Starting phenix.real_space_refine on Fri May 23 00:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyn_43672/05_2025/8vyn_43672.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyn_43672/05_2025/8vyn_43672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vyn_43672/05_2025/8vyn_43672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyn_43672/05_2025/8vyn_43672.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyn_43672/05_2025/8vyn_43672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyn_43672/05_2025/8vyn_43672.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 123 5.16 5 C 14973 2.51 5 N 3975 2.21 5 O 4692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23763 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4206 Classifications: {'peptide': 523} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 507} Chain breaks: 4 Chain: "B" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4206 Classifications: {'peptide': 523} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 507} Chain breaks: 4 Chain: "C" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4206 Classifications: {'peptide': 523} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 507} Chain breaks: 4 Chain: "D" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1017 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "E" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1017 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "I" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "J" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "L" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1017 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "M" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "N" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} 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: 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: "R" 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: "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: 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: "U" 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: "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: "W" 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: "X" 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.48, per 1000 atoms: 0.65 Number of scatterers: 23763 At special positions: 0 Unit cell: (174.139, 164.974, 112.482, 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 123 16.00 O 4692 8.00 N 3975 7.00 C 14973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 551 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS C 653 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 391 " distance=2.03 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 574 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 551 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 507 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 574 " - pdb=" SG CYS C 611 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 801 " - " ASN A 417 " " NAG A 802 " - " ASN A 302 " " NAG A 803 " - " ASN A 405 " " NAG A 804 " - " ASN A 555 " " NAG B 801 " - " ASN B 417 " " NAG B 802 " - " ASN B 302 " " NAG B 803 " - " ASN B 405 " " NAG B 804 " - " ASN B 555 " " NAG C 801 " - " ASN C 417 " " NAG C 802 " - " ASN C 302 " " NAG C 803 " - " ASN C 405 " " NAG C 804 " - " ASN C 555 " " NAG P 1 " - " ASN A 208 " " NAG Q 1 " - " ASN A 383 " " NAG R 1 " - " ASN A 281 " " NAG S 1 " - " ASN B 208 " " NAG T 1 " - " ASN B 383 " " NAG U 1 " - " ASN B 281 " " NAG V 1 " - " ASN C 208 " " NAG W 1 " - " ASN C 383 " " NAG X 1 " - " ASN C 281 " Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 3.1 seconds 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5514 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 63 sheets defined 15.2% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.614A pdb=" N SER A 288 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 392 through 408 Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 475 through 505 Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.609A pdb=" N SER B 288 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 475 through 505 Processing helix chain 'B' and resid 506 through 521 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.601A pdb=" N SER C 288 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 392 through 408 Processing helix chain 'C' and resid 438 through 447 Processing helix chain 'C' and resid 475 through 505 Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 638 through 642 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 60 through 65 removed outlier: 4.812A pdb=" N GLY D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.993A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 27A through 30 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.556A pdb=" N GLU G 83 " --> pdb=" O SER G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 60 through 65 removed outlier: 4.820A pdb=" N GLY H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 27A through 30 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.560A pdb=" N GLU K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 30 No H-bonds generated for 'chain 'L' and resid 28 through 30' Processing helix chain 'L' and resid 60 through 65 removed outlier: 4.815A pdb=" N GLY L 65 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 removed outlier: 3.991A pdb=" N THR L 87 " --> pdb=" O SER L 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 27A through 30 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.561A pdb=" N GLU O 83 " --> pdb=" O SER O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 82 removed outlier: 5.071A pdb=" N VAL A 579 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 92 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA A 538 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 removed outlier: 5.071A pdb=" N VAL A 579 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 92 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 643 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.706A pdb=" N VAL A 128 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA A 351 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET A 126 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLU A 353 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY A 124 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 355 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP A 122 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A 123 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY A 433 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASN A 417 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 435 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR A 415 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 215 removed outlier: 7.070A pdb=" N LYS A 139 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP A 335 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU A 321 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 306 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 318 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG A 320 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 186 Processing sheet with id=AA7, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 575 Processing sheet with id=AA9, first strand: chain 'A' and resid 616 through 621 removed outlier: 6.906A pdb=" N ALA A 625 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET A 636 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU A 627 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.269A pdb=" N SER A 643 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 92 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL B 579 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.269A pdb=" N SER A 643 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA B 538 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 375 through 377 removed outlier: 6.712A pdb=" N VAL B 128 " --> pdb=" O TRP B 349 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA B 351 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET B 126 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU B 353 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY B 124 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR B 355 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP B 122 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU B 123 " --> pdb=" O ILE B 434 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY B 433 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B 417 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS B 435 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR B 415 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AB5, first strand: chain 'B' and resid 214 through 215 removed outlier: 7.084A pdb=" N LYS B 139 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP B 335 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU B 321 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 316 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 306 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 318 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 304 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG B 320 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AB7, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AB8, first strand: chain 'B' and resid 573 through 575 Processing sheet with id=AB9, first strand: chain 'B' and resid 616 through 621 removed outlier: 6.909A pdb=" N ALA B 625 " --> pdb=" O MET B 636 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET B 636 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU B 627 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.253A pdb=" N SER B 643 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG C 92 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL C 579 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.253A pdb=" N SER B 643 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA C 538 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 375 through 377 removed outlier: 6.707A pdb=" N VAL C 128 " --> pdb=" O TRP C 349 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA C 351 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET C 126 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLU C 353 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLY C 124 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 355 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP C 122 " --> pdb=" O THR C 355 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU C 123 " --> pdb=" O ILE C 434 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLY C 433 " --> pdb=" O ASN C 417 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN C 417 " --> pdb=" O GLY C 433 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS C 435 " --> pdb=" O TYR C 415 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR C 415 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 167 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 214 through 215 removed outlier: 7.063A pdb=" N LYS C 139 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 335 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 321 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 316 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL C 306 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR C 318 " --> pdb=" O THR C 304 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR C 304 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG C 320 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 184 through 186 Processing sheet with id=AC7, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AC8, first strand: chain 'C' and resid 573 through 575 Processing sheet with id=AC9, first strand: chain 'C' and resid 616 through 621 removed outlier: 6.913A pdb=" N ALA C 625 " --> pdb=" O MET C 636 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N MET C 636 " --> pdb=" O ALA C 625 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU C 627 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.664A pdb=" N TYR D 33 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.792A pdb=" N VAL D 102 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER D 96 " --> pdb=" O MET D 100M" (cutoff:3.500A) removed outlier: 8.800A pdb=" N MET D 100M" --> pdb=" O SER D 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.415A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AD6, first strand: chain 'E' and resid 18 through 24 Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.650A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.347A pdb=" N TRP F 35A" --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR F 102 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.650A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.347A pdb=" N TRP F 35A" --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.339A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AE3, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.636A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.803A pdb=" N VAL H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER H 96 " --> pdb=" O MET H 100M" (cutoff:3.500A) removed outlier: 8.806A pdb=" N MET H 100M" --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.417A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 9 through 11 Processing sheet with id=AE9, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.660A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP J 35A" --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.660A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN J 50 " --> pdb=" O TRP J 35A" (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP J 35A" --> pdb=" O ASN J 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.340A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF7, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.649A pdb=" N TYR L 33 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TRP L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP L 36 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.788A pdb=" N VAL L 102 " --> pdb=" O LYS L 94 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER L 96 " --> pdb=" O MET L 100M" (cutoff:3.500A) removed outlier: 8.794A pdb=" N MET L 100M" --> pdb=" O SER L 96 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.413A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AG3, first strand: chain 'M' and resid 18 through 24 Processing sheet with id=AG4, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.654A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN N 50 " --> pdb=" O TRP N 35A" (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP N 35A" --> pdb=" O ASN N 50 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR N 102 " --> pdb=" O THR N 94 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.654A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN N 50 " --> pdb=" O TRP N 35A" (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP N 35A" --> pdb=" O ASN N 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 9 through 12 removed outlier: 6.348A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 9 through 12 Processing sheet with id=AG9, first strand: chain 'O' and resid 19 through 23 1056 hydrogen bonds defined for protein. 2658 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: 11.06 Time building geometry restraints manager: 7.49 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: 7457 1.34 - 1.46: 4824 1.46 - 1.58: 11842 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 24303 Sorted by residual: bond pdb=" CB CYS N 92 " pdb=" SG CYS N 92 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.03e-01 bond pdb=" CB CYS J 92 " pdb=" SG CYS J 92 " ideal model delta sigma weight residual 1.808 1.779 0.029 3.30e-02 9.18e+02 7.85e-01 bond pdb=" CA ALA A 396 " pdb=" C ALA A 396 " ideal model delta sigma weight residual 1.523 1.512 0.011 1.30e-02 5.92e+03 7.67e-01 bond pdb=" CA ASN C 398 " pdb=" C ASN C 398 " ideal model delta sigma weight residual 1.523 1.511 0.012 1.35e-02 5.49e+03 7.62e-01 bond pdb=" CG1 ILE B 618 " pdb=" CD1 ILE B 618 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.32e-01 ... (remaining 24298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 30733 1.04 - 2.08: 1870 2.08 - 3.12: 293 3.12 - 4.16: 61 4.16 - 5.20: 28 Bond angle restraints: 32985 Sorted by residual: angle pdb=" C TRP C 349 " pdb=" N GLU C 350 " pdb=" CA GLU C 350 " ideal model delta sigma weight residual 121.63 117.02 4.61 1.92e+00 2.71e-01 5.75e+00 angle pdb=" C TRP A 349 " pdb=" N GLU A 350 " pdb=" CA GLU A 350 " ideal model delta sigma weight residual 121.63 117.05 4.58 1.92e+00 2.71e-01 5.68e+00 angle pdb=" C GLY M 77 " pdb=" N LEU M 78 " pdb=" CA LEU M 78 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.63e+00 angle pdb=" C TRP B 349 " pdb=" N GLU B 350 " pdb=" CA GLU B 350 " ideal model delta sigma weight residual 121.63 117.10 4.53 1.92e+00 2.71e-01 5.57e+00 angle pdb=" C GLY I 77 " pdb=" N LEU I 78 " pdb=" CA LEU I 78 " ideal model delta sigma weight residual 122.82 126.02 -3.20 1.42e+00 4.96e-01 5.09e+00 ... (remaining 32980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.46: 14152 20.46 - 40.92: 542 40.92 - 61.37: 99 61.37 - 81.83: 48 81.83 - 102.29: 12 Dihedral angle restraints: 14853 sinusoidal: 6231 harmonic: 8622 Sorted by residual: dihedral pdb=" CA VAL C 81 " pdb=" C VAL C 81 " pdb=" N VAL C 82 " pdb=" CA VAL C 82 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA VAL A 81 " pdb=" C VAL A 81 " pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA VAL B 81 " pdb=" C VAL B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 14850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2927 0.052 - 0.104: 594 0.104 - 0.156: 161 0.156 - 0.208: 8 0.208 - 0.260: 6 Chirality restraints: 3696 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN A 281 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 281 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 281 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3693 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 320 " -0.319 9.50e-02 1.11e+02 1.44e-01 1.67e+01 pdb=" NE ARG B 320 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 320 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG B 320 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 320 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 320 " -0.318 9.50e-02 1.11e+02 1.44e-01 1.66e+01 pdb=" NE ARG C 320 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG C 320 " -0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 320 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 320 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 320 " -0.319 9.50e-02 1.11e+02 1.44e-01 1.65e+01 pdb=" NE ARG A 320 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 320 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARG A 320 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 320 " -0.000 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4113 2.77 - 3.30: 21455 3.30 - 3.83: 39324 3.83 - 4.37: 48710 4.37 - 4.90: 84483 Nonbonded interactions: 198085 Sorted by model distance: nonbonded pdb=" OG SER K 2 " pdb=" ND2 ASN K 27B" model vdw 2.237 3.120 nonbonded pdb=" OG SER O 2 " pdb=" ND2 ASN O 27B" model vdw 2.241 3.120 nonbonded pdb=" OG SER G 2 " pdb=" ND2 ASN G 27B" model vdw 2.248 3.120 nonbonded pdb=" ND2 ASN A 118 " pdb=" OD1 ASP A 120 " model vdw 2.268 3.120 nonbonded pdb=" ND2 ASN B 118 " pdb=" OD1 ASP B 120 " model vdw 2.270 3.120 ... (remaining 198080 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } 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: 11.100 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: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 59.840 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.004 0.046 24369 Z= 0.160 Angle : 0.584 5.204 33150 Z= 0.315 Chirality : 0.047 0.260 3696 Planarity : 0.007 0.144 4188 Dihedral : 12.537 102.290 9240 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2904 helix: 1.97 (0.28), residues: 276 sheet: 0.09 (0.15), residues: 1005 loop : -0.70 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.005 0.001 HIS D 35 PHE 0.015 0.002 PHE G 98 TYR 0.020 0.002 TYR C 626 ARG 0.035 0.002 ARG C 320 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 21) link_NAG-ASN : angle 1.95455 ( 63) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 2.25200 ( 36) hydrogen bonds : bond 0.09972 ( 924) hydrogen bonds : angle 6.62293 ( 2658) SS BOND : bond 0.00163 ( 33) SS BOND : angle 0.68022 ( 66) covalent geometry : bond 0.00366 (24303) covalent geometry : angle 0.57394 (32985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8160 (mt-10) REVERT: A 402 GLN cc_start: 0.8245 (tt0) cc_final: 0.7966 (tm-30) REVERT: A 444 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7990 (ttp-110) REVERT: B 80 ASP cc_start: 0.8737 (m-30) cc_final: 0.8466 (m-30) REVERT: B 295 ASP cc_start: 0.7815 (t0) cc_final: 0.7571 (t0) REVERT: B 402 GLN cc_start: 0.8349 (tt0) cc_final: 0.8138 (mt0) REVERT: B 444 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7969 (ttp-110) REVERT: C 444 ARG cc_start: 0.8364 (ttp80) cc_final: 0.8028 (ttp-110) REVERT: C 612 GLN cc_start: 0.8401 (mt0) cc_final: 0.8115 (mm110) REVERT: D 3 GLN cc_start: 0.8504 (tt0) cc_final: 0.8078 (pt0) REVERT: D 69 MET cc_start: 0.8260 (mmt) cc_final: 0.7625 (mmt) REVERT: E 95 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7263 (ttp-170) REVERT: H 3 GLN cc_start: 0.8407 (tt0) cc_final: 0.8166 (pt0) REVERT: I 95 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7281 (ttp-170) REVERT: L 3 GLN cc_start: 0.8465 (tt0) cc_final: 0.8166 (pt0) REVERT: M 95 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7333 (ttp-170) outliers start: 0 outliers final: 2 residues processed: 498 average time/residue: 1.1393 time to fit residues: 664.7803 Evaluate side-chains 330 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 328 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain C residue 581 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 0.0270 chunk 225 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 341 ASN A 365 HIS A 409 ASN A 447 ASN A 478 ASN A 556 GLN B 365 HIS B 409 ASN B 447 ASN B 478 ASN B 556 GLN C 286 ASN C 341 ASN C 409 ASN C 447 ASN C 478 ASN C 556 GLN D 53 ASN E 38 GLN F 77 GLN G 17 GLN G 51 ASN I 38 GLN J 50 ASN K 17 GLN K 27BASN M 38 GLN M 53 GLN N 50 ASN O 17 GLN O 51 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.161644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130492 restraints weight = 27325.917| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.55 r_work: 0.3188 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24369 Z= 0.193 Angle : 0.591 7.953 33150 Z= 0.310 Chirality : 0.046 0.194 3696 Planarity : 0.004 0.038 4188 Dihedral : 7.471 66.419 3946 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.80 % Allowed : 8.99 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 2904 helix: 2.76 (0.28), residues: 279 sheet: 0.00 (0.15), residues: 996 loop : -0.46 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 47 HIS 0.007 0.001 HIS L 35 PHE 0.017 0.002 PHE B 265 TYR 0.017 0.002 TYR K 49 ARG 0.009 0.001 ARG A 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 21) link_NAG-ASN : angle 1.62179 ( 63) link_BETA1-4 : bond 0.00321 ( 12) link_BETA1-4 : angle 2.23141 ( 36) hydrogen bonds : bond 0.03940 ( 924) hydrogen bonds : angle 5.56676 ( 2658) SS BOND : bond 0.00153 ( 33) SS BOND : angle 0.61429 ( 66) covalent geometry : bond 0.00458 (24303) covalent geometry : angle 0.58254 (32985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 2.471 Fit side-chains revert: symmetry clash REVERT: A 96 MET cc_start: 0.7143 (ttp) cc_final: 0.6883 (ttt) REVERT: A 248 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7781 (mm) REVERT: A 326 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 402 GLN cc_start: 0.8103 (tt0) cc_final: 0.7717 (tt0) REVERT: A 444 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7630 (ttp-110) REVERT: A 483 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7146 (mm-40) REVERT: A 607 ARG cc_start: 0.8106 (mpt180) cc_final: 0.7789 (mpt180) REVERT: A 634 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7188 (tmtm) REVERT: B 295 ASP cc_start: 0.7692 (t0) cc_final: 0.7408 (t0) REVERT: B 387 SER cc_start: 0.8521 (m) cc_final: 0.8267 (p) REVERT: B 402 GLN cc_start: 0.8133 (tt0) cc_final: 0.7808 (tt0) REVERT: C 248 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7788 (mm) REVERT: C 342 VAL cc_start: 0.8293 (p) cc_final: 0.8086 (m) REVERT: C 444 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7688 (ttp-110) REVERT: C 574 CYS cc_start: 0.7094 (m) cc_final: 0.6832 (m) REVERT: C 612 GLN cc_start: 0.8397 (mt0) cc_final: 0.7776 (mm110) REVERT: D 3 GLN cc_start: 0.8393 (tt0) cc_final: 0.7577 (pt0) REVERT: E 95 ARG cc_start: 0.7840 (ttm170) cc_final: 0.6954 (ttp-170) REVERT: F 77 GLN cc_start: 0.8022 (mt0) cc_final: 0.7822 (mt0) REVERT: H 3 GLN cc_start: 0.8296 (tt0) cc_final: 0.7691 (pt0) REVERT: I 95 ARG cc_start: 0.7906 (ttm170) cc_final: 0.7046 (ttp-170) REVERT: L 3 GLN cc_start: 0.8381 (tt0) cc_final: 0.7707 (pt0) REVERT: M 78 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6909 (tt) REVERT: M 95 ARG cc_start: 0.7897 (ttm170) cc_final: 0.7102 (ttp-170) outliers start: 98 outliers final: 57 residues processed: 410 average time/residue: 1.2393 time to fit residues: 590.9945 Evaluate side-chains 389 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 327 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 44 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 286 ASN A 341 ASN A 556 GLN B 202 HIS B 534 ASN B 556 GLN C 556 GLN C 583 ASN G 51 ASN J 77 GLN O 51 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.159109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125705 restraints weight = 27290.242| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.71 r_work: 0.3190 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24369 Z= 0.185 Angle : 0.573 8.830 33150 Z= 0.299 Chirality : 0.045 0.176 3696 Planarity : 0.004 0.039 4188 Dihedral : 6.580 49.825 3942 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.68 % Allowed : 11.16 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2904 helix: 2.85 (0.29), residues: 279 sheet: -0.04 (0.15), residues: 1014 loop : -0.47 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 47 HIS 0.006 0.001 HIS D 35 PHE 0.014 0.002 PHE B 265 TYR 0.019 0.002 TYR B 206 ARG 0.009 0.001 ARG C 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 21) link_NAG-ASN : angle 1.56337 ( 63) link_BETA1-4 : bond 0.00263 ( 12) link_BETA1-4 : angle 2.22361 ( 36) hydrogen bonds : bond 0.03808 ( 924) hydrogen bonds : angle 5.40636 ( 2658) SS BOND : bond 0.00221 ( 33) SS BOND : angle 0.69255 ( 66) covalent geometry : bond 0.00438 (24303) covalent geometry : angle 0.56508 (32985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 335 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.6996 (ttp) cc_final: 0.6653 (ttt) REVERT: A 211 MET cc_start: 0.7401 (mtp) cc_final: 0.7045 (mtp) REVERT: A 248 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7486 (mm) REVERT: A 311 ARG cc_start: 0.6985 (ttm110) cc_final: 0.6759 (ttm110) REVERT: A 326 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 402 GLN cc_start: 0.7606 (tt0) cc_final: 0.6955 (tt0) REVERT: A 444 ARG cc_start: 0.7719 (ttp80) cc_final: 0.6967 (ttp-110) REVERT: B 295 ASP cc_start: 0.7775 (t0) cc_final: 0.7485 (t0) REVERT: B 354 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7060 (mmp80) REVERT: B 402 GLN cc_start: 0.7606 (tt0) cc_final: 0.7009 (tt0) REVERT: B 435 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7980 (tttp) REVERT: B 444 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6735 (ttm-80) REVERT: B 600 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8598 (tt0) REVERT: B 612 GLN cc_start: 0.7883 (mt0) cc_final: 0.7058 (mm110) REVERT: C 248 LEU cc_start: 0.8019 (tp) cc_final: 0.7437 (mm) REVERT: C 342 VAL cc_start: 0.8037 (p) cc_final: 0.7802 (m) REVERT: C 344 CYS cc_start: 0.7147 (t) cc_final: 0.6888 (t) REVERT: C 354 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7031 (mmp80) REVERT: C 402 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7004 (tm-30) REVERT: C 444 ARG cc_start: 0.7716 (ttp80) cc_final: 0.6979 (ttp-110) REVERT: C 574 CYS cc_start: 0.7293 (m) cc_final: 0.6955 (m) REVERT: C 612 GLN cc_start: 0.8110 (mt0) cc_final: 0.7262 (mm110) REVERT: E 24 SER cc_start: 0.8022 (OUTLIER) cc_final: 0.7724 (t) REVERT: E 79 ARG cc_start: 0.5391 (mtt180) cc_final: 0.5143 (mtt90) REVERT: E 95 ARG cc_start: 0.7538 (ttm170) cc_final: 0.6127 (ttp-170) REVERT: F 77 GLN cc_start: 0.7771 (mt0) cc_final: 0.7517 (mt0) REVERT: H 3 GLN cc_start: 0.8053 (tt0) cc_final: 0.7054 (pt0) REVERT: I 79 ARG cc_start: 0.5537 (mtt180) cc_final: 0.5302 (mmt90) REVERT: I 95 ARG cc_start: 0.7593 (ttm170) cc_final: 0.6183 (ttp-170) REVERT: J 77 GLN cc_start: 0.7674 (mt0) cc_final: 0.7441 (mt0) REVERT: J 86 ASP cc_start: 0.7100 (m-30) cc_final: 0.6688 (m-30) REVERT: K 83 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7378 (tt0) REVERT: M 47 LEU cc_start: 0.7703 (mt) cc_final: 0.7487 (tp) REVERT: M 79 ARG cc_start: 0.5484 (mtt180) cc_final: 0.5161 (mmt90) REVERT: M 95 ARG cc_start: 0.7531 (ttm170) cc_final: 0.6258 (ttp-170) outliers start: 95 outliers final: 68 residues processed: 393 average time/residue: 1.2382 time to fit residues: 565.1680 Evaluate side-chains 393 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 319 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 179 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 239 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 178 HIS A 286 ASN A 556 GLN B 118 ASN B 556 GLN C 118 ASN C 202 HIS C 534 ASN G 51 ASN I 53 GLN O 51 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.160090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126565 restraints weight = 27404.972| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.67 r_work: 0.3209 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24369 Z= 0.140 Angle : 0.524 5.778 33150 Z= 0.276 Chirality : 0.044 0.177 3696 Planarity : 0.004 0.038 4188 Dihedral : 5.692 41.648 3942 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.49 % Allowed : 12.40 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 2904 helix: 3.03 (0.29), residues: 279 sheet: 0.00 (0.15), residues: 1014 loop : -0.45 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 36 HIS 0.003 0.001 HIS L 35 PHE 0.013 0.001 PHE N 78 TYR 0.019 0.001 TYR A 206 ARG 0.009 0.000 ARG A 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 21) link_NAG-ASN : angle 1.29964 ( 63) link_BETA1-4 : bond 0.00310 ( 12) link_BETA1-4 : angle 2.00664 ( 36) hydrogen bonds : bond 0.03377 ( 924) hydrogen bonds : angle 5.22503 ( 2658) SS BOND : bond 0.00144 ( 33) SS BOND : angle 0.73023 ( 66) covalent geometry : bond 0.00325 (24303) covalent geometry : angle 0.51683 (32985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 336 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.6866 (ttp) cc_final: 0.6579 (ttt) REVERT: A 211 MET cc_start: 0.7461 (mtp) cc_final: 0.7187 (mtp) REVERT: A 248 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7461 (mm) REVERT: A 326 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 402 GLN cc_start: 0.7600 (tt0) cc_final: 0.6969 (tt0) REVERT: A 444 ARG cc_start: 0.7731 (ttp80) cc_final: 0.6997 (ttp-110) REVERT: B 178 HIS cc_start: 0.7096 (m-70) cc_final: 0.6865 (m170) REVERT: B 248 LEU cc_start: 0.8083 (tp) cc_final: 0.7626 (mm) REVERT: B 295 ASP cc_start: 0.7815 (t0) cc_final: 0.7490 (t0) REVERT: B 354 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7023 (mmp80) REVERT: B 402 GLN cc_start: 0.7562 (tt0) cc_final: 0.6982 (tt0) REVERT: B 444 ARG cc_start: 0.7425 (ttp80) cc_final: 0.6718 (ttm-80) REVERT: B 612 GLN cc_start: 0.7893 (mt0) cc_final: 0.7083 (mm110) REVERT: C 248 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7434 (mm) REVERT: C 251 MET cc_start: 0.8044 (ttm) cc_final: 0.7759 (ttp) REVERT: C 342 VAL cc_start: 0.8002 (p) cc_final: 0.7784 (m) REVERT: C 344 CYS cc_start: 0.7047 (t) cc_final: 0.6780 (t) REVERT: C 354 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7104 (mmp80) REVERT: C 402 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7113 (tt0) REVERT: C 444 ARG cc_start: 0.7725 (ttp80) cc_final: 0.6992 (ttp-110) REVERT: C 574 CYS cc_start: 0.7298 (m) cc_final: 0.6920 (m) REVERT: C 612 GLN cc_start: 0.8070 (mt0) cc_final: 0.7225 (mm110) REVERT: D 3 GLN cc_start: 0.8157 (tt0) cc_final: 0.7078 (pt0) REVERT: E 24 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7703 (t) REVERT: E 30 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6902 (mtpp) REVERT: E 69 THR cc_start: 0.8482 (p) cc_final: 0.7860 (m) REVERT: E 79 ARG cc_start: 0.5450 (mtt180) cc_final: 0.5225 (mtt90) REVERT: F 77 GLN cc_start: 0.7891 (mt0) cc_final: 0.7536 (mt0) REVERT: H 3 GLN cc_start: 0.8085 (tt0) cc_final: 0.7069 (pt0) REVERT: I 79 ARG cc_start: 0.5566 (mtt180) cc_final: 0.5321 (mmt90) REVERT: J 59 TYR cc_start: 0.8862 (m-80) cc_final: 0.8640 (m-80) REVERT: J 77 GLN cc_start: 0.7694 (mt0) cc_final: 0.7481 (mt0) REVERT: J 86 ASP cc_start: 0.7236 (m-30) cc_final: 0.6845 (m-30) REVERT: K 83 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7397 (tt0) REVERT: M 30 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7067 (mtpp) REVERT: M 79 ARG cc_start: 0.5559 (mtt180) cc_final: 0.5253 (mmt90) REVERT: M 95 ARG cc_start: 0.7477 (ttm170) cc_final: 0.6249 (ttp-170) outliers start: 90 outliers final: 65 residues processed: 391 average time/residue: 1.1850 time to fit residues: 540.4921 Evaluate side-chains 392 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 320 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 129 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 154 optimal weight: 0.1980 chunk 190 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 178 HIS A 286 ASN A 534 ASN A 556 GLN B 118 ASN B 556 GLN C 118 ASN G 51 ASN L 53 ASN O 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.158252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124767 restraints weight = 27387.792| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.82 r_work: 0.3169 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24369 Z= 0.195 Angle : 0.564 5.933 33150 Z= 0.296 Chirality : 0.045 0.183 3696 Planarity : 0.004 0.041 4188 Dihedral : 5.654 47.237 3942 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.72 % Allowed : 12.91 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2904 helix: 2.88 (0.29), residues: 279 sheet: -0.05 (0.15), residues: 1023 loop : -0.49 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 47 HIS 0.004 0.001 HIS B 319 PHE 0.018 0.002 PHE B 265 TYR 0.021 0.002 TYR O 49 ARG 0.008 0.000 ARG A 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 21) link_NAG-ASN : angle 1.53705 ( 63) link_BETA1-4 : bond 0.00310 ( 12) link_BETA1-4 : angle 2.15021 ( 36) hydrogen bonds : bond 0.03777 ( 924) hydrogen bonds : angle 5.32605 ( 2658) SS BOND : bond 0.00221 ( 33) SS BOND : angle 0.85539 ( 66) covalent geometry : bond 0.00463 (24303) covalent geometry : angle 0.55585 (32985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 318 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.6918 (ttp) cc_final: 0.6632 (ttt) REVERT: A 211 MET cc_start: 0.7504 (mtp) cc_final: 0.7237 (mtp) REVERT: A 248 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7503 (mm) REVERT: A 326 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7834 (mt-10) REVERT: A 354 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.6764 (mmp80) REVERT: A 402 GLN cc_start: 0.7675 (tt0) cc_final: 0.7042 (tt0) REVERT: A 444 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7006 (ttp-110) REVERT: B 178 HIS cc_start: 0.7215 (m-70) cc_final: 0.6948 (m170) REVERT: B 248 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7653 (mm) REVERT: B 295 ASP cc_start: 0.7872 (t0) cc_final: 0.7548 (t0) REVERT: B 327 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7908 (mmm160) REVERT: B 354 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7071 (mmp80) REVERT: B 402 GLN cc_start: 0.7628 (tt0) cc_final: 0.7031 (tt0) REVERT: B 444 ARG cc_start: 0.7535 (ttp80) cc_final: 0.6812 (ttm-80) REVERT: B 600 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: B 612 GLN cc_start: 0.7906 (mt0) cc_final: 0.7093 (mm110) REVERT: C 248 LEU cc_start: 0.8042 (tp) cc_final: 0.7493 (mm) REVERT: C 251 MET cc_start: 0.8002 (ttm) cc_final: 0.7646 (ttp) REVERT: C 344 CYS cc_start: 0.7095 (t) cc_final: 0.6822 (t) REVERT: C 354 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6976 (mmp80) REVERT: C 402 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7162 (tt0) REVERT: C 444 ARG cc_start: 0.7707 (ttp80) cc_final: 0.6968 (ttp-110) REVERT: C 574 CYS cc_start: 0.7381 (m) cc_final: 0.7048 (m) REVERT: C 612 GLN cc_start: 0.8094 (mt0) cc_final: 0.7262 (mm110) REVERT: E 24 SER cc_start: 0.8027 (OUTLIER) cc_final: 0.7761 (t) REVERT: E 79 ARG cc_start: 0.5546 (mtt180) cc_final: 0.5258 (mtt90) REVERT: F 77 GLN cc_start: 0.7865 (mt0) cc_final: 0.7579 (mt0) REVERT: I 79 ARG cc_start: 0.5707 (mtt180) cc_final: 0.5413 (mmt90) REVERT: J 59 TYR cc_start: 0.8890 (m-80) cc_final: 0.8642 (m-80) REVERT: J 77 GLN cc_start: 0.7709 (mt0) cc_final: 0.7412 (mt0) REVERT: J 86 ASP cc_start: 0.7343 (m-30) cc_final: 0.7009 (m-30) REVERT: K 83 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7444 (tt0) REVERT: M 79 ARG cc_start: 0.5742 (mtt180) cc_final: 0.5395 (mmt90) REVERT: M 95 ARG cc_start: 0.7602 (ttm170) cc_final: 0.6320 (ttp-170) outliers start: 96 outliers final: 75 residues processed: 384 average time/residue: 1.2230 time to fit residues: 547.6289 Evaluate side-chains 387 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 305 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 45 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 236 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 286 ASN A 556 GLN B 118 ASN B 286 ASN B 556 GLN C 118 ASN E 53 GLN G 51 ASN I 53 GLN M 53 GLN O 51 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.160613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126695 restraints weight = 27097.613| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.70 r_work: 0.3214 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24369 Z= 0.113 Angle : 0.498 6.558 33150 Z= 0.263 Chirality : 0.043 0.190 3696 Planarity : 0.004 0.041 4188 Dihedral : 5.227 46.646 3942 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.53 % Allowed : 13.49 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2904 helix: 3.12 (0.29), residues: 279 sheet: 0.10 (0.16), residues: 960 loop : -0.51 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.002 0.001 HIS L 35 PHE 0.016 0.001 PHE B 265 TYR 0.019 0.001 TYR A 206 ARG 0.011 0.000 ARG C 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 21) link_NAG-ASN : angle 1.18392 ( 63) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 1.72243 ( 36) hydrogen bonds : bond 0.03165 ( 924) hydrogen bonds : angle 5.16330 ( 2658) SS BOND : bond 0.00151 ( 33) SS BOND : angle 0.63698 ( 66) covalent geometry : bond 0.00258 (24303) covalent geometry : angle 0.49215 (32985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 329 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.6870 (ttp) cc_final: 0.6628 (ttt) REVERT: A 248 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7483 (mm) REVERT: A 311 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6914 (ttm110) REVERT: A 326 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7818 (mt-10) REVERT: A 354 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6639 (mmp80) REVERT: A 402 GLN cc_start: 0.7634 (tt0) cc_final: 0.7043 (tt0) REVERT: A 444 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7046 (ttp-110) REVERT: B 141 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8062 (mtm180) REVERT: B 178 HIS cc_start: 0.7138 (m-70) cc_final: 0.6890 (m170) REVERT: B 248 LEU cc_start: 0.8094 (tp) cc_final: 0.7667 (mm) REVERT: B 295 ASP cc_start: 0.7849 (t0) cc_final: 0.7536 (t0) REVERT: B 354 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7005 (mmp80) REVERT: B 356 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8308 (pt) REVERT: B 387 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.7822 (p) REVERT: B 402 GLN cc_start: 0.7622 (tt0) cc_final: 0.7041 (tt0) REVERT: B 435 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8014 (tttp) REVERT: B 444 ARG cc_start: 0.7500 (ttp80) cc_final: 0.6805 (ttm-80) REVERT: B 612 GLN cc_start: 0.7908 (mt0) cc_final: 0.7109 (mm110) REVERT: C 117 ILE cc_start: 0.5979 (OUTLIER) cc_final: 0.5767 (mt) REVERT: C 248 LEU cc_start: 0.8024 (tp) cc_final: 0.7454 (mm) REVERT: C 251 MET cc_start: 0.7978 (ttm) cc_final: 0.7684 (ttp) REVERT: C 344 CYS cc_start: 0.7024 (t) cc_final: 0.6748 (t) REVERT: C 354 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7027 (mmp80) REVERT: C 402 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7115 (tt0) REVERT: C 444 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7008 (ttp-110) REVERT: C 501 GLN cc_start: 0.8294 (mt0) cc_final: 0.8035 (mt0) REVERT: C 574 CYS cc_start: 0.7252 (m) cc_final: 0.6811 (m) REVERT: C 612 GLN cc_start: 0.8085 (mt0) cc_final: 0.7266 (mm110) REVERT: E 30 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6851 (mtpp) REVERT: E 69 THR cc_start: 0.8506 (p) cc_final: 0.7941 (m) REVERT: E 79 ARG cc_start: 0.5531 (mtt180) cc_final: 0.5255 (mtt90) REVERT: F 77 GLN cc_start: 0.7895 (mt0) cc_final: 0.7612 (mt0) REVERT: I 79 ARG cc_start: 0.5639 (mtt180) cc_final: 0.5384 (mmt90) REVERT: J 77 GLN cc_start: 0.7727 (mt0) cc_final: 0.7401 (mt0) REVERT: J 86 ASP cc_start: 0.7416 (m-30) cc_final: 0.7087 (m-30) REVERT: L 72 ASP cc_start: 0.7098 (t0) cc_final: 0.6514 (t0) REVERT: M 30 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7062 (mtpp) REVERT: M 79 ARG cc_start: 0.5605 (mtt180) cc_final: 0.5351 (mmt90) REVERT: M 95 ARG cc_start: 0.7510 (ttm170) cc_final: 0.6178 (ttp-170) outliers start: 91 outliers final: 58 residues processed: 387 average time/residue: 1.1728 time to fit residues: 529.3391 Evaluate side-chains 385 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 63 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 105 optimal weight: 0.0370 chunk 198 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 286 ASN A 556 GLN B 556 GLN C 286 ASN D 53 ASN G 51 ASN H 53 ASN I 53 GLN O 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.165025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134083 restraints weight = 26971.633| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.53 r_work: 0.3264 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24369 Z= 0.120 Angle : 0.497 6.205 33150 Z= 0.262 Chirality : 0.043 0.173 3696 Planarity : 0.004 0.043 4188 Dihedral : 5.075 45.963 3942 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.57 % Allowed : 13.84 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 2904 helix: 3.10 (0.29), residues: 282 sheet: 0.11 (0.15), residues: 984 loop : -0.41 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.002 0.001 HIS D 35 PHE 0.020 0.001 PHE C 265 TYR 0.017 0.001 TYR O 49 ARG 0.012 0.000 ARG C 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 21) link_NAG-ASN : angle 1.15993 ( 63) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.67637 ( 36) hydrogen bonds : bond 0.03147 ( 924) hydrogen bonds : angle 5.09294 ( 2658) SS BOND : bond 0.00160 ( 33) SS BOND : angle 0.67627 ( 66) covalent geometry : bond 0.00278 (24303) covalent geometry : angle 0.49174 (32985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 327 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7144 (ttp) cc_final: 0.6920 (ttt) REVERT: A 211 MET cc_start: 0.7840 (mtp) cc_final: 0.7623 (mtp) REVERT: A 248 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7817 (mm) REVERT: A 326 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 354 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7323 (mmp80) REVERT: A 402 GLN cc_start: 0.8306 (tt0) cc_final: 0.7964 (tt0) REVERT: A 444 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7544 (ttm-80) REVERT: A 607 ARG cc_start: 0.8018 (mpt180) cc_final: 0.7812 (mpt180) REVERT: B 248 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7944 (mm) REVERT: B 295 ASP cc_start: 0.8009 (t0) cc_final: 0.7704 (t0) REVERT: B 354 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7373 (mmp80) REVERT: B 387 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8348 (p) REVERT: B 402 GLN cc_start: 0.8341 (tt0) cc_final: 0.7961 (tt0) REVERT: B 444 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7501 (ttm-80) REVERT: B 612 GLN cc_start: 0.8171 (mt0) cc_final: 0.7472 (mm110) REVERT: C 248 LEU cc_start: 0.8133 (tp) cc_final: 0.7791 (mm) REVERT: C 354 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7456 (mmp80) REVERT: C 356 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8647 (mt) REVERT: C 402 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8012 (tt0) REVERT: C 444 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7622 (ttp-110) REVERT: C 574 CYS cc_start: 0.7394 (m) cc_final: 0.7036 (m) REVERT: C 612 GLN cc_start: 0.8431 (mt0) cc_final: 0.7766 (mm110) REVERT: E 24 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7972 (t) REVERT: E 30 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7516 (mtpp) REVERT: E 69 THR cc_start: 0.8775 (p) cc_final: 0.8398 (m) REVERT: E 79 ARG cc_start: 0.6157 (mtt180) cc_final: 0.5938 (mtt90) REVERT: F 77 GLN cc_start: 0.8256 (mt0) cc_final: 0.8033 (mt0) REVERT: J 77 GLN cc_start: 0.8152 (mt0) cc_final: 0.7866 (mt0) REVERT: J 86 ASP cc_start: 0.7661 (m-30) cc_final: 0.7402 (m-30) REVERT: L 72 ASP cc_start: 0.7652 (t0) cc_final: 0.7339 (t0) REVERT: M 30 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7697 (mtpp) REVERT: M 95 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7029 (ttp-170) outliers start: 92 outliers final: 67 residues processed: 384 average time/residue: 1.1745 time to fit residues: 525.6975 Evaluate side-chains 393 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 316 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 45 optimal weight: 0.0470 chunk 129 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 556 GLN B 118 ASN B 178 HIS B 556 GLN G 51 ASN O 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123067 restraints weight = 27292.870| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.78 r_work: 0.3145 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.006 0.058 24369 Z= 0.269 Angle : 0.625 8.909 33150 Z= 0.325 Chirality : 0.047 0.182 3696 Planarity : 0.004 0.052 4188 Dihedral : 5.782 56.232 3942 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.95 % Allowed : 14.11 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 2904 helix: 2.71 (0.29), residues: 279 sheet: 0.01 (0.15), residues: 1047 loop : -0.55 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 47 HIS 0.005 0.002 HIS B 319 PHE 0.020 0.002 PHE B 265 TYR 0.023 0.002 TYR O 49 ARG 0.010 0.001 ARG A 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 21) link_NAG-ASN : angle 1.77477 ( 63) link_BETA1-4 : bond 0.00356 ( 12) link_BETA1-4 : angle 2.28008 ( 36) hydrogen bonds : bond 0.04157 ( 924) hydrogen bonds : angle 5.39015 ( 2658) SS BOND : bond 0.00297 ( 33) SS BOND : angle 1.36900 ( 66) covalent geometry : bond 0.00645 (24303) covalent geometry : angle 0.61390 (32985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 304 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7053 (ttp) cc_final: 0.6765 (ttt) REVERT: A 248 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7536 (mm) REVERT: A 326 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7986 (mt-10) REVERT: A 354 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7329 (mmp80) REVERT: A 402 GLN cc_start: 0.7760 (tt0) cc_final: 0.7147 (tt0) REVERT: A 444 ARG cc_start: 0.7712 (ttp80) cc_final: 0.7046 (ttp-110) REVERT: A 607 ARG cc_start: 0.7672 (mpt180) cc_final: 0.7463 (mpt180) REVERT: B 248 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7703 (mm) REVERT: B 295 ASP cc_start: 0.7914 (t0) cc_final: 0.7670 (t0) REVERT: B 354 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7139 (mmp80) REVERT: B 402 GLN cc_start: 0.7700 (tt0) cc_final: 0.7116 (tt0) REVERT: B 600 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: B 612 GLN cc_start: 0.7926 (mt0) cc_final: 0.7146 (mm110) REVERT: C 248 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7492 (mm) REVERT: C 344 CYS cc_start: 0.7139 (t) cc_final: 0.6913 (t) REVERT: C 354 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6802 (mmp80) REVERT: C 402 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7265 (tt0) REVERT: C 444 ARG cc_start: 0.7756 (ttp80) cc_final: 0.6975 (ttp-110) REVERT: C 574 CYS cc_start: 0.7381 (m) cc_final: 0.6981 (m) REVERT: C 612 GLN cc_start: 0.8120 (mt0) cc_final: 0.7292 (mm110) REVERT: E 24 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7838 (t) REVERT: E 79 ARG cc_start: 0.5884 (mtt180) cc_final: 0.5588 (mtt90) REVERT: F 77 GLN cc_start: 0.7956 (mt0) cc_final: 0.7650 (mt0) REVERT: H 72 ASP cc_start: 0.7049 (t0) cc_final: 0.6545 (t0) REVERT: I 79 ARG cc_start: 0.6026 (mtt90) cc_final: 0.5754 (mmt90) REVERT: J 77 GLN cc_start: 0.7822 (mt0) cc_final: 0.7482 (mt0) REVERT: J 86 ASP cc_start: 0.7488 (m-30) cc_final: 0.7116 (m-30) outliers start: 102 outliers final: 79 residues processed: 374 average time/residue: 1.2183 time to fit residues: 530.6277 Evaluate side-chains 382 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 295 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 258 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 chunk 285 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN B 286 ASN B 556 GLN E 53 GLN G 51 ASN I 53 GLN L 53 ASN M 53 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.160145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126678 restraints weight = 26974.958| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.78 r_work: 0.3189 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24369 Z= 0.138 Angle : 0.521 6.439 33150 Z= 0.275 Chirality : 0.043 0.233 3696 Planarity : 0.004 0.053 4188 Dihedral : 5.415 59.859 3942 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.41 % Allowed : 14.92 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 2904 helix: 2.91 (0.29), residues: 282 sheet: 0.01 (0.15), residues: 996 loop : -0.42 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.003 0.001 HIS L 35 PHE 0.020 0.001 PHE B 265 TYR 0.018 0.001 TYR B 631 ARG 0.013 0.001 ARG C 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 21) link_NAG-ASN : angle 1.26604 ( 63) link_BETA1-4 : bond 0.00269 ( 12) link_BETA1-4 : angle 1.72998 ( 36) hydrogen bonds : bond 0.03306 ( 924) hydrogen bonds : angle 5.21096 ( 2658) SS BOND : bond 0.00168 ( 33) SS BOND : angle 0.73512 ( 66) covalent geometry : bond 0.00319 (24303) covalent geometry : angle 0.51482 (32985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 310 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7484 (mm) REVERT: A 311 ARG cc_start: 0.7380 (ttm110) cc_final: 0.7132 (ttm110) REVERT: A 326 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 354 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7264 (mmp80) REVERT: A 402 GLN cc_start: 0.7735 (tt0) cc_final: 0.7141 (tt0) REVERT: A 444 ARG cc_start: 0.7737 (ttp80) cc_final: 0.6879 (ttm-80) REVERT: A 607 ARG cc_start: 0.7593 (mpt180) cc_final: 0.7374 (mpt180) REVERT: B 248 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7660 (mm) REVERT: B 354 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7006 (mmp80) REVERT: B 387 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.7800 (p) REVERT: B 402 GLN cc_start: 0.7655 (tt0) cc_final: 0.7079 (tt0) REVERT: B 444 ARG cc_start: 0.7555 (ttp80) cc_final: 0.6823 (ttm-80) REVERT: B 612 GLN cc_start: 0.7915 (mt0) cc_final: 0.7145 (mm110) REVERT: C 248 LEU cc_start: 0.8032 (tp) cc_final: 0.7472 (mm) REVERT: C 354 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7011 (mmp80) REVERT: C 402 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7184 (tt0) REVERT: C 444 ARG cc_start: 0.7701 (ttp80) cc_final: 0.6917 (ttp-110) REVERT: C 501 GLN cc_start: 0.8338 (mt0) cc_final: 0.8085 (mt0) REVERT: C 522 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8572 (mttm) REVERT: C 574 CYS cc_start: 0.7321 (m) cc_final: 0.6926 (m) REVERT: C 612 GLN cc_start: 0.8068 (mt0) cc_final: 0.7264 (mm110) REVERT: E 24 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7847 (t) REVERT: E 30 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6982 (mtpp) REVERT: E 79 ARG cc_start: 0.5727 (mtt180) cc_final: 0.5402 (mtt90) REVERT: F 77 GLN cc_start: 0.7931 (mt0) cc_final: 0.7638 (mt0) REVERT: I 79 ARG cc_start: 0.5993 (mtt90) cc_final: 0.5749 (mmt90) REVERT: J 77 GLN cc_start: 0.7789 (mt0) cc_final: 0.7453 (mt0) REVERT: J 86 ASP cc_start: 0.7476 (m-30) cc_final: 0.7162 (m-30) REVERT: L 72 ASP cc_start: 0.7172 (t0) cc_final: 0.6651 (t0) REVERT: M 30 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7130 (mtpp) REVERT: M 95 ARG cc_start: 0.7605 (ttm170) cc_final: 0.6308 (ttp-170) outliers start: 88 outliers final: 66 residues processed: 368 average time/residue: 1.1800 time to fit residues: 505.5960 Evaluate side-chains 377 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 301 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 522 LYS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 56 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 119 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 131 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 111 optimal weight: 0.3980 chunk 157 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 510 GLN B 286 ASN E 53 GLN G 27BASN G 51 ASN I 53 GLN M 53 GLN O 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128055 restraints weight = 27054.239| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.70 r_work: 0.3218 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24369 Z= 0.116 Angle : 0.502 6.842 33150 Z= 0.265 Chirality : 0.043 0.175 3696 Planarity : 0.004 0.059 4188 Dihedral : 5.191 57.445 3942 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.06 % Allowed : 15.43 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 2904 helix: 3.06 (0.29), residues: 282 sheet: 0.17 (0.16), residues: 972 loop : -0.46 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.002 0.001 HIS B 178 PHE 0.020 0.001 PHE B 265 TYR 0.017 0.001 TYR O 49 ARG 0.015 0.000 ARG A 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 21) link_NAG-ASN : angle 1.15322 ( 63) link_BETA1-4 : bond 0.00319 ( 12) link_BETA1-4 : angle 1.65156 ( 36) hydrogen bonds : bond 0.03105 ( 924) hydrogen bonds : angle 5.09731 ( 2658) SS BOND : bond 0.00130 ( 33) SS BOND : angle 0.70637 ( 66) covalent geometry : bond 0.00267 (24303) covalent geometry : angle 0.49710 (32985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 320 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.7236 (mtp) cc_final: 0.6513 (mtm) REVERT: A 248 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7410 (mm) REVERT: A 311 ARG cc_start: 0.7394 (ttm110) cc_final: 0.7138 (ttm110) REVERT: A 326 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 354 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6880 (mmp80) REVERT: A 402 GLN cc_start: 0.7575 (tt0) cc_final: 0.6972 (tt0) REVERT: A 444 ARG cc_start: 0.7652 (ttp80) cc_final: 0.6812 (ttm-80) REVERT: B 248 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7616 (mm) REVERT: B 341 ASN cc_start: 0.8240 (t0) cc_final: 0.7907 (t160) REVERT: B 354 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6845 (mmp80) REVERT: B 387 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7745 (p) REVERT: B 402 GLN cc_start: 0.7553 (tt0) cc_final: 0.6966 (tt0) REVERT: B 444 ARG cc_start: 0.7490 (ttp80) cc_final: 0.6771 (ttm-80) REVERT: B 612 GLN cc_start: 0.7869 (mt0) cc_final: 0.7077 (mm110) REVERT: C 216 ASP cc_start: 0.7167 (t0) cc_final: 0.6951 (t0) REVERT: C 248 LEU cc_start: 0.7980 (tp) cc_final: 0.7364 (mm) REVERT: C 354 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6973 (mmp80) REVERT: C 356 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (pt) REVERT: C 402 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7057 (tt0) REVERT: C 444 ARG cc_start: 0.7667 (ttp80) cc_final: 0.6883 (ttp-110) REVERT: C 501 GLN cc_start: 0.8217 (mt0) cc_final: 0.7959 (mt0) REVERT: C 574 CYS cc_start: 0.7240 (m) cc_final: 0.6810 (m) REVERT: C 612 GLN cc_start: 0.8060 (mt0) cc_final: 0.7261 (mm110) REVERT: E 30 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6857 (mtpp) REVERT: E 69 THR cc_start: 0.8479 (p) cc_final: 0.7855 (m) REVERT: E 79 ARG cc_start: 0.5637 (mtt180) cc_final: 0.5327 (mtt90) REVERT: F 77 GLN cc_start: 0.7869 (mt0) cc_final: 0.7575 (mt0) REVERT: I 79 ARG cc_start: 0.5926 (mtt90) cc_final: 0.5704 (mmt90) REVERT: J 77 GLN cc_start: 0.7726 (mt0) cc_final: 0.7381 (mt0) REVERT: J 86 ASP cc_start: 0.7399 (m-30) cc_final: 0.7067 (m-30) REVERT: L 72 ASP cc_start: 0.7087 (t0) cc_final: 0.6562 (t0) REVERT: O 83 GLU cc_start: 0.7619 (tt0) cc_final: 0.6978 (mt-10) outliers start: 79 outliers final: 63 residues processed: 372 average time/residue: 1.2140 time to fit residues: 533.1698 Evaluate side-chains 382 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 387 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 ASN Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 237 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 286 ASN B 118 ASN C 118 ASN C 286 ASN G 51 ASN I 53 GLN O 51 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.157030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123821 restraints weight = 27144.867| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.77 r_work: 0.3159 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 24369 Z= 0.244 Angle : 0.616 8.519 33150 Z= 0.321 Chirality : 0.046 0.210 3696 Planarity : 0.004 0.060 4188 Dihedral : 5.620 48.625 3942 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.60 % Allowed : 14.88 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2904 helix: 2.73 (0.29), residues: 279 sheet: -0.05 (0.15), residues: 1029 loop : -0.47 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 47 HIS 0.004 0.001 HIS B 319 PHE 0.019 0.002 PHE B 265 TYR 0.022 0.002 TYR O 49 ARG 0.011 0.001 ARG C 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 21) link_NAG-ASN : angle 1.71732 ( 63) link_BETA1-4 : bond 0.00339 ( 12) link_BETA1-4 : angle 2.22733 ( 36) hydrogen bonds : bond 0.04029 ( 924) hydrogen bonds : angle 5.34221 ( 2658) SS BOND : bond 0.00259 ( 33) SS BOND : angle 1.40276 ( 66) covalent geometry : bond 0.00584 (24303) covalent geometry : angle 0.60490 (32985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18853.98 seconds wall clock time: 326 minutes 27.64 seconds (19587.64 seconds total)