Starting phenix.real_space_refine on Tue Jan 21 22:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ekf_48120/01_2025/9ekf_48120_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ekf_48120/01_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_48120/01_2025/9ekf_48120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ekf_48120/01_2025/9ekf_48120.map" model { file = "/net/cci-nas-00/data/ceres_data/9ekf_48120/01_2025/9ekf_48120_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ekf_48120/01_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-5571/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: 10.71, per 1000 atoms: 0.61 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: 4.85 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: 2.37 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: 6.86 Time building geometry restraints manager: 5.54 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.070 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.110 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.750 ------------------------------------------------------------------------------- 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 17966 Z= 0.334 Angle : 0.874 12.324 24361 Z= 0.529 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 *********************** 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 : 1.780 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: 1.3815 time to fit residues: 409.3152 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 : 1.773 ------------------------------------------------------------------------------- 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 = 65)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136719 restraints weight = 16749.868| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.20 r_work: 0.3307 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 17966 Z= 0.355 Angle : 0.675 12.641 24361 Z= 0.348 Chirality : 0.053 1.078 2672 Planarity : 0.005 0.059 3102 Dihedral : 8.945 85.339 3074 Min Nonbonded Distance : 2.539 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 *********************** 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 : 2.023 Fit side-chains REVERT: A 75 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 311 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8809 (mttm) REVERT: A 384 ASN cc_start: 0.7845 (m-40) cc_final: 0.7498 (m110) REVERT: A 392 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7357 (mttp) REVERT: A 453 TYR cc_start: 0.7386 (t80) cc_final: 0.7160 (t80) REVERT: A 483 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5441 (mpt) REVERT: B 12 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6033 (t70) REVERT: B 273 ASP cc_start: 0.8193 (t0) cc_final: 0.7734 (t70) REVERT: B 319 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8579 (mtmm) REVERT: B 392 ASN cc_start: 0.8018 (m-40) cc_final: 0.7680 (m110) REVERT: B 483 TYR cc_start: 0.4735 (OUTLIER) cc_final: 0.4264 (m-80) REVERT: C 186 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.6012 (t0) REVERT: C 319 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8808 (mttm) REVERT: C 357 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6902 (mm110) REVERT: C 392 ASN cc_start: 0.7897 (m-40) cc_final: 0.7524 (m110) REVERT: C 400 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7374 (mttp) REVERT: C 426 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8981 (tmm) REVERT: C 447 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: C 451 ASP cc_start: 0.7399 (m-30) cc_final: 0.7170 (m-30) REVERT: C 492 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6279 (pm20) REVERT: D 40 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.6778 (mpp) REVERT: G 40 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.6476 (mpp) REVERT: H 40 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.6667 (mpp) REVERT: H 81 GLN cc_start: 0.7807 (mt0) cc_final: 0.6853 (mt0) REVERT: H 101 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7809 (mt-10) REVERT: I 70 GLU cc_start: 0.7471 (tt0) cc_final: 0.7069 (tm-30) REVERT: K 70 GLU cc_start: 0.7511 (tt0) cc_final: 0.7112 (mm-30) REVERT: K 81 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6775 (pt0) REVERT: L 61 ARG cc_start: 0.7378 (ptt90) cc_final: 0.7178 (ptt-90) REVERT: L 70 GLU cc_start: 0.7632 (tt0) cc_final: 0.7069 (mm-30) REVERT: L 81 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6455 (pm20) outliers start: 77 outliers final: 32 residues processed: 282 average time/residue: 1.3101 time to fit residues: 413.9971 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 : 2.014 ------------------------------------------------------------------------------- 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: 7.9990 chunk 64 optimal weight: 0.4980 chunk 87 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 106 optimal weight: 0.0370 chunk 183 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN B 285 HIS G 81 GLN G 99 HIS I 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.181288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128471 restraints weight = 16957.209| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.49 r_work: 0.3101 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17966 Z= 0.343 Angle : 0.659 11.576 24361 Z= 0.339 Chirality : 0.057 1.484 2672 Planarity : 0.005 0.057 3102 Dihedral : 8.717 85.570 3060 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.19 % Allowed : 16.48 % Favored : 79.33 % 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: -0.80 (0.17), residues: 2121 helix: 0.56 (0.27), residues: 388 sheet: 0.12 (0.23), residues: 503 loop : -1.20 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 33 HIS 0.009 0.002 HIS D 99 PHE 0.016 0.002 PHE B 345 TYR 0.017 0.002 TYR B 168 ARG 0.006 0.000 ARG C 509 *********************** 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 297 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 219 time to evaluate : 1.961 Fit side-chains REVERT: A 75 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 311 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8780 (mttp) REVERT: A 373 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5558 (pt0) REVERT: A 384 ASN cc_start: 0.7753 (m-40) cc_final: 0.7356 (m110) REVERT: A 392 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7343 (mttm) REVERT: A 395 THR cc_start: 0.7859 (p) cc_final: 0.7658 (m) REVERT: A 406 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8413 (t0) REVERT: A 483 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5296 (mpt) REVERT: A 484 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: B 12 HIS cc_start: 0.6809 (OUTLIER) cc_final: 0.5699 (t70) REVERT: B 185 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8857 (p) REVERT: B 273 ASP cc_start: 0.8059 (t0) cc_final: 0.7502 (t70) REVERT: B 301 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7492 (mmt) REVERT: B 319 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8531 (mtmm) REVERT: B 381 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: B 392 ASN cc_start: 0.7882 (m-40) cc_final: 0.7545 (m110) REVERT: B 458 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6687 (tttm) REVERT: B 483 TYR cc_start: 0.4753 (OUTLIER) cc_final: 0.4417 (m-80) REVERT: C 23 ILE cc_start: 0.7686 (mp) cc_final: 0.7306 (mm) REVERT: C 24 MET cc_start: 0.7976 (mtt) cc_final: 0.7608 (mtm) REVERT: C 186 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.5972 (t0) REVERT: C 230 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9127 (mtt) REVERT: C 319 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8761 (mttm) REVERT: C 357 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6739 (mm110) REVERT: C 392 ASN cc_start: 0.7789 (m-40) cc_final: 0.7395 (m110) REVERT: C 444 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6596 (mtp) REVERT: C 447 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: C 451 ASP cc_start: 0.7373 (m-30) cc_final: 0.7110 (m-30) REVERT: C 492 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: D 40 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.6671 (mpp) REVERT: G 40 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.6397 (mpp) REVERT: H 40 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.6520 (mpp) REVERT: H 89 MET cc_start: 0.8888 (tpt) cc_final: 0.8199 (tpt) REVERT: H 101 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7687 (mt-10) REVERT: I 39 MET cc_start: 0.7387 (mmt) cc_final: 0.7137 (mmm) REVERT: I 70 GLU cc_start: 0.7435 (tt0) cc_final: 0.6960 (tm-30) REVERT: I 81 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: I 100 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: K 65 SER cc_start: 0.8229 (p) cc_final: 0.7934 (m) REVERT: K 70 GLU cc_start: 0.7477 (tt0) cc_final: 0.6982 (mm-30) REVERT: K 81 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6642 (pt0) REVERT: K 100 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: L 70 GLU cc_start: 0.7521 (tt0) cc_final: 0.6917 (mm-30) REVERT: L 100 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7307 (pm20) outliers start: 78 outliers final: 30 residues processed: 274 average time/residue: 1.3150 time to fit residues: 403.2729 Evaluate side-chains 259 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 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 406 ASN 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 139 CYS Chi-restraints excluded: chain B residue 185 SER 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 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 329 LEU 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 K residue 100 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 112 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 93 optimal weight: 0.0470 chunk 106 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN B 41 HIS B 285 HIS B 357 GLN G 81 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 = 0.4014 r_free = 0.4014 target = 0.181875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130130 restraints weight = 16902.818| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.41 r_work: 0.3121 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17966 Z= 0.280 Angle : 0.619 9.868 24361 Z= 0.318 Chirality : 0.051 1.000 2672 Planarity : 0.004 0.054 3102 Dihedral : 8.528 84.696 3060 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.40 % Allowed : 16.53 % Favored : 79.07 % 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: -0.70 (0.17), residues: 2121 helix: 0.65 (0.27), residues: 392 sheet: 0.15 (0.22), residues: 513 loop : -1.13 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 33 HIS 0.009 0.001 HIS G 99 PHE 0.013 0.002 PHE C 345 TYR 0.014 0.002 TYR B 168 ARG 0.002 0.000 ARG A 220 *********************** 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 304 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 222 time to evaluate : 1.798 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7069 (tt0) cc_final: 0.6829 (tt0) REVERT: A 75 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8685 (mm) REVERT: A 176 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8818 (mp) REVERT: A 230 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9008 (mtt) REVERT: A 311 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8809 (mttp) REVERT: A 373 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5474 (mt-10) REVERT: A 384 ASN cc_start: 0.7796 (m-40) cc_final: 0.7419 (m110) REVERT: A 392 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7419 (mttm) REVERT: A 395 THR cc_start: 0.7861 (p) cc_final: 0.7661 (m) REVERT: A 475 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4773 (m-80) REVERT: A 483 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5487 (mpt) REVERT: B 12 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.5749 (t70) REVERT: B 273 ASP cc_start: 0.8031 (t0) cc_final: 0.7479 (t70) REVERT: B 301 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7484 (mmt) REVERT: B 371 GLU cc_start: 0.5465 (OUTLIER) cc_final: 0.3796 (mt-10) REVERT: B 381 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: B 392 ASN cc_start: 0.7926 (m-40) cc_final: 0.7610 (m110) REVERT: B 458 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6665 (tttm) REVERT: B 483 TYR cc_start: 0.4707 (OUTLIER) cc_final: 0.4377 (m-80) REVERT: C 24 MET cc_start: 0.7991 (mtt) cc_final: 0.7664 (mtm) REVERT: C 186 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.5951 (t0) REVERT: C 319 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8797 (mttm) REVERT: C 392 ASN cc_start: 0.7830 (m-40) cc_final: 0.7456 (m110) REVERT: C 444 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6636 (mtp) REVERT: C 451 ASP cc_start: 0.7415 (m-30) cc_final: 0.7190 (m-30) REVERT: C 492 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: D 40 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.6708 (mpp) REVERT: G 40 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.6499 (mpp) REVERT: H 40 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.6550 (mpp) REVERT: H 89 MET cc_start: 0.8876 (tpt) cc_final: 0.8229 (tpt) REVERT: I 39 MET cc_start: 0.7439 (mmt) cc_final: 0.7173 (mmm) REVERT: I 70 GLU cc_start: 0.7482 (tt0) cc_final: 0.7038 (tm-30) REVERT: I 81 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6772 (pt0) REVERT: I 100 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: K 39 MET cc_start: 0.7340 (mmt) cc_final: 0.6702 (mmt) REVERT: K 65 SER cc_start: 0.8224 (p) cc_final: 0.7959 (m) REVERT: K 70 GLU cc_start: 0.7528 (tt0) cc_final: 0.7058 (mm-30) REVERT: K 81 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: K 100 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: L 70 GLU cc_start: 0.7503 (tt0) cc_final: 0.6909 (mm-30) REVERT: L 81 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6362 (pm20) REVERT: L 100 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7352 (pm20) outliers start: 82 outliers final: 35 residues processed: 277 average time/residue: 1.3056 time to fit residues: 405.0692 Evaluate side-chains 271 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 230 MET 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 30 VAL Chi-restraints excluded: chain B residue 139 CYS 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 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 323 LEU 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 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 K residue 100 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 71 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 178 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 405 ASN A 406 ASN B 285 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN 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 = 0.4014 r_free = 0.4014 target = 0.181854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128198 restraints weight = 17065.182| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.57 r_work: 0.3029 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17966 Z= 0.284 Angle : 0.632 13.819 24361 Z= 0.323 Chirality : 0.054 1.214 2672 Planarity : 0.004 0.054 3102 Dihedral : 8.591 84.570 3060 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.19 % Allowed : 17.39 % Favored : 78.42 % 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: -0.64 (0.17), residues: 2121 helix: 0.70 (0.27), residues: 393 sheet: 0.16 (0.22), residues: 513 loop : -1.08 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 33 HIS 0.007 0.001 HIS G 99 PHE 0.013 0.002 PHE C 345 TYR 0.017 0.002 TYR B 168 ARG 0.003 0.000 ARG C 417 *********************** 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 300 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 222 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6086 (t70) REVERT: A 25 GLU cc_start: 0.7117 (tt0) cc_final: 0.6875 (tt0) REVERT: A 75 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8689 (mm) REVERT: A 176 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8815 (mp) REVERT: A 230 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9001 (mtt) REVERT: A 311 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8838 (mttp) REVERT: A 373 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5528 (mt-10) REVERT: A 384 ASN cc_start: 0.7692 (m-40) cc_final: 0.7293 (m110) REVERT: A 392 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7257 (mttt) REVERT: A 475 TYR cc_start: 0.5371 (OUTLIER) cc_final: 0.4688 (m-80) REVERT: A 483 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5288 (mpt) REVERT: A 484 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6173 (pm20) REVERT: B 12 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.5791 (t70) REVERT: B 273 ASP cc_start: 0.8045 (t0) cc_final: 0.7463 (t70) REVERT: B 301 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7471 (mmt) REVERT: B 371 GLU cc_start: 0.5309 (OUTLIER) cc_final: 0.4477 (pt0) REVERT: B 392 ASN cc_start: 0.7853 (m-40) cc_final: 0.7519 (m110) REVERT: B 458 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6548 (tttm) REVERT: B 483 TYR cc_start: 0.4649 (OUTLIER) cc_final: 0.4305 (m-80) REVERT: C 23 ILE cc_start: 0.7612 (mp) cc_final: 0.7250 (mm) REVERT: C 24 MET cc_start: 0.7916 (mtt) cc_final: 0.7568 (mtm) REVERT: C 186 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.5922 (t0) REVERT: C 319 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8822 (mttm) REVERT: C 371 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.4942 (pm20) REVERT: C 392 ASN cc_start: 0.7726 (m-40) cc_final: 0.7331 (m110) REVERT: C 444 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6680 (mtp) REVERT: C 447 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: C 451 ASP cc_start: 0.7314 (m-30) cc_final: 0.7062 (m-30) REVERT: C 492 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6375 (pm20) REVERT: D 40 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.6627 (mpp) REVERT: G 40 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.6412 (mpp) REVERT: H 40 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.6500 (mpp) REVERT: H 89 MET cc_start: 0.8848 (tpt) cc_final: 0.8215 (tpt) REVERT: I 39 MET cc_start: 0.7455 (mmt) cc_final: 0.7159 (mmm) REVERT: I 70 GLU cc_start: 0.7454 (tt0) cc_final: 0.6968 (tm-30) REVERT: I 81 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: I 100 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: K 39 MET cc_start: 0.7300 (mmt) cc_final: 0.6682 (mmt) REVERT: K 65 SER cc_start: 0.8171 (p) cc_final: 0.7912 (m) REVERT: K 70 GLU cc_start: 0.7477 (tt0) cc_final: 0.6928 (mm-30) REVERT: K 81 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: K 100 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: L 70 GLU cc_start: 0.7513 (tt0) cc_final: 0.6882 (mm-30) REVERT: L 81 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6351 (pm20) REVERT: L 100 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7246 (pm20) outliers start: 78 outliers final: 40 residues processed: 275 average time/residue: 1.2961 time to fit residues: 399.5972 Evaluate side-chains 280 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 26 LYS 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 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 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 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 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 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 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 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 K residue 100 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 168 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 121 optimal weight: 0.0010 chunk 96 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 349 GLN A 405 ASN A 406 ASN B 285 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4021 r_free = 0.4021 target = 0.182590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135412 restraints weight = 17030.903| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.20 r_work: 0.3105 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17966 Z= 0.236 Angle : 0.600 8.505 24361 Z= 0.309 Chirality : 0.049 0.840 2672 Planarity : 0.004 0.051 3102 Dihedral : 8.387 83.539 3060 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.13 % Allowed : 18.14 % Favored : 77.72 % 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: -0.55 (0.17), residues: 2121 helix: 0.78 (0.27), residues: 392 sheet: 0.21 (0.22), residues: 513 loop : -1.02 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 33 HIS 0.006 0.001 HIS A 277 PHE 0.010 0.002 PHE A 245 TYR 0.021 0.002 TYR G 27 ARG 0.003 0.000 ARG G 96 *********************** 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 291 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 214 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6048 (t70) REVERT: A 75 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8676 (mm) REVERT: A 176 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8778 (mp) REVERT: A 230 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8940 (mtt) REVERT: A 311 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8744 (mttp) REVERT: A 384 ASN cc_start: 0.7685 (m-40) cc_final: 0.7293 (m110) REVERT: A 392 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7427 (mttm) REVERT: A 475 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.4733 (m-80) REVERT: A 484 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.6029 (pm20) REVERT: B 12 HIS cc_start: 0.6697 (OUTLIER) cc_final: 0.5749 (t70) REVERT: B 273 ASP cc_start: 0.7807 (t0) cc_final: 0.7257 (t70) REVERT: B 301 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7323 (mmt) REVERT: B 371 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.3703 (mt-10) REVERT: B 392 ASN cc_start: 0.7830 (m-40) cc_final: 0.7497 (m110) REVERT: B 458 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6471 (tttm) REVERT: B 483 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.4235 (m-80) REVERT: C 24 MET cc_start: 0.7869 (mtt) cc_final: 0.7527 (mtm) REVERT: C 186 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.5859 (t0) REVERT: C 319 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8711 (mttm) REVERT: C 371 GLU cc_start: 0.5447 (OUTLIER) cc_final: 0.4983 (pm20) REVERT: C 392 ASN cc_start: 0.7693 (m-40) cc_final: 0.7311 (m110) REVERT: C 444 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6729 (mtp) REVERT: C 492 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: D 101 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7702 (mt-10) REVERT: G 40 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.6487 (mpp) REVERT: H 40 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.6543 (mpp) REVERT: H 89 MET cc_start: 0.8773 (tpt) cc_final: 0.8106 (tpt) REVERT: I 39 MET cc_start: 0.7433 (mmt) cc_final: 0.7200 (mmt) REVERT: I 70 GLU cc_start: 0.7356 (tt0) cc_final: 0.6933 (tm-30) REVERT: I 81 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6616 (pt0) REVERT: I 100 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: K 39 MET cc_start: 0.7310 (mmt) cc_final: 0.6656 (mmt) REVERT: K 65 SER cc_start: 0.8192 (p) cc_final: 0.7935 (m) REVERT: K 70 GLU cc_start: 0.7367 (tt0) cc_final: 0.6916 (mm-30) REVERT: K 81 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6521 (pt0) REVERT: K 100 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: L 70 GLU cc_start: 0.7354 (tt0) cc_final: 0.6775 (mm-30) REVERT: L 81 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: L 100 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7289 (pm20) outliers start: 77 outliers final: 40 residues processed: 264 average time/residue: 1.3173 time to fit residues: 390.9406 Evaluate side-chains 273 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS 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 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 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 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 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 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 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 10 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 5 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=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: 0.6980 chunk 183 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 349 GLN A 405 ASN A 406 ASN B 285 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4025 r_free = 0.4025 target = 0.183000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3422 r_free = 0.3422 target = 0.130278 restraints weight = 16985.394| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.53 r_work: 0.3131 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17966 Z= 0.229 Angle : 0.589 8.946 24361 Z= 0.303 Chirality : 0.050 1.030 2672 Planarity : 0.004 0.051 3102 Dihedral : 8.269 82.957 3060 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.92 % Allowed : 18.57 % 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: -0.55 (0.17), residues: 2121 helix: 0.83 (0.27), residues: 393 sheet: -0.01 (0.22), residues: 543 loop : -0.93 (0.16), residues: 1185 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 0.010 0.002 PHE A 245 TYR 0.015 0.001 TYR B 168 ARG 0.002 0.000 ARG C 417 *********************** 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 285 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 212 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8020 (t70) REVERT: A 75 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 176 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8786 (mp) REVERT: A 230 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8974 (mtt) REVERT: A 311 LYS cc_start: 0.9071 (mtmt) cc_final: 0.8831 (mttp) REVERT: A 384 ASN cc_start: 0.7746 (m-40) cc_final: 0.7362 (m110) REVERT: A 392 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7395 (mttm) REVERT: A 475 TYR cc_start: 0.5340 (OUTLIER) cc_final: 0.4678 (m-80) REVERT: A 484 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.6176 (mm-30) REVERT: B 301 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7452 (mmt) REVERT: B 371 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.3698 (mt-10) REVERT: B 392 ASN cc_start: 0.7880 (m-40) cc_final: 0.7564 (m110) REVERT: B 458 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6548 (tttm) REVERT: B 483 TYR cc_start: 0.4665 (OUTLIER) cc_final: 0.4276 (m-80) REVERT: C 24 MET cc_start: 0.7917 (mtt) cc_final: 0.7576 (mtm) REVERT: C 186 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.5898 (t0) REVERT: C 319 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8787 (mttm) REVERT: C 371 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.5048 (pm20) REVERT: C 392 ASN cc_start: 0.7732 (m-40) cc_final: 0.7360 (m110) REVERT: C 417 ARG cc_start: 0.8766 (mmt-90) cc_final: 0.8552 (mmp80) REVERT: C 444 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6729 (mtp) REVERT: D 101 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7779 (mt-10) REVERT: G 40 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.6517 (mpp) REVERT: H 40 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.6530 (mpp) REVERT: H 89 MET cc_start: 0.8836 (tpt) cc_final: 0.8188 (tpt) REVERT: I 39 MET cc_start: 0.7519 (mmt) cc_final: 0.7243 (mmm) REVERT: I 70 GLU cc_start: 0.7371 (tt0) cc_final: 0.6909 (tm-30) REVERT: I 81 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: I 100 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: K 39 MET cc_start: 0.7376 (mmt) cc_final: 0.6688 (mmt) REVERT: K 65 SER cc_start: 0.8183 (p) cc_final: 0.7930 (m) REVERT: K 70 GLU cc_start: 0.7427 (tt0) cc_final: 0.6918 (mm-30) REVERT: K 81 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6552 (pt0) REVERT: L 70 GLU cc_start: 0.7415 (tt0) cc_final: 0.6791 (mm-30) REVERT: L 81 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6300 (pm20) REVERT: L 100 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7334 (pm20) outliers start: 73 outliers final: 40 residues processed: 263 average time/residue: 1.3261 time to fit residues: 390.6358 Evaluate side-chains 270 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 72 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 198 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 349 GLN A 405 ASN A 406 ASN ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 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 = 0.3991 r_free = 0.3991 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127090 restraints weight = 16941.163| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.44 r_work: 0.3066 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 17966 Z= 0.444 Angle : 0.701 9.449 24361 Z= 0.361 Chirality : 0.052 0.437 2672 Planarity : 0.005 0.058 3102 Dihedral : 8.885 87.857 3059 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.81 % Allowed : 18.73 % Favored : 77.46 % 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: -0.65 (0.17), residues: 2121 helix: 0.72 (0.27), residues: 388 sheet: 0.07 (0.22), residues: 523 loop : -1.05 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 33 HIS 0.008 0.002 HIS G 99 PHE 0.019 0.003 PHE C 412 TYR 0.021 0.002 TYR B 168 ARG 0.004 0.001 ARG G 50 *********************** 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 283 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 212 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6290 (t70) REVERT: A 25 GLU cc_start: 0.7003 (tt0) cc_final: 0.6781 (tt0) REVERT: A 75 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8645 (mm) REVERT: A 116 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: A 311 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8830 (mttp) REVERT: A 384 ASN cc_start: 0.7777 (m-40) cc_final: 0.7396 (m110) REVERT: A 392 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7330 (mttt) REVERT: A 475 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4632 (m-80) REVERT: A 484 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: B 273 ASP cc_start: 0.8134 (t0) cc_final: 0.7590 (t70) REVERT: B 371 GLU cc_start: 0.5481 (OUTLIER) cc_final: 0.3776 (mt-10) REVERT: B 392 ASN cc_start: 0.8010 (m-40) cc_final: 0.7696 (m110) REVERT: B 458 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6667 (tttm) REVERT: B 483 TYR cc_start: 0.4785 (OUTLIER) cc_final: 0.4394 (m-80) REVERT: C 23 ILE cc_start: 0.7642 (mp) cc_final: 0.7242 (mm) REVERT: C 24 MET cc_start: 0.8026 (mtt) cc_final: 0.7696 (mtm) REVERT: C 186 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.5940 (t0) REVERT: C 319 LYS cc_start: 0.9077 (mtmt) cc_final: 0.8788 (mttm) REVERT: C 371 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5259 (pm20) REVERT: C 392 ASN cc_start: 0.7838 (m-40) cc_final: 0.7470 (m110) REVERT: D 101 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7828 (mt-10) REVERT: G 40 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.6460 (mpp) REVERT: H 40 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.6515 (mpp) REVERT: I 70 GLU cc_start: 0.7660 (tt0) cc_final: 0.7208 (tm-30) REVERT: I 100 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: K 39 MET cc_start: 0.7395 (mmt) cc_final: 0.6797 (mmt) REVERT: K 65 SER cc_start: 0.8238 (p) cc_final: 0.7962 (m) REVERT: K 70 GLU cc_start: 0.7667 (tt0) cc_final: 0.7166 (mm-30) REVERT: K 100 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: L 70 GLU cc_start: 0.7671 (tt0) cc_final: 0.7042 (mm-30) REVERT: L 100 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7347 (pm20) outliers start: 71 outliers final: 39 residues processed: 264 average time/residue: 1.2707 time to fit residues: 377.7045 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 : 1.890 ------------------------------------------------------------------------------- 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 187 ASN Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 235 THR 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 30 VAL 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 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 14 ASN 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 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 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 100 GLN 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: 5.9990 chunk 88 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 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 = 0.4029 r_free = 0.4029 target = 0.183252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127606 restraints weight = 17096.191| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.52 r_work: 0.3133 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17966 Z= 0.197 Angle : 0.580 8.068 24361 Z= 0.300 Chirality : 0.046 0.349 2672 Planarity : 0.004 0.049 3102 Dihedral : 8.391 83.820 3057 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.90 % Allowed : 19.75 % Favored : 77.35 % 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: -0.47 (0.18), residues: 2121 helix: 1.15 (0.28), residues: 374 sheet: -0.12 (0.22), residues: 549 loop : -0.87 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 33 HIS 0.007 0.001 HIS A 277 PHE 0.015 0.002 PHE A 245 TYR 0.017 0.001 TYR D 79 ARG 0.005 0.000 ARG L 54 *********************** 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 270 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 311 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8837 (mttp) REVERT: A 384 ASN cc_start: 0.7657 (m-40) cc_final: 0.7262 (m110) REVERT: A 392 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7380 (mttm) REVERT: A 475 TYR cc_start: 0.5148 (OUTLIER) cc_final: 0.4492 (m-80) REVERT: A 484 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6156 (mm-30) REVERT: B 12 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.6305 (t-90) REVERT: B 301 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7431 (mmt) REVERT: B 371 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.3742 (mt-10) REVERT: B 392 ASN cc_start: 0.7835 (m-40) cc_final: 0.7514 (m110) REVERT: B 458 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6448 (tttm) REVERT: B 483 TYR cc_start: 0.4724 (OUTLIER) cc_final: 0.4337 (m-80) REVERT: C 24 MET cc_start: 0.7873 (mtt) cc_final: 0.7536 (mtm) REVERT: C 186 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.5782 (t0) REVERT: C 319 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8765 (mttm) REVERT: C 371 GLU cc_start: 0.5423 (OUTLIER) cc_final: 0.4961 (pm20) REVERT: C 392 ASN cc_start: 0.7706 (m-40) cc_final: 0.7313 (m110) REVERT: C 417 ARG cc_start: 0.8754 (mmt-90) cc_final: 0.8531 (mmp80) REVERT: D 101 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7815 (mt-10) REVERT: H 40 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.6503 (mpp) REVERT: I 70 GLU cc_start: 0.7332 (tt0) cc_final: 0.6867 (tm-30) REVERT: I 100 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: K 65 SER cc_start: 0.8191 (p) cc_final: 0.7951 (m) REVERT: K 70 GLU cc_start: 0.7440 (tt0) cc_final: 0.6886 (mm-30) REVERT: K 100 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7187 (pm20) REVERT: L 70 GLU cc_start: 0.7497 (tt0) cc_final: 0.6833 (mm-30) REVERT: L 81 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6340 (pm20) REVERT: L 100 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7209 (pm20) outliers start: 54 outliers final: 33 residues processed: 254 average time/residue: 1.3238 time to fit residues: 376.4947 Evaluate side-chains 257 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 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 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 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 477 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 201 optimal weight: 0.0870 chunk 43 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- 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 A 406 ASN B 285 HIS B 413 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 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 = 0.4002 r_free = 0.4002 target = 0.180658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3396 r_free = 0.3396 target = 0.127872 restraints weight = 16961.075| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.61 r_work: 0.3075 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17966 Z= 0.353 Angle : 0.655 8.920 24361 Z= 0.338 Chirality : 0.050 0.407 2672 Planarity : 0.005 0.055 3102 Dihedral : 8.579 86.700 3055 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.95 % Allowed : 19.81 % Favored : 77.24 % 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: -0.54 (0.17), residues: 2121 helix: 1.08 (0.28), residues: 372 sheet: -0.16 (0.22), residues: 549 loop : -0.91 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 33 HIS 0.008 0.002 HIS A 277 PHE 0.016 0.003 PHE C 412 TYR 0.018 0.002 TYR B 168 ARG 0.005 0.001 ARG G 96 ********************** 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 266 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8707 (mm) REVERT: A 230 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9014 (mtt) REVERT: A 311 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8837 (mttp) REVERT: A 384 ASN cc_start: 0.7720 (m-40) cc_final: 0.7342 (m110) REVERT: A 392 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7409 (mttm) REVERT: A 475 TYR cc_start: 0.5132 (OUTLIER) cc_final: 0.4497 (m-80) REVERT: A 484 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6153 (mm-30) REVERT: B 273 ASP cc_start: 0.8076 (t0) cc_final: 0.7531 (t70) REVERT: B 301 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7669 (mmt) REVERT: B 371 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.3797 (mp0) REVERT: B 392 ASN cc_start: 0.7951 (m-40) cc_final: 0.7633 (m110) REVERT: B 458 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6584 (tttm) REVERT: B 483 TYR cc_start: 0.4784 (OUTLIER) cc_final: 0.4399 (m-80) REVERT: C 23 ILE cc_start: 0.7476 (mp) cc_final: 0.7045 (mm) REVERT: C 24 MET cc_start: 0.7992 (mtt) cc_final: 0.7677 (mtm) REVERT: C 186 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.5890 (t0) REVERT: C 319 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8776 (mttm) REVERT: C 371 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5252 (pm20) REVERT: C 392 ASN cc_start: 0.7732 (m-40) cc_final: 0.7350 (m110) REVERT: D 101 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 40 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.6526 (mpp) REVERT: I 70 GLU cc_start: 0.7484 (tt0) cc_final: 0.7024 (tm-30) REVERT: I 100 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: K 65 SER cc_start: 0.8226 (p) cc_final: 0.7967 (m) REVERT: K 70 GLU cc_start: 0.7667 (tt0) cc_final: 0.7162 (mm-30) REVERT: K 100 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7252 (pm20) REVERT: L 70 GLU cc_start: 0.7572 (tt0) cc_final: 0.6940 (mm-30) REVERT: L 100 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7305 (pm20) outliers start: 55 outliers final: 36 residues processed: 250 average time/residue: 1.2866 time to fit residues: 360.5737 Evaluate side-chains 255 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain A residue 235 THR 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 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 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 447 GLU Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL 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 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 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: 0.7980 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS B 413 ASN C 357 GLN H 6 GLN 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 = 0.4033 r_free = 0.4033 target = 0.183681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132192 restraints weight = 17065.767| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.43 r_work: 0.3147 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17966 Z= 0.193 Angle : 0.579 9.963 24361 Z= 0.298 Chirality : 0.048 0.672 2672 Planarity : 0.004 0.049 3102 Dihedral : 8.159 83.037 3055 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.47 % Allowed : 20.34 % Favored : 77.19 % 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: -0.41 (0.18), residues: 2121 helix: 1.19 (0.27), residues: 373 sheet: -0.08 (0.22), residues: 549 loop : -0.83 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 33 HIS 0.007 0.001 HIS A 277 PHE 0.016 0.002 PHE A 245 TYR 0.016 0.001 TYR A 11 ARG 0.004 0.000 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16649.25 seconds wall clock time: 294 minutes 3.57 seconds (17643.57 seconds total)