Starting phenix.real_space_refine on Fri Jun 13 20:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq6_25377/06_2025/7sq6_25377_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq6_25377/06_2025/7sq6_25377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sq6_25377/06_2025/7sq6_25377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq6_25377/06_2025/7sq6_25377.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq6_25377/06_2025/7sq6_25377_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq6_25377/06_2025/7sq6_25377_neut_trim.cif" } resolution = 2.32 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= 0.006 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 2 4.78 5 C 10064 2.51 5 N 2532 2.21 5 O 2648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15342 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "B" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "C" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "D" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' NA': 1, 'AQV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' NA': 1, 'AQV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.39, per 1000 atoms: 0.61 Number of scatterers: 15342 At special positions: 0 Unit cell: (108.73, 108.73, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 2 11.00 O 2648 8.00 N 2532 7.00 C 10064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 4.57 Conformation dependent library (CDL) restraints added in 2.1 seconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 67.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.707A pdb=" N LYS A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.586A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 297 through 338 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.785A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 412 through 448 Proline residue: A 423 - end of helix removed outlier: 3.627A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.119A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.823A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.707A pdb=" N LYS B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.585A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 143 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 297 through 338 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.785A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 412 through 448 Proline residue: B 423 - end of helix removed outlier: 3.627A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 4.118A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.823A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 508 through 525 Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.706A pdb=" N LYS C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.585A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 143 Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 297 through 338 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.785A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 412 through 448 Proline residue: C 423 - end of helix removed outlier: 3.627A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 4.118A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.823A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.707A pdb=" N LYS D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.586A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 143 Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 297 through 338 Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.785A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 412 through 448 Proline residue: D 423 - end of helix removed outlier: 3.626A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.118A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.823A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 508 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.715A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLY A 173 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP A 185 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.716A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY B 173 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP B 185 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.716A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY C 173 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASP C 185 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.715A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) 1144 hydrogen bonds defined for protein. 3216 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: 5.26 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2280 1.31 - 1.44: 4596 1.44 - 1.57: 8700 1.57 - 1.70: 4 1.70 - 1.83: 132 Bond restraints: 15712 Sorted by residual: bond pdb=" C15 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C10 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.367 1.482 -0.115 2.00e-02 2.50e+03 3.29e+01 ... (remaining 15707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 20612 2.14 - 4.28: 630 4.28 - 6.42: 66 6.42 - 8.56: 20 8.56 - 10.70: 4 Bond angle restraints: 21332 Sorted by residual: angle pdb=" CA LEU B 348 " pdb=" C LEU B 348 " pdb=" O LEU B 348 " ideal model delta sigma weight residual 121.00 116.82 4.18 1.05e+00 9.07e-01 1.59e+01 angle pdb=" CA LEU A 348 " pdb=" C LEU A 348 " pdb=" O LEU A 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" CA LEU D 348 " pdb=" C LEU D 348 " pdb=" O LEU D 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" CA LEU C 348 " pdb=" C LEU C 348 " pdb=" O LEU C 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" N ARG A 347 " pdb=" CA ARG A 347 " pdb=" C ARG A 347 " ideal model delta sigma weight residual 111.11 106.45 4.66 1.20e+00 6.94e-01 1.51e+01 ... (remaining 21327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8160 17.97 - 35.94: 908 35.94 - 53.92: 176 53.92 - 71.89: 48 71.89 - 89.86: 32 Dihedral angle restraints: 9324 sinusoidal: 3840 harmonic: 5484 Sorted by residual: dihedral pdb=" C VAL C 332 " pdb=" N VAL C 332 " pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C VAL B 332 " pdb=" N VAL B 332 " pdb=" CA VAL B 332 " pdb=" CB VAL B 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C VAL A 332 " pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" CB VAL A 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2059 0.067 - 0.133: 305 0.133 - 0.200: 49 0.200 - 0.267: 37 0.267 - 0.334: 10 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA ARG B 338 " pdb=" N ARG B 338 " pdb=" C ARG B 338 " pdb=" CB ARG B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG C 338 " pdb=" N ARG C 338 " pdb=" C ARG C 338 " pdb=" CB ARG C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ARG D 338 " pdb=" N ARG D 338 " pdb=" C ARG D 338 " pdb=" CB ARG D 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2457 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 57 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ARG D 57 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG D 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA D 58 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 57 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ARG A 57 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG A 57 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 58 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 57 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C ARG C 57 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG C 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 58 " -0.017 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6274 2.91 - 3.40: 15447 3.40 - 3.90: 26807 3.90 - 4.40: 30913 4.40 - 4.90: 49847 Nonbonded interactions: 129288 Sorted by model distance: nonbonded pdb=" OH TYR A 109 " pdb=" OD1 ASP A 114 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR B 109 " pdb=" OD1 ASP B 114 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR D 109 " pdb=" OD1 ASP D 114 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR C 109 " pdb=" OD1 ASP C 114 " model vdw 2.408 3.040 nonbonded pdb=" O TYR A 47 " pdb=" NZ LYS A 55 " model vdw 2.436 3.120 ... (remaining 129283 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: 0.10 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.560 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.007 0.120 15720 Z= 0.414 Angle : 0.817 10.700 21356 Z= 0.509 Chirality : 0.060 0.334 2460 Planarity : 0.005 0.044 2600 Dihedral : 16.321 89.861 5788 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 17.94 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.19), residues: 1844 helix: 1.57 (0.15), residues: 1116 sheet: 0.95 (0.31), residues: 252 loop : -0.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 491 HIS 0.007 0.002 HIS C 234 PHE 0.021 0.002 PHE A 474 TYR 0.014 0.002 TYR D 497 ARG 0.006 0.001 ARG D 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 4) link_NAG-ASN : angle 3.07730 ( 12) link_BETA1-4 : bond 0.00564 ( 4) link_BETA1-4 : angle 2.20311 ( 12) hydrogen bonds : bond 0.12539 ( 1052) hydrogen bonds : angle 6.59061 ( 3216) covalent geometry : bond 0.00686 (15712) covalent geometry : angle 0.81228 (21332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.808 Fit side-chains REVERT: C 303 VAL cc_start: 0.7753 (t) cc_final: 0.7550 (p) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 1.0887 time to fit residues: 235.8404 Evaluate side-chains 153 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 469 ASN B 234 HIS B 469 ASN C 234 HIS C 469 ASN D 234 HIS D 469 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094591 restraints weight = 15544.729| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.78 r_work: 0.2788 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15720 Z= 0.191 Angle : 0.583 6.366 21356 Z= 0.310 Chirality : 0.042 0.140 2460 Planarity : 0.005 0.039 2600 Dihedral : 6.703 53.993 2316 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.53 % Allowed : 14.95 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.93 (0.20), residues: 1844 helix: 1.83 (0.15), residues: 1120 sheet: 1.15 (0.32), residues: 252 loop : 0.12 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 157 HIS 0.006 0.002 HIS D 234 PHE 0.019 0.002 PHE B 235 TYR 0.014 0.002 TYR A 497 ARG 0.004 0.001 ARG C 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 2.59947 ( 12) link_BETA1-4 : bond 0.00087 ( 4) link_BETA1-4 : angle 1.82001 ( 12) hydrogen bonds : bond 0.06214 ( 1052) hydrogen bonds : angle 5.25827 ( 3216) covalent geometry : bond 0.00421 (15712) covalent geometry : angle 0.57894 (21332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.4891 (ptm-80) REVERT: A 65 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7152 (mtmp) REVERT: A 358 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7964 (mp) REVERT: B 44 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.5189 (ptm160) REVERT: B 65 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7135 (mtmp) REVERT: B 276 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: B 358 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7970 (mp) REVERT: C 44 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.5188 (ptm160) REVERT: C 65 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7148 (mtmp) REVERT: C 276 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: C 303 VAL cc_start: 0.7615 (t) cc_final: 0.7400 (p) REVERT: C 358 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7988 (mp) REVERT: D 44 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.4862 (ptm-80) REVERT: D 65 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7168 (mtmp) REVERT: D 95 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: D 123 GLU cc_start: 0.8057 (mp0) cc_final: 0.7815 (mp0) REVERT: D 358 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7950 (mp) outliers start: 59 outliers final: 19 residues processed: 185 average time/residue: 1.4254 time to fit residues: 290.8680 Evaluate side-chains 178 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 21 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094622 restraints weight = 15625.753| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.49 r_work: 0.2894 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15720 Z= 0.119 Angle : 0.493 5.981 21356 Z= 0.256 Chirality : 0.039 0.130 2460 Planarity : 0.004 0.036 2600 Dihedral : 6.432 53.493 2316 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.57 % Allowed : 15.73 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.41 (0.20), residues: 1844 helix: 2.23 (0.15), residues: 1108 sheet: 1.23 (0.31), residues: 252 loop : 0.39 (0.32), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 157 HIS 0.003 0.001 HIS B 234 PHE 0.012 0.001 PHE C 235 TYR 0.013 0.001 TYR D 497 ARG 0.003 0.000 ARG B 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 4) link_NAG-ASN : angle 1.37490 ( 12) link_BETA1-4 : bond 0.00074 ( 4) link_BETA1-4 : angle 1.77452 ( 12) hydrogen bonds : bond 0.04863 ( 1052) hydrogen bonds : angle 4.78751 ( 3216) covalent geometry : bond 0.00227 (15712) covalent geometry : angle 0.49034 (21332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 2.376 Fit side-chains REVERT: A 44 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5575 (mtm-85) REVERT: A 65 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6899 (ttmt) REVERT: A 95 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: A 355 TYR cc_start: 0.8328 (m-10) cc_final: 0.8032 (m-10) REVERT: A 358 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 44 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5577 (mtm-85) REVERT: B 65 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6951 (ttmt) REVERT: B 95 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: B 355 TYR cc_start: 0.8311 (m-10) cc_final: 0.8016 (m-10) REVERT: B 358 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7880 (mp) REVERT: C 44 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5612 (mtm-85) REVERT: C 65 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6965 (ttmt) REVERT: C 95 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: C 355 TYR cc_start: 0.8308 (m-10) cc_final: 0.8011 (m-10) REVERT: C 358 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7879 (mp) REVERT: D 44 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.5624 (mtm-85) REVERT: D 65 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6850 (ttmt) REVERT: D 95 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: D 355 TYR cc_start: 0.8338 (m-10) cc_final: 0.7970 (m-10) REVERT: D 358 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7889 (mp) outliers start: 43 outliers final: 4 residues processed: 188 average time/residue: 1.3778 time to fit residues: 286.4431 Evaluate side-chains 169 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN B 247 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.090974 restraints weight = 15484.136| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.45 r_work: 0.2839 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15720 Z= 0.190 Angle : 0.579 6.085 21356 Z= 0.307 Chirality : 0.042 0.131 2460 Planarity : 0.005 0.058 2600 Dihedral : 6.587 54.271 2316 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 14.89 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.20), residues: 1844 helix: 2.04 (0.15), residues: 1124 sheet: 1.19 (0.31), residues: 252 loop : 0.31 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 491 HIS 0.007 0.002 HIS A 486 PHE 0.019 0.002 PHE B 474 TYR 0.016 0.002 TYR C 497 ARG 0.003 0.000 ARG D 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 2.56629 ( 12) link_BETA1-4 : bond 0.00207 ( 4) link_BETA1-4 : angle 1.87079 ( 12) hydrogen bonds : bond 0.05955 ( 1052) hydrogen bonds : angle 5.06843 ( 3216) covalent geometry : bond 0.00424 (15712) covalent geometry : angle 0.57481 (21332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 1.720 Fit side-chains REVERT: A 44 ARG cc_start: 0.5853 (ptm160) cc_final: 0.5519 (mtm-85) REVERT: A 65 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7186 (mtmp) REVERT: A 95 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: A 276 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: A 358 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (mp) REVERT: B 44 ARG cc_start: 0.5869 (ptm160) cc_final: 0.5542 (mtm-85) REVERT: B 65 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7184 (mtmp) REVERT: B 95 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: B 115 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: B 276 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: B 358 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7958 (mp) REVERT: C 44 ARG cc_start: 0.5907 (ptm160) cc_final: 0.5569 (mtm-85) REVERT: C 65 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7176 (mtmp) REVERT: C 95 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 276 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: C 358 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7967 (mp) REVERT: D 44 ARG cc_start: 0.5885 (ptm160) cc_final: 0.5536 (mtm-85) REVERT: D 65 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7151 (mtmp) REVERT: D 95 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: D 115 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: D 276 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: D 358 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7958 (mp) outliers start: 46 outliers final: 20 residues processed: 177 average time/residue: 1.2128 time to fit residues: 238.1380 Evaluate side-chains 176 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 24 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.091184 restraints weight = 15652.403| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.46 r_work: 0.2855 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15720 Z= 0.175 Angle : 0.551 6.068 21356 Z= 0.291 Chirality : 0.042 0.127 2460 Planarity : 0.005 0.039 2600 Dihedral : 6.620 53.810 2316 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 14.11 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.19), residues: 1844 helix: 2.08 (0.15), residues: 1124 sheet: 1.16 (0.31), residues: 252 loop : 0.31 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 491 HIS 0.006 0.002 HIS B 486 PHE 0.019 0.002 PHE B 474 TYR 0.014 0.002 TYR B 497 ARG 0.002 0.000 ARG D 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 4) link_NAG-ASN : angle 2.29790 ( 12) link_BETA1-4 : bond 0.00151 ( 4) link_BETA1-4 : angle 1.91951 ( 12) hydrogen bonds : bond 0.05685 ( 1052) hydrogen bonds : angle 5.00286 ( 3216) covalent geometry : bond 0.00388 (15712) covalent geometry : angle 0.54634 (21332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 135 time to evaluate : 1.691 Fit side-chains REVERT: A 44 ARG cc_start: 0.5848 (ptm160) cc_final: 0.5514 (mtm-85) REVERT: A 65 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6989 (ttmt) REVERT: A 95 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: A 276 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: A 358 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7958 (mp) REVERT: B 44 ARG cc_start: 0.5841 (ptm160) cc_final: 0.5546 (mtm-85) REVERT: B 65 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7023 (ttmt) REVERT: B 95 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: B 115 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: B 276 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: B 358 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (mp) REVERT: C 44 ARG cc_start: 0.5862 (ptm160) cc_final: 0.5524 (mtm-85) REVERT: C 65 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7020 (ttmt) REVERT: C 95 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 276 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: C 358 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7991 (mp) REVERT: D 44 ARG cc_start: 0.5863 (ptm160) cc_final: 0.5627 (mtm-85) REVERT: D 65 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6976 (ttmt) REVERT: D 95 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: D 115 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: D 276 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: D 358 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7956 (mp) outliers start: 58 outliers final: 20 residues processed: 178 average time/residue: 1.2662 time to fit residues: 249.3232 Evaluate side-chains 177 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 178 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094012 restraints weight = 15663.507| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.50 r_work: 0.2898 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15720 Z= 0.123 Angle : 0.503 6.021 21356 Z= 0.261 Chirality : 0.039 0.126 2460 Planarity : 0.004 0.035 2600 Dihedral : 6.437 53.345 2316 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.51 % Allowed : 15.13 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.54 (0.20), residues: 1844 helix: 2.33 (0.15), residues: 1112 sheet: 1.24 (0.31), residues: 252 loop : 0.47 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 491 HIS 0.003 0.001 HIS D 234 PHE 0.012 0.001 PHE C 474 TYR 0.012 0.001 TYR A 497 ARG 0.002 0.000 ARG C 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00019 ( 4) link_NAG-ASN : angle 1.62051 ( 12) link_BETA1-4 : bond 0.00047 ( 4) link_BETA1-4 : angle 1.91712 ( 12) hydrogen bonds : bond 0.04872 ( 1052) hydrogen bonds : angle 4.73652 ( 3216) covalent geometry : bond 0.00244 (15712) covalent geometry : angle 0.49942 (21332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.978 Fit side-chains REVERT: A 44 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5540 (mtm-85) REVERT: A 65 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6947 (ttmt) REVERT: A 95 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: A 276 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 358 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 44 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.5543 (mtm-85) REVERT: B 65 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6958 (ttmt) REVERT: B 95 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: B 276 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: B 358 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7895 (mp) REVERT: C 44 ARG cc_start: 0.5840 (ptm160) cc_final: 0.5519 (mtm-85) REVERT: C 65 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6961 (ttmt) REVERT: C 95 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: C 276 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: C 318 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7283 (tmm-80) REVERT: C 358 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7912 (mp) REVERT: D 44 ARG cc_start: 0.5898 (OUTLIER) cc_final: 0.5551 (mtm-85) REVERT: D 65 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6995 (ttmt) REVERT: D 95 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: D 276 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: D 358 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7887 (mp) outliers start: 42 outliers final: 13 residues processed: 188 average time/residue: 1.3823 time to fit residues: 288.7449 Evaluate side-chains 161 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 327 GLN B 247 ASN B 327 GLN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 327 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.091211 restraints weight = 15660.650| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.46 r_work: 0.2857 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15720 Z= 0.192 Angle : 0.572 6.145 21356 Z= 0.302 Chirality : 0.042 0.128 2460 Planarity : 0.004 0.037 2600 Dihedral : 6.588 54.251 2316 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.59 % Allowed : 14.11 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.37 (0.19), residues: 1844 helix: 2.17 (0.15), residues: 1124 sheet: 1.19 (0.31), residues: 252 loop : 0.39 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 491 HIS 0.007 0.002 HIS A 486 PHE 0.019 0.002 PHE C 474 TYR 0.015 0.002 TYR C 404 ARG 0.003 0.000 ARG C 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 2.41909 ( 12) link_BETA1-4 : bond 0.00212 ( 4) link_BETA1-4 : angle 1.97010 ( 12) hydrogen bonds : bond 0.05793 ( 1052) hydrogen bonds : angle 4.99288 ( 3216) covalent geometry : bond 0.00433 (15712) covalent geometry : angle 0.56760 (21332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 1.770 Fit side-chains REVERT: A 65 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7026 (ttmt) REVERT: A 95 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 276 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: A 358 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7967 (mp) REVERT: B 65 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7062 (ttmt) REVERT: B 95 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: B 115 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: B 276 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: B 358 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7988 (mp) REVERT: C 65 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7098 (ttmt) REVERT: C 95 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: C 276 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: C 358 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7993 (mp) REVERT: D 65 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7054 (ttmt) REVERT: D 95 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: D 276 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: D 358 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7983 (mp) outliers start: 60 outliers final: 16 residues processed: 179 average time/residue: 1.3247 time to fit residues: 261.9194 Evaluate side-chains 163 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 87 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 168 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.096063 restraints weight = 15520.603| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.75 r_work: 0.2829 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15720 Z= 0.144 Angle : 0.526 6.067 21356 Z= 0.275 Chirality : 0.040 0.125 2460 Planarity : 0.004 0.035 2600 Dihedral : 6.504 53.486 2316 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.29 % Allowed : 13.58 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.47 (0.19), residues: 1844 helix: 2.26 (0.15), residues: 1112 sheet: 1.24 (0.31), residues: 252 loop : 0.44 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 491 HIS 0.004 0.001 HIS A 486 PHE 0.015 0.002 PHE A 474 TYR 0.014 0.002 TYR B 497 ARG 0.002 0.000 ARG D 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00039 ( 4) link_NAG-ASN : angle 1.98148 ( 12) link_BETA1-4 : bond 0.00052 ( 4) link_BETA1-4 : angle 1.97208 ( 12) hydrogen bonds : bond 0.05222 ( 1052) hydrogen bonds : angle 4.84150 ( 3216) covalent geometry : bond 0.00306 (15712) covalent geometry : angle 0.52172 (21332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 1.716 Fit side-chains REVERT: A 44 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5381 (mtm-85) REVERT: A 65 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7004 (ttmt) REVERT: A 95 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: A 276 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: A 318 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7313 (tmm-80) REVERT: A 358 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 44 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5389 (mtm-85) REVERT: B 65 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7026 (ttmt) REVERT: B 95 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: B 276 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: B 318 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7326 (tmm-80) REVERT: B 358 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7949 (mp) REVERT: C 44 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5617 (mtm-85) REVERT: C 65 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7084 (ttmt) REVERT: C 95 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: C 276 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: C 358 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7976 (mp) REVERT: D 44 ARG cc_start: 0.5879 (OUTLIER) cc_final: 0.5368 (mtm-85) REVERT: D 65 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7088 (ttmt) REVERT: D 95 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: D 276 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: D 358 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7981 (mp) outliers start: 55 outliers final: 24 residues processed: 182 average time/residue: 1.1444 time to fit residues: 232.7344 Evaluate side-chains 177 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 104 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.094745 restraints weight = 15585.038| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.48 r_work: 0.2907 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15720 Z= 0.116 Angle : 0.494 6.128 21356 Z= 0.255 Chirality : 0.039 0.126 2460 Planarity : 0.004 0.034 2600 Dihedral : 6.343 53.712 2316 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.33 % Allowed : 14.95 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.69 (0.20), residues: 1844 helix: 2.45 (0.15), residues: 1112 sheet: 1.30 (0.31), residues: 252 loop : 0.52 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 354 HIS 0.003 0.001 HIS A 234 PHE 0.011 0.001 PHE A 235 TYR 0.012 0.001 TYR A 404 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 4) link_NAG-ASN : angle 1.44211 ( 12) link_BETA1-4 : bond 0.00061 ( 4) link_BETA1-4 : angle 1.92593 ( 12) hydrogen bonds : bond 0.04570 ( 1052) hydrogen bonds : angle 4.63459 ( 3216) covalent geometry : bond 0.00230 (15712) covalent geometry : angle 0.49131 (21332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.697 Fit side-chains REVERT: A 44 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5543 (mtm-85) REVERT: A 65 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6986 (ttmt) REVERT: A 95 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 276 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: A 358 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7848 (mp) REVERT: B 44 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5538 (mtm-85) REVERT: B 65 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7008 (ttmt) REVERT: B 95 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: B 276 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: B 358 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7874 (mp) REVERT: C 44 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.5520 (mtm-85) REVERT: C 65 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7009 (ttmt) REVERT: C 95 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: C 276 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: C 358 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7876 (mp) REVERT: D 44 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5563 (mtm-85) REVERT: D 65 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6864 (ttmt) REVERT: D 95 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: D 276 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: D 358 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7857 (mp) outliers start: 39 outliers final: 14 residues processed: 172 average time/residue: 1.2640 time to fit residues: 243.5647 Evaluate side-chains 169 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 34 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095437 restraints weight = 15725.349| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.45 r_work: 0.2919 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15720 Z= 0.121 Angle : 0.504 6.058 21356 Z= 0.262 Chirality : 0.039 0.126 2460 Planarity : 0.004 0.034 2600 Dihedral : 6.312 53.751 2316 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.45 % Allowed : 15.43 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.67 (0.20), residues: 1844 helix: 2.44 (0.15), residues: 1112 sheet: 1.25 (0.30), residues: 252 loop : 0.51 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 491 HIS 0.003 0.001 HIS A 234 PHE 0.013 0.001 PHE A 474 TYR 0.013 0.001 TYR D 355 ARG 0.002 0.000 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 4) link_NAG-ASN : angle 1.56601 ( 12) link_BETA1-4 : bond 0.00094 ( 4) link_BETA1-4 : angle 1.90545 ( 12) hydrogen bonds : bond 0.04640 ( 1052) hydrogen bonds : angle 4.63855 ( 3216) covalent geometry : bond 0.00247 (15712) covalent geometry : angle 0.50075 (21332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.978 Fit side-chains REVERT: A 44 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.5572 (mtm-85) REVERT: A 65 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6934 (ttmt) REVERT: A 95 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: A 276 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: A 358 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7867 (mp) REVERT: B 44 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.5550 (mtm-85) REVERT: B 65 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6991 (ttmt) REVERT: B 95 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: B 276 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: B 327 GLN cc_start: 0.5691 (OUTLIER) cc_final: 0.5489 (tm-30) REVERT: B 358 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7893 (mp) REVERT: C 44 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.5546 (mtm-85) REVERT: C 65 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6922 (ttmt) REVERT: C 95 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: C 276 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: C 358 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7892 (mp) REVERT: D 44 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5564 (mtm-85) REVERT: D 95 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: D 115 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: D 276 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: D 358 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7885 (mp) outliers start: 41 outliers final: 14 residues processed: 175 average time/residue: 1.1275 time to fit residues: 222.7720 Evaluate side-chains 175 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 26 optimal weight: 0.0040 chunk 155 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN D 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.094969 restraints weight = 15597.676| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.49 r_work: 0.2910 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 15720 Z= 0.155 Angle : 0.753 59.174 21356 Z= 0.426 Chirality : 0.040 0.573 2460 Planarity : 0.004 0.034 2600 Dihedral : 6.312 53.751 2316 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.39 % Allowed : 15.61 % Favored : 82.00 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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: 2.66 (0.20), residues: 1844 helix: 2.43 (0.15), residues: 1112 sheet: 1.25 (0.30), residues: 252 loop : 0.51 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 491 HIS 0.003 0.001 HIS A 234 PHE 0.013 0.001 PHE A 474 TYR 0.013 0.001 TYR A 404 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00025 ( 4) link_NAG-ASN : angle 1.56537 ( 12) link_BETA1-4 : bond 0.00106 ( 4) link_BETA1-4 : angle 1.90485 ( 12) hydrogen bonds : bond 0.04650 ( 1052) hydrogen bonds : angle 4.64015 ( 3216) covalent geometry : bond 0.00304 (15712) covalent geometry : angle 0.75072 (21332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13063.68 seconds wall clock time: 226 minutes 12.69 seconds (13572.69 seconds total)