Starting phenix.real_space_refine on Tue Sep 24 05:25:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk0_19254/09_2024/8rk0_19254.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk0_19254/09_2024/8rk0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk0_19254/09_2024/8rk0_19254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk0_19254/09_2024/8rk0_19254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk0_19254/09_2024/8rk0_19254.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk0_19254/09_2024/8rk0_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-5461/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: 5.05, per 1000 atoms: 0.73 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: 2.08 Conformation dependent library (CDL) restraints added in 850.2 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: 0.69 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: 1.57 Time building geometry restraints manager: 2.38 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.110 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- 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 7138 Z= 0.285 Angle : 0.916 11.595 9756 Z= 0.428 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.779 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1671 time to fit residues: 16.5706 Evaluate side-chains 66 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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: 3.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 7138 Z= 0.261 Angle : 0.821 8.029 9756 Z= 0.390 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 *********************** 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 fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 0.792 Fit side-chains REVERT: D 415 ASN cc_start: 0.9293 (t0) cc_final: 0.9052 (t0) REVERT: D 536 ASP cc_start: 0.7240 (t0) cc_final: 0.6930 (t0) REVERT: D 673 HIS cc_start: 0.7642 (t-90) cc_final: 0.7260 (t-90) REVERT: D 706 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8744 (tp40) outliers start: 32 outliers final: 13 residues processed: 92 average time/residue: 0.1517 time to fit residues: 20.2365 Evaluate side-chains 76 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 40 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 49 optimal weight: 30.0000 chunk 20 optimal weight: 0.0370 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- 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 222 HIS A 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7138 Z= 0.177 Angle : 0.793 9.514 9756 Z= 0.374 Chirality : 0.051 0.253 1185 Planarity : 0.006 0.048 1192 Dihedral : 15.355 116.126 1832 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 4.11 % Allowed : 22.80 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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: -2.42 (0.29), residues: 796 helix: -1.00 (0.70), residues: 58 sheet: -0.31 (0.61), residues: 80 loop : -2.03 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 622 HIS 0.003 0.001 HIS B 669 PHE 0.010 0.001 PHE B 442 TYR 0.029 0.002 TYR C 250 ARG 0.002 0.000 ARG C 195 *********************** 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 114 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: D 415 ASN cc_start: 0.9266 (t0) cc_final: 0.9047 (t0) REVERT: D 536 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6706 (t0) REVERT: D 673 HIS cc_start: 0.7618 (t-90) cc_final: 0.7016 (t-90) REVERT: A 250 TYR cc_start: 0.8655 (p90) cc_final: 0.8400 (p90) outliers start: 29 outliers final: 7 residues processed: 103 average time/residue: 0.1407 time to fit residues: 20.9194 Evaluate side-chains 75 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 536 ASP 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 246 VAL Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.0050 chunk 73 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7138 Z= 0.203 Angle : 0.769 9.160 9756 Z= 0.366 Chirality : 0.050 0.274 1185 Planarity : 0.005 0.045 1192 Dihedral : 13.349 113.566 1832 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 3.82 % Allowed : 24.08 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % 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: -2.36 (0.29), residues: 796 helix: -1.06 (0.71), residues: 58 sheet: -0.39 (0.59), residues: 80 loop : -1.96 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 652 HIS 0.004 0.001 HIS A 222 PHE 0.016 0.001 PHE D 447 TYR 0.022 0.001 TYR D 617 ARG 0.002 0.000 ARG A 294 *********************** 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 96 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.807 Fit side-chains REVERT: D 415 ASN cc_start: 0.9258 (t0) cc_final: 0.9011 (t0) REVERT: D 536 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6856 (t0) REVERT: D 673 HIS cc_start: 0.7736 (t-90) cc_final: 0.7317 (t-90) REVERT: D 706 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8777 (tp40) REVERT: B 523 LYS cc_start: 0.8451 (ptpp) cc_final: 0.7966 (mmtt) outliers start: 27 outliers final: 16 residues processed: 84 average time/residue: 0.1490 time to fit residues: 17.9953 Evaluate side-chains 83 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 246 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 591 CYS Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 53 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7138 Z= 0.403 Angle : 0.849 9.299 9756 Z= 0.408 Chirality : 0.051 0.314 1185 Planarity : 0.006 0.048 1192 Dihedral : 12.317 109.638 1832 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 5.38 % Allowed : 23.09 % Favored : 71.53 % 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: -2.47 (0.29), residues: 796 helix: -1.16 (0.68), residues: 58 sheet: -0.57 (0.54), residues: 100 loop : -2.05 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 420 HIS 0.009 0.002 HIS A 222 PHE 0.012 0.002 PHE D 538 TYR 0.029 0.002 TYR C 250 ARG 0.005 0.001 ARG C 294 *********************** 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 100 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 62 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2090 (OUTLIER) cc_final: -0.0122 (mpt180) REVERT: D 482 ASP cc_start: 0.9069 (t0) cc_final: 0.8747 (t0) REVERT: D 536 ASP cc_start: 0.7521 (t0) cc_final: 0.7289 (t0) REVERT: D 673 HIS cc_start: 0.7921 (t-90) cc_final: 0.7259 (t-90) REVERT: A 250 TYR cc_start: 0.8980 (p90) cc_final: 0.8645 (p90) REVERT: A 294 ARG cc_start: 0.2150 (OUTLIER) cc_final: -0.0207 (mpt180) REVERT: B 536 ASP cc_start: 0.7917 (m-30) cc_final: 0.7409 (t0) outliers start: 38 outliers final: 28 residues processed: 90 average time/residue: 0.1689 time to fit residues: 21.0712 Evaluate side-chains 88 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 58 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 497 VAL Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 556 MET Chi-restraints excluded: chain D residue 591 CYS Chi-restraints excluded: chain D residue 615 VAL 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 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 591 CYS Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 678 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7138 Z= 0.195 Angle : 0.760 9.695 9756 Z= 0.368 Chirality : 0.049 0.261 1185 Planarity : 0.006 0.044 1192 Dihedral : 11.530 107.951 1832 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 4.39 % Allowed : 24.79 % Favored : 70.82 % 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: -1.11 (0.69), residues: 58 sheet: -0.61 (0.59), residues: 80 loop : -1.91 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 622 HIS 0.003 0.001 HIS B 669 PHE 0.010 0.001 PHE B 538 TYR 0.016 0.001 TYR D 709 ARG 0.001 0.000 ARG C 294 *********************** 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 fitting. rotamer outliers: 31 poor density : 73 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2158 (OUTLIER) cc_final: -0.0060 (mpt180) REVERT: D 536 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7089 (t0) REVERT: D 668 GLN cc_start: 0.8944 (mm110) cc_final: 0.8668 (mm110) REVERT: D 673 HIS cc_start: 0.7768 (t-90) cc_final: 0.7109 (t-90) REVERT: D 688 MET cc_start: 0.8469 (mtp) cc_final: 0.8054 (mtp) REVERT: A 294 ARG cc_start: 0.2391 (OUTLIER) cc_final: -0.0088 (mpt180) REVERT: B 536 ASP cc_start: 0.7690 (m-30) cc_final: 0.7230 (t0) outliers start: 31 outliers final: 19 residues processed: 94 average time/residue: 0.1778 time to fit residues: 23.5817 Evaluate side-chains 89 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 ILE 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 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 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 A residue 212 ILE 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 A residue 313 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 591 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7138 Z= 0.243 Angle : 0.760 8.809 9756 Z= 0.368 Chirality : 0.049 0.276 1185 Planarity : 0.005 0.042 1192 Dihedral : 10.843 102.442 1832 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 6.37 % Allowed : 24.36 % Favored : 69.26 % 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: -2.32 (0.29), residues: 796 helix: -1.15 (0.68), residues: 58 sheet: -0.26 (0.58), residues: 90 loop : -1.95 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 622 HIS 0.005 0.001 HIS A 222 PHE 0.017 0.001 PHE B 447 TYR 0.016 0.001 TYR D 709 ARG 0.004 0.000 ARG C 294 *********************** 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 109 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 64 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2172 (OUTLIER) cc_final: -0.0271 (mtt90) REVERT: D 536 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7170 (t0) REVERT: D 673 HIS cc_start: 0.7797 (t-90) cc_final: 0.7122 (t-90) REVERT: A 294 ARG cc_start: 0.2271 (OUTLIER) cc_final: -0.0021 (mpt180) REVERT: B 536 ASP cc_start: 0.7782 (m-30) cc_final: 0.7347 (t0) outliers start: 45 outliers final: 30 residues processed: 97 average time/residue: 0.1816 time to fit residues: 23.9701 Evaluate side-chains 96 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 63 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 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 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 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 307 SER Chi-restraints excluded: chain A residue 313 VAL 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 507 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 532 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7138 Z= 0.234 Angle : 0.767 9.391 9756 Z= 0.370 Chirality : 0.050 0.264 1185 Planarity : 0.006 0.043 1192 Dihedral : 10.390 97.905 1832 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 5.52 % Allowed : 24.50 % 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: -2.28 (0.30), residues: 796 helix: -1.15 (0.69), residues: 58 sheet: -0.26 (0.58), residues: 90 loop : -1.92 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 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 *********************** 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 103 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 64 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2069 (OUTLIER) cc_final: -0.0439 (mtt90) REVERT: D 536 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7145 (t0) REVERT: D 673 HIS cc_start: 0.7810 (t-90) cc_final: 0.7123 (t-90) REVERT: D 706 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8719 (tp40) REVERT: A 294 ARG cc_start: 0.2335 (OUTLIER) cc_final: 0.0070 (mpt180) REVERT: B 536 ASP cc_start: 0.7774 (m-30) cc_final: 0.7353 (t0) outliers start: 39 outliers final: 33 residues processed: 91 average time/residue: 0.1768 time to fit residues: 22.2745 Evaluate side-chains 99 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 62 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 237 THR 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 482 ASP 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 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 307 SER Chi-restraints excluded: chain A residue 313 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7138 Z= 0.239 Angle : 0.769 9.079 9756 Z= 0.372 Chirality : 0.049 0.251 1185 Planarity : 0.005 0.043 1192 Dihedral : 9.630 88.651 1832 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % 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: -2.28 (0.30), residues: 796 helix: -1.19 (0.68), residues: 58 sheet: -0.24 (0.58), residues: 90 loop : -1.91 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 622 HIS 0.004 0.001 HIS C 222 PHE 0.011 0.001 PHE B 538 TYR 0.016 0.001 TYR D 709 ARG 0.004 0.000 ARG C 294 *********************** 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 100 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 62 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2150 (OUTLIER) cc_final: -0.0129 (mpt180) REVERT: D 536 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7165 (t0) REVERT: D 673 HIS cc_start: 0.7849 (t-90) cc_final: 0.7120 (t-90) REVERT: D 688 MET cc_start: 0.8458 (mtp) cc_final: 0.8197 (mtp) REVERT: D 691 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7619 (mp) REVERT: D 706 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8708 (tp40) REVERT: A 294 ARG cc_start: 0.2297 (OUTLIER) cc_final: -0.0294 (mtt90) REVERT: B 536 ASP cc_start: 0.7737 (m-30) cc_final: 0.7382 (t0) outliers start: 38 outliers final: 29 residues processed: 89 average time/residue: 0.1748 time to fit residues: 21.5382 Evaluate side-chains 91 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 57 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 237 THR 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 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 313 VAL 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 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 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 36 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 0.0870 overall best weight: 1.7362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7138 Z= 0.231 Angle : 0.774 9.263 9756 Z= 0.374 Chirality : 0.049 0.243 1185 Planarity : 0.005 0.043 1192 Dihedral : 8.921 79.066 1832 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.31 % Favored : 87.56 % Rotamer: Outliers : 4.96 % Allowed : 26.20 % Favored : 68.84 % 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: -2.30 (0.30), residues: 796 helix: -1.15 (0.69), residues: 58 sheet: -0.44 (0.57), residues: 94 loop : -1.91 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 530 HIS 0.004 0.001 HIS A 222 PHE 0.010 0.001 PHE B 538 TYR 0.017 0.001 TYR B 709 ARG 0.003 0.000 ARG C 294 ********************** 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 97 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 62 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 294 ARG cc_start: 0.2343 (OUTLIER) cc_final: 0.0079 (mpt180) REVERT: D 536 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7157 (t0) REVERT: D 673 HIS cc_start: 0.8010 (t-90) cc_final: 0.7420 (t-90) REVERT: D 688 MET cc_start: 0.8456 (mtp) cc_final: 0.8194 (mtp) REVERT: D 706 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8693 (tp40) REVERT: A 294 ARG cc_start: 0.2324 (OUTLIER) cc_final: 0.0258 (mpt180) REVERT: B 536 ASP cc_start: 0.7719 (m-30) cc_final: 0.7409 (t0) outliers start: 35 outliers final: 31 residues processed: 91 average time/residue: 0.1833 time to fit residues: 23.1203 Evaluate side-chains 93 residues out of total 708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 58 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 237 THR 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 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 313 VAL 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 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 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 58 optimal weight: 0.9990 chunk 9 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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 = 0.3610 r_free = 0.3610 target = 0.083005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060680 restraints weight = 24390.680| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 6.54 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7138 Z= 0.188 Angle : 0.770 9.691 9756 Z= 0.371 Chirality : 0.049 0.252 1185 Planarity : 0.005 0.045 1192 Dihedral : 8.333 71.622 1832 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 4.96 % Allowed : 26.20 % Favored : 68.84 % 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: -2.24 (0.30), residues: 796 helix: -1.13 (0.70), residues: 58 sheet: -0.42 (0.56), residues: 94 loop : -1.86 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 622 HIS 0.005 0.001 HIS B 669 PHE 0.010 0.001 PHE B 538 TYR 0.016 0.001 TYR B 709 ARG 0.002 0.000 ARG C 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1653.66 seconds wall clock time: 30 minutes 37.90 seconds (1837.90 seconds total)