Starting phenix.real_space_refine on Wed Sep 17 08:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rk0_19254/09_2025/8rk0_19254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rk0_19254/09_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_19254/09_2025/8rk0_19254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rk0_19254/09_2025/8rk0_19254.map" model { file = "/net/cci-nas-00/data/ceres_data/8rk0_19254/09_2025/8rk0_19254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rk0_19254/09_2025/8rk0_19254.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.97, per 1000 atoms: 0.28 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: 0.91 Conformation dependent library (CDL) restraints added in 323.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 0.96 Time building geometry restraints manager: 1.12 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: 0.00 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- 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 : 16.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 297 TYR 0.021 0.002 TYR D 709 PHE 0.009 0.001 PHE D 538 TRP 0.019 0.001 TRP B 622 HIS 0.003 0.001 HIS B 673 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 7138) covalent geometry : angle 0.91611 ( 9756) SS BOND : bond 0.00262 ( 22) SS BOND : angle 1.21276 ( 44) hydrogen bonds : bond 0.22450 ( 108) hydrogen bonds : angle 8.03004 ( 273) Misc. bond : bond 0.00126 ( 2) link_BETA1-4 : bond 0.00554 ( 26) link_BETA1-4 : angle 2.12385 ( 78) link_NAG-ASN : bond 0.00347 ( 11) link_NAG-ASN : angle 2.35814 ( 33) *********************** 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 : 0.207 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.0783 time to fit residues: 7.7787 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 : 0.276 ------------------------------------------------------------------------------- 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 49 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 D 423 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS B 409 GLN B 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.079617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057702 restraints weight = 25344.335| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 6.40 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7199 Z= 0.302 Angle : 0.926 7.498 9911 Z= 0.434 Chirality : 0.053 0.212 1185 Planarity : 0.006 0.057 1192 Dihedral : 19.004 114.734 1835 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 5.81 % Allowed : 24.08 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.30), residues: 796 helix: -1.07 (0.69), residues: 58 sheet: -0.45 (0.55), residues: 100 loop : -2.15 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 294 TYR 0.022 0.002 TYR D 709 PHE 0.013 0.002 PHE D 538 TRP 0.015 0.002 TRP B 622 HIS 0.006 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 7138) covalent geometry : angle 0.89093 ( 9756) SS BOND : bond 0.00460 ( 22) SS BOND : angle 1.38477 ( 44) hydrogen bonds : bond 0.04981 ( 108) hydrogen bonds : angle 6.77590 ( 273) Misc. bond : bond 0.00055 ( 2) link_BETA1-4 : bond 0.00586 ( 26) link_BETA1-4 : angle 2.39519 ( 78) link_NAG-ASN : bond 0.00643 ( 11) link_NAG-ASN : angle 2.60880 ( 33) *********************** 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 101 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 60 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: D 536 ASP cc_start: 0.7481 (t0) cc_final: 0.7227 (t0) REVERT: D 673 HIS cc_start: 0.7764 (t-90) cc_final: 0.7381 (t-90) REVERT: D 706 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8774 (tp-100) REVERT: A 250 TYR cc_start: 0.8914 (p90) cc_final: 0.8589 (p90) outliers start: 41 outliers final: 19 residues processed: 92 average time/residue: 0.0661 time to fit residues: 8.9351 Evaluate side-chains 77 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 614 MET Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 705 VAL 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 427 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 556 MET 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 67 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.081029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059484 restraints weight = 24579.508| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 6.34 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1447 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= 0.179 Angle : 0.849 9.062 9911 Z= 0.396 Chirality : 0.051 0.230 1185 Planarity : 0.006 0.055 1192 Dihedral : 16.539 115.656 1832 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.32 % Favored : 86.56 % Rotamer: Outliers : 4.67 % Allowed : 24.50 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.30), residues: 796 helix: -1.01 (0.70), residues: 58 sheet: -0.60 (0.53), residues: 100 loop : -2.06 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 294 TYR 0.028 0.002 TYR C 250 PHE 0.010 0.001 PHE B 538 TRP 0.013 0.001 TRP B 622 HIS 0.003 0.001 HIS D 669 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7138) covalent geometry : angle 0.82040 ( 9756) SS BOND : bond 0.00314 ( 22) SS BOND : angle 1.11956 ( 44) hydrogen bonds : bond 0.04237 ( 108) hydrogen bonds : angle 6.64408 ( 273) Misc. bond : bond 0.00049 ( 2) link_BETA1-4 : bond 0.00590 ( 26) link_BETA1-4 : angle 2.08459 ( 78) link_NAG-ASN : bond 0.00204 ( 11) link_NAG-ASN : angle 2.31785 ( 33) *********************** 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 100 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.321 Fit side-chains REVERT: D 536 ASP cc_start: 0.7381 (t0) cc_final: 0.7090 (t0) REVERT: D 673 HIS cc_start: 0.7693 (t-90) cc_final: 0.7108 (t-90) outliers start: 33 outliers final: 17 residues processed: 88 average time/residue: 0.0698 time to fit residues: 9.0147 Evaluate side-chains 77 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 D residue 446 LYS 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 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 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 678 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 668 GLN A 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.082325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060200 restraints weight = 24382.093| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 6.48 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1651 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= 0.138 Angle : 0.810 9.058 9911 Z= 0.379 Chirality : 0.050 0.260 1185 Planarity : 0.006 0.048 1192 Dihedral : 13.806 114.067 1832 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.32 % Favored : 86.68 % Rotamer: Outliers : 4.53 % Allowed : 23.51 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.29), residues: 796 helix: -0.96 (0.70), residues: 58 sheet: -0.59 (0.59), residues: 80 loop : -1.94 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 195 TYR 0.018 0.001 TYR D 709 PHE 0.016 0.001 PHE D 447 TRP 0.009 0.001 TRP B 622 HIS 0.004 0.001 HIS D 595 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7138) covalent geometry : angle 0.78247 ( 9756) SS BOND : bond 0.00256 ( 22) SS BOND : angle 1.12909 ( 44) hydrogen bonds : bond 0.03557 ( 108) hydrogen bonds : angle 6.55740 ( 273) Misc. bond : bond 0.00077 ( 2) link_BETA1-4 : bond 0.00647 ( 26) link_BETA1-4 : angle 1.95612 ( 78) link_NAG-ASN : bond 0.00226 ( 11) link_NAG-ASN : angle 2.34719 ( 33) *********************** 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 107 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.240 Fit side-chains REVERT: C 294 ARG cc_start: 0.1961 (OUTLIER) cc_final: -0.0415 (mpt180) REVERT: D 536 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6953 (t0) REVERT: D 668 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8669 (mm110) REVERT: D 673 HIS cc_start: 0.7745 (t-90) cc_final: 0.7139 (t-90) REVERT: D 706 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8753 (tp40) REVERT: A 294 ARG cc_start: 0.1916 (OUTLIER) cc_final: -0.0396 (mpt180) REVERT: B 523 LYS cc_start: 0.8360 (ptpp) cc_final: 0.7917 (mmtt) outliers start: 32 outliers final: 16 residues processed: 92 average time/residue: 0.0746 time to fit residues: 9.6039 Evaluate side-chains 87 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 304 CYS Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 520 THR 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 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 556 MET Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 628 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3613 r_free = 0.3613 target = 0.083669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061665 restraints weight = 24646.395| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 6.56 r_work: 0.2983 rms_B_bonded: 6.55 restraints_weight: 2.0000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7199 Z= 0.133 Angle : 0.792 10.145 9911 Z= 0.372 Chirality : 0.050 0.266 1185 Planarity : 0.005 0.046 1192 Dihedral : 12.194 111.029 1832 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer: Outliers : 5.10 % Allowed : 23.80 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.29), residues: 796 helix: -0.93 (0.72), residues: 58 sheet: -0.55 (0.58), residues: 80 loop : -1.86 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 195 TYR 0.016 0.001 TYR D 709 PHE 0.011 0.001 PHE B 538 TRP 0.010 0.001 TRP D 622 HIS 0.005 0.001 HIS D 595 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7138) covalent geometry : angle 0.76725 ( 9756) SS BOND : bond 0.00283 ( 22) SS BOND : angle 1.05998 ( 44) hydrogen bonds : bond 0.03313 ( 108) hydrogen bonds : angle 6.42539 ( 273) Misc. bond : bond 0.00076 ( 2) link_BETA1-4 : bond 0.00616 ( 26) link_BETA1-4 : angle 1.86953 ( 78) link_NAG-ASN : bond 0.00189 ( 11) link_NAG-ASN : angle 2.15090 ( 33) *********************** 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 107 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.4887 (OUTLIER) cc_final: 0.1406 (mpt180) REVERT: D 536 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6939 (t0) REVERT: D 668 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8784 (mm110) REVERT: D 673 HIS cc_start: 0.7712 (t-90) cc_final: 0.7062 (t-90) REVERT: D 706 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8863 (tp40) REVERT: A 294 ARG cc_start: 0.5043 (OUTLIER) cc_final: 0.1345 (mpt180) REVERT: B 536 ASP cc_start: 0.7815 (m-30) cc_final: 0.7252 (t0) outliers start: 36 outliers final: 22 residues processed: 92 average time/residue: 0.0727 time to fit residues: 9.3036 Evaluate side-chains 86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 446 LYS Chi-restraints excluded: chain D residue 472 LEU 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 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 446 LYS Chi-restraints excluded: chain B residue 520 THR 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 6 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 40.0000 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3596 r_free = 0.3596 target = 0.082651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060647 restraints weight = 24756.442| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 6.54 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2059 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= 0.156 Angle : 0.778 8.996 9911 Z= 0.369 Chirality : 0.049 0.280 1185 Planarity : 0.005 0.044 1192 Dihedral : 11.414 107.149 1832 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 5.24 % Allowed : 24.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.29), residues: 796 helix: -1.09 (0.71), residues: 58 sheet: -0.86 (0.53), residues: 90 loop : -1.88 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 620 TYR 0.016 0.001 TYR D 709 PHE 0.016 0.001 PHE B 447 TRP 0.008 0.001 TRP B 622 HIS 0.005 0.001 HIS D 623 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7138) covalent geometry : angle 0.75009 ( 9756) SS BOND : bond 0.00268 ( 22) SS BOND : angle 1.26382 ( 44) hydrogen bonds : bond 0.03383 ( 108) hydrogen bonds : angle 6.34684 ( 273) Misc. bond : bond 0.00054 ( 2) link_BETA1-4 : bond 0.00585 ( 26) link_BETA1-4 : angle 1.89131 ( 78) link_NAG-ASN : bond 0.00206 ( 11) link_NAG-ASN : angle 2.21903 ( 33) *********************** 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 104 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1921 (OUTLIER) cc_final: -0.0343 (mpt180) REVERT: D 536 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7091 (t0) REVERT: D 668 GLN cc_start: 0.9000 (mm110) cc_final: 0.8717 (mm110) REVERT: D 673 HIS cc_start: 0.7726 (t-90) cc_final: 0.7063 (t-90) REVERT: D 706 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8809 (tp40) REVERT: A 294 ARG cc_start: 0.1892 (OUTLIER) cc_final: -0.0493 (mpt180) REVERT: B 536 ASP cc_start: 0.7778 (m-30) cc_final: 0.7341 (t0) outliers start: 37 outliers final: 27 residues processed: 91 average time/residue: 0.0770 time to fit residues: 9.6085 Evaluate side-chains 92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 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 520 THR Chi-restraints excluded: chain D residue 532 GLU 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 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 446 LYS Chi-restraints excluded: chain B residue 472 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 0.0040 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.082669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060439 restraints weight = 24607.673| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 6.53 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7199 Z= 0.143 Angle : 0.775 9.586 9911 Z= 0.368 Chirality : 0.049 0.262 1185 Planarity : 0.005 0.045 1192 Dihedral : 10.691 101.717 1832 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 4.67 % Allowed : 25.92 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.29), residues: 796 helix: -1.08 (0.71), residues: 58 sheet: -0.56 (0.59), residues: 80 loop : -1.85 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.016 0.001 TYR B 709 PHE 0.010 0.001 PHE B 538 TRP 0.010 0.001 TRP B 622 HIS 0.003 0.001 HIS D 669 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7138) covalent geometry : angle 0.75052 ( 9756) SS BOND : bond 0.00290 ( 22) SS BOND : angle 1.12249 ( 44) hydrogen bonds : bond 0.03265 ( 108) hydrogen bonds : angle 6.26936 ( 273) Misc. bond : bond 0.00079 ( 2) link_BETA1-4 : bond 0.00609 ( 26) link_BETA1-4 : angle 1.83283 ( 78) link_NAG-ASN : bond 0.00178 ( 11) link_NAG-ASN : angle 2.02232 ( 33) *********************** 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 101 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1999 (OUTLIER) cc_final: -0.0328 (mpt180) REVERT: D 536 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7103 (t0) REVERT: D 668 GLN cc_start: 0.8916 (mm110) cc_final: 0.8641 (mm110) REVERT: D 673 HIS cc_start: 0.7767 (t-90) cc_final: 0.7073 (t-90) REVERT: D 706 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8756 (tp40) REVERT: A 294 ARG cc_start: 0.1923 (OUTLIER) cc_final: -0.0491 (mpt180) outliers start: 33 outliers final: 27 residues processed: 89 average time/residue: 0.0845 time to fit residues: 10.2040 Evaluate side-chains 94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 644 HIS D 668 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.083482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061181 restraints weight = 24604.913| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 6.56 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7199 Z= 0.130 Angle : 0.767 9.400 9911 Z= 0.365 Chirality : 0.049 0.249 1185 Planarity : 0.005 0.047 1192 Dihedral : 9.820 93.355 1832 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 5.24 % Allowed : 25.64 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.30), residues: 796 helix: -1.07 (0.72), residues: 58 sheet: -0.28 (0.67), residues: 66 loop : -1.77 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 195 TYR 0.015 0.001 TYR D 709 PHE 0.022 0.001 PHE D 447 TRP 0.011 0.001 TRP D 622 HIS 0.003 0.001 HIS D 669 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7138) covalent geometry : angle 0.74485 ( 9756) SS BOND : bond 0.00237 ( 22) SS BOND : angle 0.98627 ( 44) hydrogen bonds : bond 0.03130 ( 108) hydrogen bonds : angle 6.24911 ( 273) Misc. bond : bond 0.00081 ( 2) link_BETA1-4 : bond 0.00647 ( 26) link_BETA1-4 : angle 1.81846 ( 78) link_NAG-ASN : bond 0.00166 ( 11) link_NAG-ASN : angle 1.93953 ( 33) *********************** 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 107 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1788 (OUTLIER) cc_final: -0.0445 (mpt180) REVERT: D 536 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7025 (t0) REVERT: D 668 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8647 (mm110) REVERT: D 673 HIS cc_start: 0.7752 (t-90) cc_final: 0.7041 (t-90) REVERT: D 706 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8753 (tp40) REVERT: A 294 ARG cc_start: 0.1852 (OUTLIER) cc_final: -0.0498 (mpt180) outliers start: 37 outliers final: 25 residues processed: 93 average time/residue: 0.0784 time to fit residues: 10.1308 Evaluate side-chains 90 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 VAL Chi-restraints excluded: chain D residue 403 PHE 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 212 ILE Chi-restraints excluded: chain A residue 213 VAL 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 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ** 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 = 0.3586 r_free = 0.3586 target = 0.081730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059526 restraints weight = 24806.010| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 6.53 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2484 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= 0.185 Angle : 0.801 8.950 9911 Z= 0.380 Chirality : 0.049 0.241 1185 Planarity : 0.005 0.044 1192 Dihedral : 9.291 85.333 1832 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 5.24 % Allowed : 25.78 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.29), residues: 796 helix: -1.15 (0.70), residues: 58 sheet: -0.33 (0.67), residues: 66 loop : -1.82 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 620 TYR 0.016 0.001 TYR B 709 PHE 0.011 0.001 PHE B 538 TRP 0.010 0.002 TRP B 420 HIS 0.006 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7138) covalent geometry : angle 0.77375 ( 9756) SS BOND : bond 0.00324 ( 22) SS BOND : angle 1.01853 ( 44) hydrogen bonds : bond 0.03424 ( 108) hydrogen bonds : angle 6.15913 ( 273) Misc. bond : bond 0.00067 ( 2) link_BETA1-4 : bond 0.00582 ( 26) link_BETA1-4 : angle 1.98830 ( 78) link_NAG-ASN : bond 0.00366 ( 11) link_NAG-ASN : angle 2.19033 ( 33) *********************** 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 97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1887 (OUTLIER) cc_final: -0.0208 (mpt180) REVERT: D 536 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7225 (t0) REVERT: D 673 HIS cc_start: 0.7919 (t-90) cc_final: 0.7355 (t-90) REVERT: D 706 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8650 (tp40) REVERT: A 294 ARG cc_start: 0.1905 (OUTLIER) cc_final: -0.0437 (mpt180) outliers start: 37 outliers final: 29 residues processed: 85 average time/residue: 0.0792 time to fit residues: 9.2829 Evaluate side-chains 89 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 392 VAL Chi-restraints excluded: chain D residue 403 PHE 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 212 ILE Chi-restraints excluded: chain A residue 213 VAL 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 392 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 overall best weight: 0.4640 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.083958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061559 restraints weight = 24330.722| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 6.57 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7199 Z= 0.129 Angle : 0.790 9.713 9911 Z= 0.376 Chirality : 0.049 0.247 1185 Planarity : 0.005 0.047 1192 Dihedral : 8.708 79.238 1832 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.44 % Favored : 87.44 % Rotamer: Outliers : 4.67 % Allowed : 26.35 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.30), residues: 796 helix: -1.08 (0.72), residues: 58 sheet: -0.32 (0.66), residues: 66 loop : -1.75 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 663 TYR 0.016 0.001 TYR B 709 PHE 0.009 0.001 PHE B 538 TRP 0.013 0.001 TRP D 530 HIS 0.003 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7138) covalent geometry : angle 0.76915 ( 9756) SS BOND : bond 0.00231 ( 22) SS BOND : angle 0.94620 ( 44) hydrogen bonds : bond 0.03099 ( 108) hydrogen bonds : angle 6.22725 ( 273) Misc. bond : bond 0.00090 ( 2) link_BETA1-4 : bond 0.00657 ( 26) link_BETA1-4 : angle 1.85799 ( 78) link_NAG-ASN : bond 0.00258 ( 11) link_NAG-ASN : angle 1.78081 ( 33) ********************** 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 107 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.1903 (OUTLIER) cc_final: -0.0259 (mpt180) REVERT: D 617 TYR cc_start: 0.9539 (p90) cc_final: 0.9128 (p90) REVERT: D 673 HIS cc_start: 0.7819 (t-90) cc_final: 0.7193 (t-90) REVERT: D 706 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8738 (tp40) REVERT: A 294 ARG cc_start: 0.2007 (OUTLIER) cc_final: -0.0542 (mtt90) REVERT: B 622 TRP cc_start: 0.9248 (m100) cc_final: 0.9022 (m100) outliers start: 33 outliers final: 26 residues processed: 97 average time/residue: 0.0826 time to fit residues: 10.9208 Evaluate side-chains 92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 VAL Chi-restraints excluded: chain D residue 403 PHE 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 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 212 ILE Chi-restraints excluded: chain A residue 213 VAL 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 392 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 472 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 70 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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** ** 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 = 0.3630 r_free = 0.3630 target = 0.084074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061948 restraints weight = 24169.213| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 6.51 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7199 Z= 0.128 Angle : 0.790 9.481 9911 Z= 0.376 Chirality : 0.049 0.251 1185 Planarity : 0.005 0.047 1192 Dihedral : 8.043 71.610 1832 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 4.67 % Allowed : 26.91 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.30), residues: 796 helix: -1.17 (0.71), residues: 58 sheet: -0.29 (0.67), residues: 66 loop : -1.75 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 636 TYR 0.015 0.001 TYR B 709 PHE 0.010 0.001 PHE D 538 TRP 0.011 0.001 TRP D 530 HIS 0.004 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7138) covalent geometry : angle 0.76759 ( 9756) SS BOND : bond 0.00198 ( 22) SS BOND : angle 0.91278 ( 44) hydrogen bonds : bond 0.03135 ( 108) hydrogen bonds : angle 6.14484 ( 273) Misc. bond : bond 0.00087 ( 2) link_BETA1-4 : bond 0.00584 ( 26) link_BETA1-4 : angle 1.93807 ( 78) link_NAG-ASN : bond 0.00194 ( 11) link_NAG-ASN : angle 1.85524 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1512.43 seconds wall clock time: 26 minutes 59.31 seconds (1619.31 seconds total)