Starting phenix.real_space_refine on Sun Jun 15 15:46:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ekf_48120/06_2025/9ekf_48120_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ekf_48120/06_2025/9ekf_48120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ekf_48120/06_2025/9ekf_48120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ekf_48120/06_2025/9ekf_48120.map" model { file = "/net/cci-nas-00/data/ceres_data/9ekf_48120/06_2025/9ekf_48120_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ekf_48120/06_2025/9ekf_48120_neut.cif" } resolution = 2.68 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 11051 2.51 5 N 2967 2.21 5 O 3426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17537 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3926 Classifications: {'peptide': 491} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 958 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 958 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 958 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 810 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.07, per 1000 atoms: 0.63 Number of scatterers: 17537 At special positions: 0 Unit cell: (132, 136.125, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 3426 8.00 N 2967 7.00 C 11051 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 482 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 314 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 314 " distance=2.03 Simple disulfide: pdb=" SG CYS C 486 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " BETA1-2 " MAN E 4 " - " NAG E 5 " " MAN F 4 " - " NAG F 5 " " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG E 5 " - " GAL E 6 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG J 5 " - " GAL J 6 " BETA2-3 " GAL E 6 " - " SIA E 7 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL F 6 " - " SIA F 7 " " GAL J 6 " - " SIA J 7 " NAG-ASN " NAG A 601 " - " ASN A 27 " " NAG A 602 " - " ASN A 290 " " NAG A 603 " - " ASN A 14 " " NAG A 604 " - " ASN A 488 " " NAG B 601 " - " ASN B 27 " " NAG B 602 " - " ASN B 298 " " NAG B 603 " - " ASN B 14 " " NAG B 604 " - " ASN B 496 " " NAG C 601 " - " ASN C 27 " " NAG C 602 " - " ASN C 298 " " NAG C 603 " - " ASN C 14 " " NAG C 604 " - " ASN C 496 " Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.1 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3970 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 48 sheets defined 19.8% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 68 through 75 removed outlier: 4.126A pdb=" N ASP A 72 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLU A 73 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.927A pdb=" N TRP A 126 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 374 through 393 removed outlier: 3.551A pdb=" N MET A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 460 removed outlier: 3.698A pdb=" N GLU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.776A pdb=" N TYR A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLU A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 67 Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.975A pdb=" N ASP B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU B 73 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 110 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.897A pdb=" N TRP B 126 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.646A pdb=" N MET B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 469 Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.677A pdb=" N SER B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.510A pdb=" N GLN B 503 " --> pdb=" O ASP B 500 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 504 " --> pdb=" O TYR B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 504' Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.732A pdb=" N LEU B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 68 through 75 removed outlier: 4.103A pdb=" N ASP C 72 " --> pdb=" O PRO C 69 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU C 73 " --> pdb=" O MET C 70 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 74 " --> pdb=" O CYS C 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.971A pdb=" N TRP C 126 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.702A pdb=" N MET C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 469 Processing helix chain 'C' and resid 487 through 495 removed outlier: 3.514A pdb=" N SER C 493 " --> pdb=" O GLU C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 512 removed outlier: 4.073A pdb=" N TYR C 504 " --> pdb=" O ASP C 500 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 506 " --> pdb=" O PRO C 502 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLU C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG C 509 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 3.553A pdb=" N GLN A 6 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.396A pdb=" N GLU A 18 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.089A pdb=" N LEU A 45 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N CYS A 278 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.740A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 83 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.500A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS A 114 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A 263 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 112 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.500A pdb=" N SER A 98 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TRP A 234 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.536A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 210 through 213 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.341A pdb=" N GLU B 18 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AB6, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'B' and resid 45 through 48 removed outlier: 7.084A pdb=" N LEU B 45 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N CYS B 286 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.698A pdb=" N LEU B 54 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 83 " --> pdb=" O MET B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.445A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU B 179 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR B 264 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS B 114 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS B 271 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE B 112 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.445A pdb=" N SER B 98 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N TRP B 234 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU B 179 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.548A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 210 through 213 Processing sheet with id=AC4, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AC5, first strand: chain 'C' and resid 6 through 11 removed outlier: 3.552A pdb=" N GLN C 6 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AC7, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'C' and resid 37 through 38 Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 48 removed outlier: 7.054A pdb=" N LEU C 45 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N CYS C 286 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.667A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 83 " --> pdb=" O MET C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.512A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C 179 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR C 264 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS C 114 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS C 271 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 112 " --> pdb=" O LYS C 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.512A pdb=" N SER C 98 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N TRP C 234 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 179 " --> pdb=" O PRO C 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.542A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 210 through 213 removed outlier: 7.976A pdb=" N PHE G 100 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER C 167 " --> pdb=" O PHE G 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AD7, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.613A pdb=" N TYR D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP D 52 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE D 32 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AE1, first strand: chain 'G' and resid 56 through 59 removed outlier: 3.613A pdb=" N TYR G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP G 52 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE G 32 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AE3, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.613A pdb=" N TYR H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE H 32 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.365A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1746 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: 6.47 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2877 1.31 - 1.44: 5197 1.44 - 1.57: 9751 1.57 - 1.71: 3 1.71 - 1.84: 138 Bond restraints: 17966 Sorted by residual: bond pdb=" C ILE A 166 " pdb=" O ILE A 166 " ideal model delta sigma weight residual 1.236 1.175 0.061 9.90e-03 1.02e+04 3.82e+01 bond pdb=" C PRO A 162 " pdb=" O PRO A 162 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.19e-02 7.06e+03 2.70e+01 bond pdb=" C PHE B 245 " pdb=" O PHE B 245 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.20e-02 6.94e+03 2.33e+01 bond pdb=" C HIS B 244 " pdb=" O HIS B 244 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.21e-02 6.83e+03 2.12e+01 bond pdb=" C ILE A 164 " pdb=" O ILE A 164 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.03e-02 9.43e+03 1.82e+01 ... (remaining 17961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 23731 2.46 - 4.93: 565 4.93 - 7.39: 57 7.39 - 9.86: 6 9.86 - 12.32: 2 Bond angle restraints: 24361 Sorted by residual: angle pdb=" N ILE B 243 " pdb=" CA ILE B 243 " pdb=" C ILE B 243 " ideal model delta sigma weight residual 108.11 98.68 9.43 1.40e+00 5.10e-01 4.54e+01 angle pdb=" CA ASP B 92 " pdb=" CB ASP B 92 " pdb=" CG ASP B 92 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.00e+00 1.00e+00 3.21e+01 angle pdb=" N HIS C 244 " pdb=" CA HIS C 244 " pdb=" C HIS C 244 " ideal model delta sigma weight residual 110.91 117.39 -6.48 1.17e+00 7.31e-01 3.07e+01 angle pdb=" C ILE B 243 " pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta sigma weight residual 110.63 118.65 -8.02 1.48e+00 4.57e-01 2.94e+01 angle pdb=" C LYS B 380 " pdb=" N GLU B 381 " pdb=" CA GLU B 381 " ideal model delta sigma weight residual 121.54 131.78 -10.24 1.91e+00 2.74e-01 2.88e+01 ... (remaining 24356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9676 17.98 - 35.96: 1027 35.96 - 53.94: 311 53.94 - 71.92: 67 71.92 - 89.90: 32 Dihedral angle restraints: 11113 sinusoidal: 4899 harmonic: 6214 Sorted by residual: dihedral pdb=" CB CYS C 486 " pdb=" SG CYS C 486 " pdb=" SG CYS C 490 " pdb=" CB CYS C 490 " ideal model delta sinusoidal sigma weight residual 93.00 161.79 -68.79 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS A 478 " pdb=" SG CYS A 478 " pdb=" SG CYS A 482 " pdb=" CB CYS A 482 " ideal model delta sinusoidal sigma weight residual 93.00 158.09 -65.09 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS B 486 " pdb=" SG CYS B 486 " pdb=" SG CYS B 490 " pdb=" CB CYS B 490 " ideal model delta sinusoidal sigma weight residual 93.00 158.00 -65.00 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 11110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 2656 0.214 - 0.429: 14 0.429 - 0.643: 1 0.643 - 0.858: 0 0.858 - 1.072: 1 Chirality restraints: 2672 Sorted by residual: chirality pdb=" C2 SIA J 7 " pdb=" O3 GAL J 6 " pdb=" C1 SIA J 7 " pdb=" O6 SIA J 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.85 0.35 2.00e-02 2.50e+03 3.08e+02 chirality pdb=" C2 SIA E 7 " pdb=" O3 GAL E 6 " pdb=" C1 SIA E 7 " pdb=" O6 SIA E 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.76e+02 chirality pdb=" C2 SIA F 7 " pdb=" O3 GAL F 6 " pdb=" C1 SIA F 7 " pdb=" O6 SIA F 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.71e+02 ... (remaining 2669 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 14 " 0.020 2.00e-02 2.50e+03 7.21e-02 6.50e+01 pdb=" CG ASN B 14 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN B 14 " 0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN B 14 " -0.066 2.00e-02 2.50e+03 pdb=" C1 NAG B 603 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 14 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" CG ASN B 14 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN B 14 " -0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 14 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 242 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C ALA B 242 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA B 242 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE B 243 " 0.020 2.00e-02 2.50e+03 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 9 1.65 - 2.46: 22 2.46 - 3.27: 16549 3.27 - 4.09: 47257 4.09 - 4.90: 85208 Warning: very small nonbonded interaction distances. Nonbonded interactions: 149045 Sorted by model distance: nonbonded pdb=" OE1 GLU A 189 " pdb=" CZ TYR D 27 " model vdw 0.836 3.260 nonbonded pdb=" OE1 GLU B 189 " pdb=" CZ TYR G 27 " model vdw 0.960 3.260 nonbonded pdb=" OE1 GLU A 189 " pdb=" CE1 TYR D 27 " model vdw 1.131 3.340 nonbonded pdb=" OE1 GLU B 189 " pdb=" CE1 TYR G 27 " model vdw 1.134 3.340 nonbonded pdb=" OE2 GLU B 189 " pdb=" OH TYR G 27 " model vdw 1.236 3.040 ... (remaining 149040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 through 513 or resid 601 through 604)) selection = (chain 'C' and (resid 5 through 241 or (resid 242 and (name N or name CA or name \ C or name O )) or resid 243 through 513 or resid 601 through 604)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } 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=0.55 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: 3.550 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.480 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 18017 Z= 0.311 Angle : 0.936 23.646 24493 Z= 0.540 Chirality : 0.059 1.072 2672 Planarity : 0.006 0.064 3102 Dihedral : 16.751 89.902 7080 Min Nonbonded Distance : 0.836 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.15 % Allowed : 18.36 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.19 (0.17), residues: 2121 helix: -0.16 (0.25), residues: 391 sheet: 0.09 (0.23), residues: 503 loop : -1.41 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP H 100G HIS 0.009 0.002 HIS B 244 PHE 0.023 0.002 PHE B 245 TYR 0.030 0.002 TYR A 11 ARG 0.013 0.001 ARG A 440 Details of bonding type rmsd link_BETA2-3 : bond 0.00083 ( 3) link_BETA2-3 : angle 6.64578 ( 9) link_NAG-ASN : bond 0.01355 ( 12) link_NAG-ASN : angle 7.42245 ( 36) link_BETA1-2 : bond 0.00368 ( 3) link_BETA1-2 : angle 1.44248 ( 9) link_BETA1-4 : bond 0.00502 ( 9) link_BETA1-4 : angle 3.28165 ( 27) link_ALPHA1-3 : bond 0.00948 ( 3) link_ALPHA1-3 : angle 0.84806 ( 9) hydrogen bonds : bond 0.13824 ( 636) hydrogen bonds : angle 7.26580 ( 1746) SS BOND : bond 0.00343 ( 21) SS BOND : angle 1.71419 ( 42) covalent geometry : bond 0.00509 (17966) covalent geometry : angle 0.87437 (24361) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.7498 (mt) cc_final: 0.7269 (mm) REVERT: A 116 GLU cc_start: 0.7421 (tt0) cc_final: 0.7129 (tt0) REVERT: A 262 LYS cc_start: 0.6816 (tppt) cc_final: 0.6428 (tttp) REVERT: A 265 ASP cc_start: 0.7645 (t0) cc_final: 0.7346 (t70) REVERT: A 274 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6573 (pt0) REVERT: A 311 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7699 (mttp) REVERT: A 349 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6684 (mm110) REVERT: A 384 ASN cc_start: 0.6771 (m110) cc_final: 0.6410 (m110) REVERT: A 392 LYS cc_start: 0.6459 (mmtt) cc_final: 0.6081 (mttp) REVERT: A 440 ARG cc_start: 0.5409 (mtt90) cc_final: 0.5184 (mmm160) REVERT: A 453 TYR cc_start: 0.7029 (t80) cc_final: 0.6741 (t80) REVERT: B 58 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6766 (t0) REVERT: B 73 GLU cc_start: 0.7376 (tt0) cc_final: 0.7144 (tt0) REVERT: B 199 ILE cc_start: 0.7790 (mp) cc_final: 0.7545 (mm) REVERT: B 273 ASP cc_start: 0.7360 (t0) cc_final: 0.6707 (t70) REVERT: B 282 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6612 (pt0) REVERT: B 319 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7574 (mtmm) REVERT: B 329 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6876 (pp) REVERT: B 392 ASN cc_start: 0.6807 (m110) cc_final: 0.6442 (m110) REVERT: B 448 ARG cc_start: 0.5531 (mtt90) cc_final: 0.5230 (mmm160) REVERT: B 483 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.4195 (m-80) REVERT: C 73 GLU cc_start: 0.6844 (tt0) cc_final: 0.6547 (pt0) REVERT: C 116 GLU cc_start: 0.7493 (tt0) cc_final: 0.7171 (tt0) REVERT: C 270 LYS cc_start: 0.6815 (tppt) cc_final: 0.6206 (tttm) REVERT: C 273 ASP cc_start: 0.7498 (t0) cc_final: 0.7248 (t70) REVERT: C 282 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6482 (pt0) REVERT: C 319 LYS cc_start: 0.8376 (mtmt) cc_final: 0.7658 (mttm) REVERT: C 329 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7031 (mp) REVERT: C 392 ASN cc_start: 0.7016 (m110) cc_final: 0.6589 (m110) REVERT: C 401 MET cc_start: 0.7635 (mmt) cc_final: 0.7432 (mmt) REVERT: C 403 THR cc_start: 0.7338 (OUTLIER) cc_final: 0.6841 (t) REVERT: C 411 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: C 428 ASP cc_start: 0.6862 (t70) cc_final: 0.6477 (m-30) REVERT: C 451 ASP cc_start: 0.6533 (m-30) cc_final: 0.6177 (m-30) REVERT: D 89 MET cc_start: 0.8688 (tpt) cc_final: 0.8483 (tpp) REVERT: G 52 ASP cc_start: 0.8038 (t0) cc_final: 0.7458 (t0) REVERT: H 81 GLN cc_start: 0.7633 (mt0) cc_final: 0.6635 (mt0) REVERT: I 39 MET cc_start: 0.7170 (mmm) cc_final: 0.6714 (mmt) REVERT: I 45 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.8167 (ptt-90) REVERT: I 70 GLU cc_start: 0.6829 (tt0) cc_final: 0.6379 (tm-30) REVERT: K 65 SER cc_start: 0.8025 (p) cc_final: 0.7705 (m) REVERT: K 70 GLU cc_start: 0.6907 (tt0) cc_final: 0.6399 (mm-30) REVERT: L 70 GLU cc_start: 0.6888 (tt0) cc_final: 0.6296 (mm-30) outliers start: 40 outliers final: 12 residues processed: 266 average time/residue: 1.6163 time to fit residues: 478.4685 Evaluate side-chains 228 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0060 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 186 ASN A 197 ASN A 224 ASN A 384 ASN A 448 ASN B 32 HIS B 142 GLN B 186 ASN B 197 ASN B 285 HIS B 357 GLN B 392 ASN B 467 GLN C 6 GLN C 187 ASN C 197 ASN C 392 ASN C 404 GLN C 421 ASN C 456 ASN G 81 GLN I 27 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.184216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128230 restraints weight = 16749.846| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.56 r_work: 0.3073 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18017 Z= 0.233 Angle : 0.737 21.801 24493 Z= 0.362 Chirality : 0.053 1.080 2672 Planarity : 0.005 0.059 3102 Dihedral : 8.945 85.338 3074 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.13 % Allowed : 16.32 % Favored : 79.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2121 helix: 0.41 (0.27), residues: 390 sheet: 0.22 (0.23), residues: 499 loop : -1.29 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 33 HIS 0.011 0.002 HIS G 99 PHE 0.019 0.003 PHE C 345 TYR 0.020 0.002 TYR D 27 ARG 0.004 0.001 ARG A 461 Details of bonding type rmsd link_BETA2-3 : bond 0.01505 ( 3) link_BETA2-3 : angle 6.07610 ( 9) link_NAG-ASN : bond 0.00583 ( 12) link_NAG-ASN : angle 6.29345 ( 36) link_BETA1-2 : bond 0.00379 ( 3) link_BETA1-2 : angle 1.66910 ( 9) link_BETA1-4 : bond 0.00476 ( 9) link_BETA1-4 : angle 3.30024 ( 27) link_ALPHA1-3 : bond 0.00519 ( 3) link_ALPHA1-3 : angle 1.58928 ( 9) hydrogen bonds : bond 0.04623 ( 636) hydrogen bonds : angle 5.62533 ( 1746) SS BOND : bond 0.00415 ( 21) SS BOND : angle 1.50570 ( 42) covalent geometry : bond 0.00543 (17966) covalent geometry : angle 0.67511 (24361) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 225 time to evaluate : 1.808 Fit side-chains REVERT: A 75 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8558 (mm) REVERT: A 311 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8790 (mttm) REVERT: A 349 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7171 (mm-40) REVERT: A 384 ASN cc_start: 0.7670 (m-40) cc_final: 0.7300 (m110) REVERT: A 392 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7265 (mttp) REVERT: A 453 TYR cc_start: 0.7227 (t80) cc_final: 0.7006 (t80) REVERT: A 483 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5171 (mpt) REVERT: B 12 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.5975 (t70) REVERT: B 273 ASP cc_start: 0.8158 (t0) cc_final: 0.7668 (t70) REVERT: B 319 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8562 (mtmm) REVERT: B 392 ASN cc_start: 0.7880 (m-40) cc_final: 0.7516 (m110) REVERT: B 483 TYR cc_start: 0.4729 (OUTLIER) cc_final: 0.4284 (m-80) REVERT: C 186 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.5947 (t0) REVERT: C 282 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7972 (pt0) REVERT: C 319 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8786 (mttm) REVERT: C 357 GLN cc_start: 0.7041 (mm-40) cc_final: 0.6755 (mm110) REVERT: C 392 ASN cc_start: 0.7757 (m-40) cc_final: 0.7361 (m110) REVERT: C 400 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7284 (mttp) REVERT: C 426 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8962 (tmm) REVERT: C 447 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: C 451 ASP cc_start: 0.7343 (m-30) cc_final: 0.7089 (m-30) REVERT: C 492 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: D 40 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.6684 (mpp) REVERT: G 40 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.6396 (mpp) REVERT: H 40 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.6570 (mpp) REVERT: H 81 GLN cc_start: 0.7736 (mt0) cc_final: 0.6700 (mt0) REVERT: H 101 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7770 (mt-10) REVERT: I 70 GLU cc_start: 0.7420 (tt0) cc_final: 0.6944 (tm-30) REVERT: K 70 GLU cc_start: 0.7440 (tt0) cc_final: 0.6933 (mm-30) REVERT: K 81 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6692 (pt0) REVERT: L 70 GLU cc_start: 0.7518 (tt0) cc_final: 0.6857 (mm-30) REVERT: L 81 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6391 (pm20) outliers start: 77 outliers final: 32 residues processed: 282 average time/residue: 1.2473 time to fit residues: 394.5051 Evaluate side-chains 250 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 143 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 459 GLN B 285 HIS G 81 GLN G 99 HIS I 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.179713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125179 restraints weight = 16935.852| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.41 r_work: 0.3062 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 18017 Z= 0.285 Angle : 0.777 16.031 24493 Z= 0.383 Chirality : 0.058 1.391 2672 Planarity : 0.005 0.061 3102 Dihedral : 9.036 87.774 3060 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.94 % Allowed : 15.41 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2121 helix: 0.46 (0.27), residues: 388 sheet: -0.02 (0.22), residues: 523 loop : -1.27 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 33 HIS 0.013 0.002 HIS H 99 PHE 0.019 0.003 PHE B 345 TYR 0.019 0.002 TYR A 201 ARG 0.009 0.001 ARG C 509 Details of bonding type rmsd link_BETA2-3 : bond 0.01028 ( 3) link_BETA2-3 : angle 6.68237 ( 9) link_NAG-ASN : bond 0.00873 ( 12) link_NAG-ASN : angle 5.73096 ( 36) link_BETA1-2 : bond 0.00368 ( 3) link_BETA1-2 : angle 1.88611 ( 9) link_BETA1-4 : bond 0.00498 ( 9) link_BETA1-4 : angle 3.43031 ( 27) link_ALPHA1-3 : bond 0.00360 ( 3) link_ALPHA1-3 : angle 1.62803 ( 9) hydrogen bonds : bond 0.04823 ( 636) hydrogen bonds : angle 5.69134 ( 1746) SS BOND : bond 0.00243 ( 21) SS BOND : angle 1.78656 ( 42) covalent geometry : bond 0.00673 (17966) covalent geometry : angle 0.72157 (24361) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 226 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6323 (t70) REVERT: A 75 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8611 (mm) REVERT: A 116 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8687 (tt0) REVERT: A 311 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8791 (mttp) REVERT: A 373 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5553 (pt0) REVERT: A 384 ASN cc_start: 0.7824 (m-40) cc_final: 0.7436 (m110) REVERT: A 392 LYS cc_start: 0.7800 (mmtt) cc_final: 0.7358 (mttm) REVERT: A 475 TYR cc_start: 0.5453 (OUTLIER) cc_final: 0.4758 (m-80) REVERT: A 483 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5264 (mpt) REVERT: B 12 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.5885 (t70) REVERT: B 273 ASP cc_start: 0.8160 (t0) cc_final: 0.7619 (t70) REVERT: B 301 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7602 (mmt) REVERT: B 319 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8566 (mtmm) REVERT: B 371 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.3880 (mt-10) REVERT: B 381 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6301 (tm-30) REVERT: B 392 ASN cc_start: 0.7976 (m-40) cc_final: 0.7646 (m110) REVERT: B 403 THR cc_start: 0.7580 (p) cc_final: 0.7339 (m) REVERT: B 458 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6715 (tttm) REVERT: B 483 TYR cc_start: 0.4805 (OUTLIER) cc_final: 0.4408 (m-80) REVERT: C 23 ILE cc_start: 0.7730 (mp) cc_final: 0.7361 (mm) REVERT: C 24 MET cc_start: 0.8011 (mtt) cc_final: 0.7652 (mtm) REVERT: C 186 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.5988 (t0) REVERT: C 230 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.9153 (mtt) REVERT: C 319 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8781 (mttm) REVERT: C 357 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6874 (mm110) REVERT: C 360 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7370 (p) REVERT: C 392 ASN cc_start: 0.7842 (m-40) cc_final: 0.7472 (m110) REVERT: C 444 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6651 (mtp) REVERT: C 447 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: C 451 ASP cc_start: 0.7373 (m-30) cc_final: 0.7141 (m-30) REVERT: C 492 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6311 (pm20) REVERT: D 40 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.6586 (mpp) REVERT: G 40 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.6335 (mpp) REVERT: H 40 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.6530 (mpp) REVERT: H 101 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7775 (mt-10) REVERT: I 39 MET cc_start: 0.7431 (mmt) cc_final: 0.7176 (mmm) REVERT: I 70 GLU cc_start: 0.7698 (tt0) cc_final: 0.7254 (tm-30) REVERT: I 81 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6713 (pt0) REVERT: I 100 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: K 39 MET cc_start: 0.7408 (mmt) cc_final: 0.6682 (mmt) REVERT: K 70 GLU cc_start: 0.7647 (tt0) cc_final: 0.7213 (mm-30) REVERT: K 81 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6618 (pt0) REVERT: L 70 GLU cc_start: 0.7652 (tt0) cc_final: 0.7055 (mm-30) REVERT: L 81 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6328 (pm20) REVERT: L 100 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7318 (pm20) outliers start: 92 outliers final: 36 residues processed: 291 average time/residue: 1.6081 time to fit residues: 527.0869 Evaluate side-chains 274 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 112 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 406 ASN B 285 HIS B 357 GLN G 6 GLN G 81 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.181232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129208 restraints weight = 16915.287| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.48 r_work: 0.3098 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18017 Z= 0.195 Angle : 0.679 10.912 24493 Z= 0.337 Chirality : 0.052 1.110 2672 Planarity : 0.004 0.054 3102 Dihedral : 8.800 86.264 3060 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.03 % Allowed : 16.91 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2121 helix: 0.60 (0.27), residues: 390 sheet: 0.02 (0.22), residues: 523 loop : -1.15 (0.16), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 33 HIS 0.007 0.001 HIS G 99 PHE 0.014 0.002 PHE C 412 TYR 0.016 0.002 TYR B 168 ARG 0.003 0.000 ARG A 220 Details of bonding type rmsd link_BETA2-3 : bond 0.00846 ( 3) link_BETA2-3 : angle 6.11080 ( 9) link_NAG-ASN : bond 0.00829 ( 12) link_NAG-ASN : angle 4.80713 ( 36) link_BETA1-2 : bond 0.00265 ( 3) link_BETA1-2 : angle 1.53982 ( 9) link_BETA1-4 : bond 0.00391 ( 9) link_BETA1-4 : angle 3.17719 ( 27) link_ALPHA1-3 : bond 0.00650 ( 3) link_ALPHA1-3 : angle 1.36319 ( 9) hydrogen bonds : bond 0.04201 ( 636) hydrogen bonds : angle 5.49041 ( 1746) SS BOND : bond 0.00157 ( 21) SS BOND : angle 2.15659 ( 42) covalent geometry : bond 0.00455 (17966) covalent geometry : angle 0.62840 (24361) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 2.328 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7113 (tt0) cc_final: 0.6877 (tt0) REVERT: A 75 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8704 (mm) REVERT: A 116 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: A 176 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 230 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.8990 (mtt) REVERT: A 311 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8804 (mttp) REVERT: A 349 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7189 (mm110) REVERT: A 373 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5600 (pt0) REVERT: A 384 ASN cc_start: 0.7740 (m-40) cc_final: 0.7367 (m110) REVERT: A 392 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7363 (mttm) REVERT: A 483 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5280 (mpt) REVERT: A 484 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5993 (pm20) REVERT: B 12 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.5980 (t70) REVERT: B 273 ASP cc_start: 0.8031 (t0) cc_final: 0.7474 (t70) REVERT: B 301 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7486 (mmt) REVERT: B 319 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8519 (mtmm) REVERT: B 392 ASN cc_start: 0.7929 (m-40) cc_final: 0.7605 (m110) REVERT: B 403 THR cc_start: 0.7569 (p) cc_final: 0.7324 (m) REVERT: B 458 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6617 (tttm) REVERT: B 483 TYR cc_start: 0.4800 (OUTLIER) cc_final: 0.4454 (m-80) REVERT: C 24 MET cc_start: 0.7964 (mtt) cc_final: 0.7639 (mtm) REVERT: C 186 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.5980 (t0) REVERT: C 319 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8772 (mttm) REVERT: C 371 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.4954 (pm20) REVERT: C 392 ASN cc_start: 0.7797 (m-40) cc_final: 0.7415 (m110) REVERT: C 444 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6696 (mtp) REVERT: C 492 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: D 40 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.6593 (mpp) REVERT: G 40 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.6442 (mpp) REVERT: H 40 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.6538 (mpp) REVERT: H 89 MET cc_start: 0.8875 (tpt) cc_final: 0.8265 (tpt) REVERT: I 39 MET cc_start: 0.7451 (mmt) cc_final: 0.7153 (mmm) REVERT: I 70 GLU cc_start: 0.7503 (tt0) cc_final: 0.7074 (tm-30) REVERT: I 81 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6763 (pt0) REVERT: I 100 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: K 39 MET cc_start: 0.7416 (mmt) cc_final: 0.6713 (mmt) REVERT: K 65 SER cc_start: 0.8249 (p) cc_final: 0.7976 (m) REVERT: K 70 GLU cc_start: 0.7511 (tt0) cc_final: 0.7046 (mm-30) REVERT: K 81 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: K 100 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7284 (pm20) REVERT: L 70 GLU cc_start: 0.7591 (tt0) cc_final: 0.7011 (mm-30) REVERT: L 100 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7325 (pm20) outliers start: 75 outliers final: 32 residues processed: 271 average time/residue: 1.7773 time to fit residues: 540.5353 Evaluate side-chains 264 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 4.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 71 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 177 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 406 ASN B 41 HIS B 285 HIS B 413 ASN B 414 ASN B 477 ASN H 81 GLN I 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.182627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126526 restraints weight = 17091.448| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.56 r_work: 0.3112 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18017 Z= 0.150 Angle : 0.639 9.514 24493 Z= 0.317 Chirality : 0.048 0.674 2672 Planarity : 0.004 0.050 3102 Dihedral : 8.526 83.604 3060 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.81 % Allowed : 17.71 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2121 helix: 0.76 (0.27), residues: 393 sheet: 0.10 (0.22), residues: 523 loop : -1.05 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 33 HIS 0.005 0.001 HIS C 285 PHE 0.012 0.002 PHE A 245 TYR 0.015 0.002 TYR B 168 ARG 0.005 0.000 ARG G 96 Details of bonding type rmsd link_BETA2-3 : bond 0.00836 ( 3) link_BETA2-3 : angle 5.73512 ( 9) link_NAG-ASN : bond 0.00951 ( 12) link_NAG-ASN : angle 4.32825 ( 36) link_BETA1-2 : bond 0.00177 ( 3) link_BETA1-2 : angle 1.38870 ( 9) link_BETA1-4 : bond 0.00344 ( 9) link_BETA1-4 : angle 3.01284 ( 27) link_ALPHA1-3 : bond 0.00746 ( 3) link_ALPHA1-3 : angle 1.23186 ( 9) hydrogen bonds : bond 0.03868 ( 636) hydrogen bonds : angle 5.29849 ( 1746) SS BOND : bond 0.00164 ( 21) SS BOND : angle 2.41202 ( 42) covalent geometry : bond 0.00344 (17966) covalent geometry : angle 0.59072 (24361) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6997 (tt0) cc_final: 0.6777 (tt0) REVERT: A 75 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8691 (mm) REVERT: A 176 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8784 (mp) REVERT: A 230 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8992 (mtt) REVERT: A 311 LYS cc_start: 0.9125 (mtmt) cc_final: 0.8851 (mttp) REVERT: A 349 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7241 (mm110) REVERT: A 384 ASN cc_start: 0.7699 (m-40) cc_final: 0.7302 (m110) REVERT: A 392 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7336 (mttm) REVERT: A 475 TYR cc_start: 0.5431 (OUTLIER) cc_final: 0.4763 (m-80) REVERT: A 483 MET cc_start: 0.5906 (OUTLIER) cc_final: 0.5353 (mpt) REVERT: A 484 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5943 (tm-30) REVERT: B 12 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.5925 (t70) REVERT: B 273 ASP cc_start: 0.7969 (t0) cc_final: 0.7409 (t70) REVERT: B 301 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7372 (mmt) REVERT: B 392 ASN cc_start: 0.7845 (m-40) cc_final: 0.7511 (m110) REVERT: B 403 THR cc_start: 0.7514 (p) cc_final: 0.7263 (m) REVERT: B 458 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6533 (tttm) REVERT: B 483 TYR cc_start: 0.4656 (OUTLIER) cc_final: 0.4304 (m-80) REVERT: C 23 ILE cc_start: 0.7616 (mp) cc_final: 0.7247 (mm) REVERT: C 24 MET cc_start: 0.7880 (mtt) cc_final: 0.7530 (mtm) REVERT: C 186 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.5849 (t0) REVERT: C 319 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8817 (mttm) REVERT: C 371 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.4914 (pm20) REVERT: C 392 ASN cc_start: 0.7739 (m-40) cc_final: 0.7349 (m110) REVERT: C 417 ARG cc_start: 0.8759 (mmt-90) cc_final: 0.8553 (mmp80) REVERT: C 444 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6838 (mtp) REVERT: C 492 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: G 40 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.6451 (mpp) REVERT: H 40 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.6489 (mpp) REVERT: H 101 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: I 39 MET cc_start: 0.7486 (mmt) cc_final: 0.7186 (mmm) REVERT: I 70 GLU cc_start: 0.7382 (tt0) cc_final: 0.6904 (tm-30) REVERT: I 81 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6711 (pt0) REVERT: I 100 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: K 39 MET cc_start: 0.7450 (mmt) cc_final: 0.6729 (mmt) REVERT: K 65 SER cc_start: 0.8203 (p) cc_final: 0.7945 (m) REVERT: K 70 GLU cc_start: 0.7460 (tt0) cc_final: 0.6923 (mm-30) REVERT: K 81 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6548 (pt0) REVERT: K 100 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7197 (pm20) REVERT: L 70 GLU cc_start: 0.7417 (tt0) cc_final: 0.6786 (mm-30) REVERT: L 100 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7252 (pm20) outliers start: 71 outliers final: 34 residues processed: 268 average time/residue: 1.2686 time to fit residues: 380.9313 Evaluate side-chains 268 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 168 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 121 optimal weight: 0.0870 chunk 96 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN A 406 ASN B 285 HIS B 413 ASN B 477 ASN H 81 GLN I 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129070 restraints weight = 17032.434| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.53 r_work: 0.3089 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18017 Z= 0.163 Angle : 0.649 15.526 24493 Z= 0.321 Chirality : 0.048 0.613 2672 Planarity : 0.004 0.050 3102 Dihedral : 8.394 83.513 3060 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.76 % Allowed : 18.30 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2121 helix: 0.81 (0.27), residues: 392 sheet: 0.15 (0.22), residues: 523 loop : -1.01 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 33 HIS 0.005 0.001 HIS G 99 PHE 0.011 0.002 PHE C 412 TYR 0.016 0.002 TYR B 168 ARG 0.005 0.000 ARG G 96 Details of bonding type rmsd link_BETA2-3 : bond 0.00825 ( 3) link_BETA2-3 : angle 5.81894 ( 9) link_NAG-ASN : bond 0.00773 ( 12) link_NAG-ASN : angle 4.71856 ( 36) link_BETA1-2 : bond 0.00179 ( 3) link_BETA1-2 : angle 1.40594 ( 9) link_BETA1-4 : bond 0.00365 ( 9) link_BETA1-4 : angle 3.03144 ( 27) link_ALPHA1-3 : bond 0.00656 ( 3) link_ALPHA1-3 : angle 1.25371 ( 9) hydrogen bonds : bond 0.03934 ( 636) hydrogen bonds : angle 5.24164 ( 1746) SS BOND : bond 0.00304 ( 21) SS BOND : angle 2.47588 ( 42) covalent geometry : bond 0.00377 (17966) covalent geometry : angle 0.59650 (24361) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8689 (mm) REVERT: A 176 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 230 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8976 (mtt) REVERT: A 311 LYS cc_start: 0.9071 (mtmt) cc_final: 0.8812 (mttp) REVERT: A 349 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7214 (mm110) REVERT: A 384 ASN cc_start: 0.7693 (m-40) cc_final: 0.7296 (m110) REVERT: A 392 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7400 (mttm) REVERT: A 475 TYR cc_start: 0.5332 (OUTLIER) cc_final: 0.4690 (m-80) REVERT: A 484 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.6007 (pm20) REVERT: B 12 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6124 (t70) REVERT: B 273 ASP cc_start: 0.7910 (t0) cc_final: 0.7356 (t70) REVERT: B 301 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7434 (mmt) REVERT: B 371 GLU cc_start: 0.5325 (OUTLIER) cc_final: 0.3665 (mt-10) REVERT: B 392 ASN cc_start: 0.7833 (m-40) cc_final: 0.7509 (m110) REVERT: B 403 THR cc_start: 0.7515 (p) cc_final: 0.7266 (m) REVERT: B 458 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6526 (tttm) REVERT: B 483 TYR cc_start: 0.4700 (OUTLIER) cc_final: 0.4321 (m-80) REVERT: C 24 MET cc_start: 0.7863 (mtt) cc_final: 0.7526 (mtm) REVERT: C 186 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.5856 (t0) REVERT: C 319 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8774 (mttm) REVERT: C 371 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.4975 (pm20) REVERT: C 392 ASN cc_start: 0.7702 (m-40) cc_final: 0.7324 (m110) REVERT: C 444 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6719 (mtp) REVERT: C 492 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6389 (pm20) REVERT: G 40 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.6474 (mpp) REVERT: H 40 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.6494 (mpp) REVERT: I 39 MET cc_start: 0.7472 (mmt) cc_final: 0.7227 (mmt) REVERT: I 70 GLU cc_start: 0.7368 (tt0) cc_final: 0.6895 (tm-30) REVERT: I 81 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6672 (pt0) REVERT: I 100 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: K 39 MET cc_start: 0.7434 (mmt) cc_final: 0.6720 (mmt) REVERT: K 65 SER cc_start: 0.8207 (p) cc_final: 0.7947 (m) REVERT: K 70 GLU cc_start: 0.7414 (tt0) cc_final: 0.6889 (mm-30) REVERT: K 81 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6478 (pt0) REVERT: K 100 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7187 (pm20) REVERT: L 70 GLU cc_start: 0.7410 (tt0) cc_final: 0.6767 (mm-30) REVERT: L 100 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7251 (pm20) outliers start: 70 outliers final: 39 residues processed: 262 average time/residue: 1.2848 time to fit residues: 378.3827 Evaluate side-chains 270 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 6 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 405 ASN A 406 ASN B 285 HIS B 413 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN I 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.181398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134833 restraints weight = 16933.330| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.27 r_work: 0.3298 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18017 Z= 0.188 Angle : 0.668 12.282 24493 Z= 0.331 Chirality : 0.049 0.595 2672 Planarity : 0.004 0.052 3102 Dihedral : 8.452 84.786 3060 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.76 % Allowed : 18.68 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2121 helix: 0.81 (0.27), residues: 392 sheet: -0.09 (0.22), residues: 543 loop : -0.98 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 33 HIS 0.007 0.001 HIS A 277 PHE 0.013 0.002 PHE C 412 TYR 0.017 0.002 TYR B 168 ARG 0.004 0.000 ARG G 96 Details of bonding type rmsd link_BETA2-3 : bond 0.00891 ( 3) link_BETA2-3 : angle 6.04815 ( 9) link_NAG-ASN : bond 0.00830 ( 12) link_NAG-ASN : angle 4.45666 ( 36) link_BETA1-2 : bond 0.00240 ( 3) link_BETA1-2 : angle 1.47025 ( 9) link_BETA1-4 : bond 0.00392 ( 9) link_BETA1-4 : angle 3.11272 ( 27) link_ALPHA1-3 : bond 0.00546 ( 3) link_ALPHA1-3 : angle 1.30426 ( 9) hydrogen bonds : bond 0.04079 ( 636) hydrogen bonds : angle 5.31184 ( 1746) SS BOND : bond 0.00289 ( 21) SS BOND : angle 2.67144 ( 42) covalent geometry : bond 0.00441 (17966) covalent geometry : angle 0.61734 (24361) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 213 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6129 (t70) REVERT: A 75 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8743 (mm) REVERT: A 116 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: A 176 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8826 (mp) REVERT: A 349 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7433 (mm110) REVERT: A 384 ASN cc_start: 0.7889 (m-40) cc_final: 0.7523 (m110) REVERT: A 392 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7494 (mttm) REVERT: A 475 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.4654 (m-80) REVERT: A 483 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.5685 (mmt) REVERT: A 484 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: B 12 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6214 (t70) REVERT: B 273 ASP cc_start: 0.8143 (t0) cc_final: 0.7611 (t70) REVERT: B 301 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7659 (mmt) REVERT: B 371 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.3751 (mp0) REVERT: B 392 ASN cc_start: 0.8089 (m-40) cc_final: 0.7807 (m110) REVERT: B 403 THR cc_start: 0.7612 (p) cc_final: 0.7367 (m) REVERT: B 458 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6746 (tttm) REVERT: B 483 TYR cc_start: 0.4765 (OUTLIER) cc_final: 0.4357 (m-80) REVERT: C 24 MET cc_start: 0.8034 (mtt) cc_final: 0.7710 (mtm) REVERT: C 186 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.5966 (t0) REVERT: C 319 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8860 (mttm) REVERT: C 371 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5185 (pm20) REVERT: C 392 ASN cc_start: 0.7960 (m-40) cc_final: 0.7599 (m110) REVERT: C 444 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6825 (mtp) REVERT: C 492 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: G 40 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.6506 (mpp) REVERT: H 40 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.6565 (mpp) REVERT: I 39 MET cc_start: 0.7576 (mmt) cc_final: 0.7363 (mmt) REVERT: I 70 GLU cc_start: 0.7564 (tt0) cc_final: 0.7157 (tm-30) REVERT: I 81 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6757 (pt0) REVERT: I 100 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: K 39 MET cc_start: 0.7558 (mmt) cc_final: 0.6909 (mmt) REVERT: K 65 SER cc_start: 0.8280 (p) cc_final: 0.8038 (m) REVERT: K 70 GLU cc_start: 0.7611 (tt0) cc_final: 0.7165 (mm-30) REVERT: K 100 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7407 (pm20) REVERT: L 70 GLU cc_start: 0.7748 (tt0) cc_final: 0.7212 (mm-30) REVERT: L 100 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7413 (pm20) outliers start: 70 outliers final: 38 residues processed: 262 average time/residue: 1.3278 time to fit residues: 388.6953 Evaluate side-chains 269 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 406 ASN B 285 HIS B 413 ASN C 357 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129162 restraints weight = 16894.941| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.59 r_work: 0.3056 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18017 Z= 0.152 Angle : 0.641 11.425 24493 Z= 0.317 Chirality : 0.049 0.855 2672 Planarity : 0.004 0.049 3102 Dihedral : 8.256 83.488 3055 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.60 % Allowed : 18.73 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2121 helix: 0.87 (0.27), residues: 392 sheet: -0.04 (0.22), residues: 543 loop : -0.93 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 33 HIS 0.006 0.001 HIS A 277 PHE 0.011 0.002 PHE A 245 TYR 0.015 0.001 TYR B 168 ARG 0.004 0.000 ARG G 96 Details of bonding type rmsd link_BETA2-3 : bond 0.00831 ( 3) link_BETA2-3 : angle 5.77844 ( 9) link_NAG-ASN : bond 0.00691 ( 12) link_NAG-ASN : angle 4.10079 ( 36) link_BETA1-2 : bond 0.00170 ( 3) link_BETA1-2 : angle 1.35237 ( 9) link_BETA1-4 : bond 0.00345 ( 9) link_BETA1-4 : angle 2.97702 ( 27) link_ALPHA1-3 : bond 0.00697 ( 3) link_ALPHA1-3 : angle 1.18847 ( 9) hydrogen bonds : bond 0.03841 ( 636) hydrogen bonds : angle 5.23474 ( 1746) SS BOND : bond 0.00217 ( 21) SS BOND : angle 2.63207 ( 42) covalent geometry : bond 0.00351 (17966) covalent geometry : angle 0.59380 (24361) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 211 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.5957 (t70) REVERT: A 35 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7997 (t70) REVERT: A 75 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8702 (mm) REVERT: A 176 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8800 (mp) REVERT: A 230 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8978 (mtt) REVERT: A 349 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7302 (mm110) REVERT: A 384 ASN cc_start: 0.7702 (m-40) cc_final: 0.7317 (m110) REVERT: A 392 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7379 (mttm) REVERT: A 475 TYR cc_start: 0.5172 (OUTLIER) cc_final: 0.4521 (m-80) REVERT: A 484 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6184 (mm-30) REVERT: B 12 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6007 (t70) REVERT: B 273 ASP cc_start: 0.7946 (t0) cc_final: 0.7398 (t70) REVERT: B 301 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7485 (mmt) REVERT: B 371 GLU cc_start: 0.5327 (OUTLIER) cc_final: 0.4494 (pt0) REVERT: B 392 ASN cc_start: 0.7864 (m-40) cc_final: 0.7548 (m110) REVERT: B 403 THR cc_start: 0.7527 (p) cc_final: 0.7264 (m) REVERT: B 458 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6470 (tttm) REVERT: B 483 TYR cc_start: 0.4721 (OUTLIER) cc_final: 0.4337 (m-80) REVERT: C 24 MET cc_start: 0.7865 (mtt) cc_final: 0.7533 (mtm) REVERT: C 186 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.5828 (t0) REVERT: C 319 LYS cc_start: 0.9105 (mtmt) cc_final: 0.8803 (mttm) REVERT: C 371 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.5084 (pm20) REVERT: C 392 ASN cc_start: 0.7746 (m-40) cc_final: 0.7368 (m110) REVERT: C 417 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8557 (mmp80) REVERT: C 444 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6750 (mtp) REVERT: C 492 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6563 (pm20) REVERT: H 40 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.6555 (mpp) REVERT: I 39 MET cc_start: 0.7519 (mmt) cc_final: 0.7282 (mmt) REVERT: I 70 GLU cc_start: 0.7426 (tt0) cc_final: 0.6938 (tm-30) REVERT: I 81 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6694 (pt0) REVERT: I 100 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: K 39 MET cc_start: 0.7469 (mmt) cc_final: 0.6812 (mmt) REVERT: K 65 SER cc_start: 0.8212 (p) cc_final: 0.7966 (m) REVERT: K 70 GLU cc_start: 0.7418 (tt0) cc_final: 0.6891 (mm-30) REVERT: K 81 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6559 (pt0) REVERT: K 100 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7207 (pm20) REVERT: L 70 GLU cc_start: 0.7467 (tt0) cc_final: 0.6809 (mm-30) REVERT: L 100 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7272 (pm20) outliers start: 67 outliers final: 40 residues processed: 257 average time/residue: 1.2927 time to fit residues: 374.6375 Evaluate side-chains 268 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 171 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 0.0370 chunk 179 optimal weight: 1.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 405 ASN A 406 ASN B 285 HIS B 413 ASN C 357 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131270 restraints weight = 17091.333| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.57 r_work: 0.3111 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18017 Z= 0.128 Angle : 0.602 9.276 24493 Z= 0.300 Chirality : 0.047 0.647 2672 Planarity : 0.004 0.048 3102 Dihedral : 7.934 81.654 3055 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.22 % Allowed : 19.27 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2121 helix: 0.91 (0.27), residues: 393 sheet: 0.05 (0.22), residues: 543 loop : -0.87 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 33 HIS 0.007 0.001 HIS A 277 PHE 0.014 0.002 PHE A 245 TYR 0.014 0.001 TYR B 168 ARG 0.004 0.000 ARG G 96 Details of bonding type rmsd link_BETA2-3 : bond 0.00730 ( 3) link_BETA2-3 : angle 5.43328 ( 9) link_NAG-ASN : bond 0.00736 ( 12) link_NAG-ASN : angle 3.79041 ( 36) link_BETA1-2 : bond 0.00099 ( 3) link_BETA1-2 : angle 1.21683 ( 9) link_BETA1-4 : bond 0.00321 ( 9) link_BETA1-4 : angle 2.83114 ( 27) link_ALPHA1-3 : bond 0.00730 ( 3) link_ALPHA1-3 : angle 1.08488 ( 9) hydrogen bonds : bond 0.03649 ( 636) hydrogen bonds : angle 5.10821 ( 1746) SS BOND : bond 0.00250 ( 21) SS BOND : angle 2.41195 ( 42) covalent geometry : bond 0.00293 (17966) covalent geometry : angle 0.55890 (24361) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.5858 (t70) REVERT: A 75 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8718 (mm) REVERT: A 230 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8964 (mtt) REVERT: A 349 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7307 (mm110) REVERT: A 384 ASN cc_start: 0.7619 (m-40) cc_final: 0.7226 (m110) REVERT: A 392 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7358 (mttm) REVERT: A 475 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.4497 (m-80) REVERT: A 484 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6194 (mm-30) REVERT: B 12 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6006 (t70) REVERT: B 301 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7440 (mmt) REVERT: B 371 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.3713 (mp0) REVERT: B 392 ASN cc_start: 0.7805 (m-40) cc_final: 0.7487 (m110) REVERT: B 458 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6340 (tttm) REVERT: B 483 TYR cc_start: 0.4687 (OUTLIER) cc_final: 0.4346 (m-80) REVERT: C 24 MET cc_start: 0.7935 (mtt) cc_final: 0.7594 (mtm) REVERT: C 186 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.5798 (t0) REVERT: C 319 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8813 (mttm) REVERT: C 371 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5090 (pm20) REVERT: C 392 ASN cc_start: 0.7692 (m-40) cc_final: 0.7315 (m110) REVERT: H 40 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.6575 (mpp) REVERT: I 39 MET cc_start: 0.7541 (mmt) cc_final: 0.7300 (mmm) REVERT: I 70 GLU cc_start: 0.7341 (tt0) cc_final: 0.6863 (tm-30) REVERT: I 81 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6720 (pt0) REVERT: I 100 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: K 39 MET cc_start: 0.7496 (mmt) cc_final: 0.6853 (mmt) REVERT: K 65 SER cc_start: 0.8216 (p) cc_final: 0.7979 (m) REVERT: K 70 GLU cc_start: 0.7389 (tt0) cc_final: 0.6855 (mm-30) REVERT: K 81 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6532 (pt0) REVERT: L 70 GLU cc_start: 0.7412 (tt0) cc_final: 0.6774 (mm-30) REVERT: L 100 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7292 (pm20) outliers start: 60 outliers final: 33 residues processed: 250 average time/residue: 1.7354 time to fit residues: 488.9784 Evaluate side-chains 253 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 283 GLN A 405 ASN A 406 ASN B 285 HIS B 413 ASN C 287 ASN C 357 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.182053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127646 restraints weight = 16936.903| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.45 r_work: 0.3055 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18017 Z= 0.183 Angle : 0.671 14.207 24493 Z= 0.332 Chirality : 0.049 0.787 2672 Planarity : 0.004 0.051 3102 Dihedral : 8.050 83.110 3054 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.22 % Allowed : 19.22 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2121 helix: 0.89 (0.27), residues: 390 sheet: 0.04 (0.22), residues: 543 loop : -0.88 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 33 HIS 0.007 0.001 HIS A 277 PHE 0.013 0.002 PHE C 412 TYR 0.018 0.002 TYR A 11 ARG 0.005 0.000 ARG G 96 Details of bonding type rmsd link_BETA2-3 : bond 0.00908 ( 3) link_BETA2-3 : angle 5.86957 ( 9) link_NAG-ASN : bond 0.00769 ( 12) link_NAG-ASN : angle 4.32980 ( 36) link_BETA1-2 : bond 0.00190 ( 3) link_BETA1-2 : angle 1.36268 ( 9) link_BETA1-4 : bond 0.00381 ( 9) link_BETA1-4 : angle 3.00170 ( 27) link_ALPHA1-3 : bond 0.00525 ( 3) link_ALPHA1-3 : angle 1.23702 ( 9) hydrogen bonds : bond 0.03988 ( 636) hydrogen bonds : angle 5.24780 ( 1746) SS BOND : bond 0.00191 ( 21) SS BOND : angle 3.43740 ( 42) covalent geometry : bond 0.00429 (17966) covalent geometry : angle 0.61717 (24361) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.5841 (t70) REVERT: A 75 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8715 (mm) REVERT: A 230 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.9002 (mtt) REVERT: A 349 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7300 (mm110) REVERT: A 384 ASN cc_start: 0.7639 (m-40) cc_final: 0.7260 (m110) REVERT: A 392 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7334 (mttm) REVERT: A 475 TYR cc_start: 0.5089 (OUTLIER) cc_final: 0.4436 (m-80) REVERT: A 484 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: B 12 HIS cc_start: 0.7189 (OUTLIER) cc_final: 0.6057 (t70) REVERT: B 301 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7558 (mmt) REVERT: B 371 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.3703 (mp0) REVERT: B 392 ASN cc_start: 0.7847 (m-40) cc_final: 0.7534 (m110) REVERT: B 403 THR cc_start: 0.7529 (p) cc_final: 0.7264 (m) REVERT: B 458 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6413 (tttm) REVERT: B 483 TYR cc_start: 0.4729 (OUTLIER) cc_final: 0.4388 (m-80) REVERT: C 24 MET cc_start: 0.7952 (mtt) cc_final: 0.7612 (mtm) REVERT: C 186 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.5841 (t0) REVERT: C 319 LYS cc_start: 0.9107 (mtmt) cc_final: 0.8805 (mttm) REVERT: C 371 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5132 (pm20) REVERT: C 392 ASN cc_start: 0.7736 (m-40) cc_final: 0.7358 (m110) REVERT: C 444 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6755 (mtp) REVERT: H 40 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.6551 (mpp) REVERT: I 39 MET cc_start: 0.7523 (mmt) cc_final: 0.7284 (mmm) REVERT: I 70 GLU cc_start: 0.7416 (tt0) cc_final: 0.6910 (tm-30) REVERT: I 81 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6743 (pt0) REVERT: I 100 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: K 39 MET cc_start: 0.7484 (mmt) cc_final: 0.6844 (mmt) REVERT: K 65 SER cc_start: 0.8225 (p) cc_final: 0.7971 (m) REVERT: K 70 GLU cc_start: 0.7438 (tt0) cc_final: 0.6881 (mm-30) REVERT: K 81 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6552 (pt0) REVERT: K 100 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7210 (pm20) REVERT: L 70 GLU cc_start: 0.7545 (tt0) cc_final: 0.6858 (mm-30) REVERT: L 100 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7295 (pm20) outliers start: 60 outliers final: 38 residues processed: 248 average time/residue: 1.7129 time to fit residues: 475.2026 Evaluate side-chains 260 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 483 TYR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 132 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 405 ASN B 285 HIS B 357 GLN B 413 ASN C 357 GLN H 81 GLN I 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.182060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127931 restraints weight = 16983.026| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.53 r_work: 0.3068 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18017 Z= 0.177 Angle : 0.666 13.228 24493 Z= 0.330 Chirality : 0.049 0.757 2672 Planarity : 0.004 0.051 3102 Dihedral : 8.089 83.870 3054 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.17 % Allowed : 19.27 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2121 helix: 0.85 (0.27), residues: 390 sheet: 0.04 (0.22), residues: 543 loop : -0.88 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 33 HIS 0.007 0.001 HIS B 285 PHE 0.013 0.002 PHE C 412 TYR 0.016 0.002 TYR B 168 ARG 0.005 0.000 ARG G 96 Details of bonding type rmsd link_BETA2-3 : bond 0.00871 ( 3) link_BETA2-3 : angle 5.90447 ( 9) link_NAG-ASN : bond 0.00746 ( 12) link_NAG-ASN : angle 4.22174 ( 36) link_BETA1-2 : bond 0.00198 ( 3) link_BETA1-2 : angle 1.37241 ( 9) link_BETA1-4 : bond 0.00375 ( 9) link_BETA1-4 : angle 3.00814 ( 27) link_ALPHA1-3 : bond 0.00563 ( 3) link_ALPHA1-3 : angle 1.21899 ( 9) hydrogen bonds : bond 0.03969 ( 636) hydrogen bonds : angle 5.29752 ( 1746) SS BOND : bond 0.00225 ( 21) SS BOND : angle 3.28461 ( 42) covalent geometry : bond 0.00415 (17966) covalent geometry : angle 0.61409 (24361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22837.87 seconds wall clock time: 405 minutes 24.55 seconds (24324.55 seconds total)