 0.222 Angle : 0.815 8.793 9911 Z= 0.384 Chirality : 0.050 0.291 1185 Planarity : 0.005 0.044 1192 Dihedral : 11.705 106.314 1832 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 6.23 % Allowed : 23.80 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -2.38 (0.29), residues: 796 helix: -1.13 (0.68), residues: 58 sheet: -0.60 (0.54), residues: 100 loop : -1.97 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 420 HIS 0.006 0.001 HIS C 222 PHE 0.010 0.001 PHE B 538 TYR 0.017 0.002 TYR D 709 ARG 0.005 0.000 ARG C 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 11) link_NAG-ASN : angle 2.41887 ( 33) link_BETA1-4 : bond 0.00556 ( 26) link_BETA1-4 : angle 1.98886 ( 78) hydrogen bonds : bond 0.03639 ( 108) hydrogen bonds : angle 6.35405 ( 273) SS BOND : bond 0.00447 ( 22) SS BOND : angle 1.12186 ( 44) covalent geometry : bond 0.00477 ( 7138) covalent geometry : angle 0.78624 ( 9756) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 63 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1873 (OUTLIER) cc_final: -0.0191 (mpt180) REVERT: D 536 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7233 (t0) REVERT: D 673 HIS cc_start: 0.7852 (t-90) cc_final: 0.7182 (t-90) REVERT: D 706 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8738 (tp40) REVERT: A 294 ARG cc_start: 0.1941 (OUTLIER) cc_final: -0.0351 (mpt180) REVERT: B 536 ASP cc_start: 0.7887 (m-30) cc_final: 0.7417 (t0) outliers start: 44 outliers final: 33 residues processed: 94 average time/residue: 0.1764 time to fit residues: 22.7520 Evaluate side-chains 97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 9 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.082614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060721 restraints weight = 24357.506| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 6.44 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7199 Z= 0.146 Angle : 0.787 9.870 9911 Z= 0.374 Chirality : 0.049 0.264 1185 Planarity : 0.005 0.044 1192 Dihedral : 11.212 103.120 1832 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.56 % Favored : 87.31 % Rotamer: Outliers : 5.24 % Allowed : 25.07 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -2.35 (0.29), residues: 796 helix: -1.13 (0.68), residues: 58 sheet: -0.81 (0.58), residues: 84 loop : -1.88 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 622 HIS 0.004 0.001 HIS B 595 PHE 0.010 0.001 PHE B 538 TYR 0.016 0.001 TYR B 709 ARG 0.002 0.000 ARG C 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 11) link_NAG-ASN : angle 2.11601 ( 33) link_BETA1-4 : bond 0.00639 ( 26) link_BETA1-4 : angle 1.84360 ( 78) hydrogen bonds : bond 0.03252 ( 108) hydrogen bonds : angle 6.36998 ( 273) SS BOND : bond 0.00277 ( 22) SS BOND : angle 0.95826 ( 44) covalent geometry : bond 0.00318 ( 7138) covalent geometry : angle 0.76374 ( 9756) Misc. bond : bond 0.00072 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1859 (OUTLIER) cc_final: -0.0408 (mpt180) REVERT: D 536 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7137 (t0) REVERT: D 617 TYR cc_start: 0.9455 (p90) cc_final: 0.9212 (p90) REVERT: D 673 HIS cc_start: 0.7793 (t-90) cc_final: 0.7103 (t-90) REVERT: D 706 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8724 (tp40) REVERT: A 294 ARG cc_start: 0.2066 (OUTLIER) cc_final: -0.0628 (mtt90) REVERT: B 536 ASP cc_start: 0.7774 (m-30) cc_final: 0.7310 (t0) outliers start: 37 outliers final: 29 residues processed: 94 average time/residue: 0.1847 time to fit residues: 23.5501 Evaluate side-chains 96 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.081033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059136 restraints weight = 24922.504| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 6.45 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7199 Z= 0.225 Angle : 0.821 8.829 9911 Z= 0.390 Chirality : 0.050 0.291 1185 Planarity : 0.006 0.042 1192 Dihedral : 10.795 97.205 1832 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 6.23 % Allowed : 24.08 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -2.37 (0.29), residues: 796 helix: -1.20 (0.67), residues: 58 sheet: -0.33 (0.58), residues: 90 loop : -1.99 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 420 HIS 0.006 0.001 HIS C 222 PHE 0.011 0.001 PHE B 538 TYR 0.017 0.002 TYR D 709 ARG 0.005 0.000 ARG C 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 11) link_NAG-ASN : angle 2.38574 ( 33) link_BETA1-4 : bond 0.00581 ( 26) link_BETA1-4 : angle 2.01239 ( 78) hydrogen bonds : bond 0.03566 ( 108) hydrogen bonds : angle 6.29514 ( 273) SS BOND : bond 0.00578 ( 22) SS BOND : angle 1.09837 ( 44) covalent geometry : bond 0.00484 ( 7138) covalent geometry : angle 0.79246 ( 9756) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 62 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1999 (OUTLIER) cc_final: -0.0270 (mpt180) REVERT: D 536 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7272 (t0) REVERT: D 673 HIS cc_start: 0.7897 (t-90) cc_final: 0.7172 (t-90) REVERT: D 706 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8690 (tp40) REVERT: A 294 ARG cc_start: 0.1981 (OUTLIER) cc_final: -0.0285 (mpt180) REVERT: B 536 ASP cc_start: 0.7870 (m-30) cc_final: 0.7413 (t0) outliers start: 44 outliers final: 35 residues processed: 94 average time/residue: 0.1825 time to fit residues: 23.7066 Evaluate side-chains 96 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 57 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.080654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058328 restraints weight = 25072.139| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 6.52 r_work: 0.2929 rms_B_bonded: 6.49 restraints_weight: 2.0000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7199 Z= 0.202 Angle : 0.821 9.250 9911 Z= 0.390 Chirality : 0.050 0.278 1185 Planarity : 0.005 0.043 1192 Dihedral : 10.330 90.534 1832 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.69 % Favored : 87.19 % Rotamer: Outliers : 5.38 % Allowed : 25.07 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -2.44 (0.29), residues: 796 helix: -1.23 (0.67), residues: 58 sheet: -0.50 (0.62), residues: 80 loop : -1.99 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 622 HIS 0.005 0.001 HIS C 222 PHE 0.010 0.001 PHE B 538 TYR 0.017 0.001 TYR D 709 ARG 0.004 0.000 ARG C 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 11) link_NAG-ASN : angle 2.21959 ( 33) link_BETA1-4 : bond 0.00598 ( 26) link_BETA1-4 : angle 1.96445 ( 78) hydrogen bonds : bond 0.03491 ( 108) hydrogen bonds : angle 6.28678 ( 273) SS BOND : bond 0.00339 ( 22) SS BOND : angle 1.12675 ( 44) covalent geometry : bond 0.00435 ( 7138) covalent geometry : angle 0.79477 ( 9756) Misc. bond : bond 0.00071 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.4976 (OUTLIER) cc_final: 0.1841 (mpt180) REVERT: D 536 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7234 (t0) REVERT: D 617 TYR cc_start: 0.9621 (p90) cc_final: 0.9394 (p90) REVERT: D 673 HIS cc_start: 0.7891 (t-90) cc_final: 0.7115 (t-90) REVERT: D 706 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8591 (tp40) REVERT: A 294 ARG cc_start: 0.4995 (OUTLIER) cc_final: 0.1485 (mpt180) REVERT: B 536 ASP cc_start: 0.7989 (m-30) cc_final: 0.7439 (t0) outliers start: 38 outliers final: 34 residues processed: 93 average time/residue: 0.1875 time to fit residues: 23.9545 Evaluate side-chains 97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.082329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059934 restraints weight = 24739.388| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 6.55 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7199 Z= 0.143 Angle : 0.808 9.727 9911 Z= 0.383 Chirality : 0.050 0.249 1185 Planarity : 0.005 0.044 1192 Dihedral : 9.607 83.513 1832 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 5.38 % Allowed : 25.50 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -2.36 (0.29), residues: 796 helix: -1.23 (0.68), residues: 58 sheet: -0.50 (0.56), residues: 94 loop : -1.95 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 622 HIS 0.003 0.001 HIS B 673 PHE 0.024 0.001 PHE D 447 TYR 0.016 0.001 TYR B 709 ARG 0.002 0.000 ARG C 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 11) link_NAG-ASN : angle 2.02675 ( 33) link_BETA1-4 : bond 0.00619 ( 26) link_BETA1-4 : angle 1.91767 ( 78) hydrogen bonds : bond 0.03232 ( 108) hydrogen bonds : angle 6.28740 ( 273) SS BOND : bond 0.00290 ( 22) SS BOND : angle 1.04944 ( 44) covalent geometry : bond 0.00310 ( 7138) covalent geometry : angle 0.78467 ( 9756) Misc. bond : bond 0.00087 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 66 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2354 (OUTLIER) cc_final: 0.0196 (mpt180) REVERT: D 536 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7148 (t0) REVERT: D 617 TYR cc_start: 0.9466 (p90) cc_final: 0.9211 (p90) REVERT: D 673 HIS cc_start: 0.7978 (t-90) cc_final: 0.7379 (t-90) REVERT: D 706 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8642 (tp40) REVERT: A 294 ARG cc_start: 0.2055 (OUTLIER) cc_final: -0.0233 (mpt180) REVERT: B 536 ASP cc_start: 0.7786 (m-30) cc_final: 0.7397 (t0) outliers start: 38 outliers final: 32 residues processed: 95 average time/residue: 0.1761 time to fit residues: 23.0245 Evaluate side-chains 96 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 536 ASP Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain D residue 706 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 294 ARG Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 532 GLU Chi-restraints excluded: chain B residue 556 MET Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.081846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059826 restraints weight = 24632.108| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 6.49 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7199 Z= 0.170 Angle : 0.816 9.215 9911 Z= 0.388 Chirality : 0.050 0.250 1185 Planarity : 0.005 0.043 1192 Dihedral : 8.991 75.089 1832 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 5.38 % Allowed : 25.64 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.27 % 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: -2.35 (0.29), residues: 796 helix: -1.26 (0.67), residues: 58 sheet: -0.44 (0.57), residues: 94 loop : -1.95 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 622 HIS 0.004 0.001 HIS C 222 PHE 0.010 0.001 PHE B 538 TYR 0.016 0.001 TYR D 709 ARG 0.003 0.000 ARG C 294 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 11) link_NAG-ASN : angle 2.11630 ( 33) link_BETA1-4 : bond 0.00565 ( 26) link_BETA1-4 : angle 2.01596 ( 78) hydrogen bonds : bond 0.03297 ( 108) hydrogen bonds : angle 6.19698 ( 273) SS BOND : bond 0.00375 ( 22) SS BOND : angle 1.07500 ( 44) covalent geometry : bond 0.00369 ( 7138) covalent geometry : angle 0.78919 ( 9756) Misc. bond : bond 0.00072 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.31 seconds wall clock time: 56 minutes 35.76 seconds (3395.76 seconds total)