Starting phenix.real_space_refine on Thu May 15 09:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8on7_16981/05_2025/8on7_16981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8on7_16981/05_2025/8on7_16981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8on7_16981/05_2025/8on7_16981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8on7_16981/05_2025/8on7_16981.map" model { file = "/net/cci-nas-00/data/ceres_data/8on7_16981/05_2025/8on7_16981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8on7_16981/05_2025/8on7_16981.cif" } resolution = 2.5 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= 0.002 sd= 0.033 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 108 5.16 5 C 8289 2.51 5 N 2169 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13032 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4204 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 29, 'TRANS': 495} Chain breaks: 1 Chain: "B" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4204 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 29, 'TRANS': 495} Chain breaks: 1 Chain: "C" Number of atoms: 4204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4204 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 29, 'TRANS': 495} Chain breaks: 1 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.47, per 1000 atoms: 0.57 Number of scatterers: 13032 At special positions: 0 Unit cell: (107.31, 109.354, 135.926, 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 108 16.00 O 2466 8.00 N 2169 7.00 C 8289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 360 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 401 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 381 " distance=2.04 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 350 " distance=2.03 Simple disulfide: pdb=" SG CYS C 360 " - pdb=" SG CYS C 368 " 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=3, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 444 " " NAG A 603 " - " ASN A 460 " " NAG B 601 " - " ASN B 392 " " NAG B 602 " - " ASN B 444 " " NAG B 603 " - " ASN B 460 " " NAG C 601 " - " ASN C 392 " " NAG C 602 " - " ASN C 444 " " NAG C 603 " - " ASN C 460 " " NAG G 1 " - " ASN A 180 " " NAG H 1 " - " ASN A 299 " " NAG I 1 " - " ASN B 180 " " NAG J 1 " - " ASN B 299 " " NAG K 1 " - " ASN C 180 " " NAG L 1 " - " ASN C 299 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 47.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 27 through 58 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.628A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.901A pdb=" N PHE A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.631A pdb=" N CYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 365 through 390 removed outlier: 4.603A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.580A pdb=" N CYS A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 512 through 528 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 27 through 58 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.628A pdb=" N LYS B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.901A pdb=" N PHE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.631A pdb=" N CYS B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 365 through 390 removed outlier: 4.603A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 399 removed outlier: 3.580A pdb=" N CYS B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'B' and resid 512 through 528 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 27 through 58 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.628A pdb=" N LYS C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.901A pdb=" N PHE C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.630A pdb=" N CYS C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 365 through 390 removed outlier: 4.603A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 removed outlier: 3.579A pdb=" N CYS C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'C' and resid 512 through 528 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY A 218 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR A 174 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 220 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS A 172 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 222 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL A 484 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 486 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG A 289 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU A 488 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 291 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU A 490 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.777A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY B 218 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR B 174 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER B 220 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 172 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 222 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 68 removed outlier: 9.247A pdb=" N VAL B 484 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR B 486 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG B 289 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLU B 488 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 291 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU B 490 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 190 removed outlier: 6.778A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY C 218 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR C 174 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER C 220 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS C 172 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 222 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 68 removed outlier: 9.246A pdb=" N VAL C 484 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 486 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG C 289 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU C 488 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 291 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU C 490 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 190 removed outlier: 6.777A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1911 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: 3.74 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4176 1.35 - 1.47: 3312 1.47 - 1.59: 5709 1.59 - 1.71: 0 1.71 - 1.83: 162 Bond restraints: 13359 Sorted by residual: bond pdb=" N GLN C 344 " pdb=" CA GLN C 344 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.59e+00 bond pdb=" N GLN B 344 " pdb=" CA GLN B 344 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.47e+00 bond pdb=" N GLN A 344 " pdb=" CA GLN A 344 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.46e+00 bond pdb=" N ILE A 347 " pdb=" CA ILE A 347 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.24e-02 6.50e+03 6.80e+00 bond pdb=" N ILE C 347 " pdb=" CA ILE C 347 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.24e-02 6.50e+03 6.70e+00 ... (remaining 13354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 17457 1.73 - 3.46: 537 3.46 - 5.19: 71 5.19 - 6.92: 19 6.92 - 8.65: 6 Bond angle restraints: 18090 Sorted by residual: angle pdb=" N ASN B 346 " pdb=" CA ASN B 346 " pdb=" C ASN B 346 " ideal model delta sigma weight residual 113.20 108.20 5.00 1.21e+00 6.83e-01 1.71e+01 angle pdb=" N ASN C 346 " pdb=" CA ASN C 346 " pdb=" C ASN C 346 " ideal model delta sigma weight residual 113.20 108.21 4.99 1.21e+00 6.83e-01 1.70e+01 angle pdb=" N ASN A 346 " pdb=" CA ASN A 346 " pdb=" C ASN A 346 " ideal model delta sigma weight residual 113.20 108.21 4.99 1.21e+00 6.83e-01 1.70e+01 angle pdb=" CA PHE F 612 " pdb=" CB PHE F 612 " pdb=" CG PHE F 612 " ideal model delta sigma weight residual 113.80 117.45 -3.65 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA PHE D 612 " pdb=" CB PHE D 612 " pdb=" CG PHE D 612 " ideal model delta sigma weight residual 113.80 117.45 -3.65 1.00e+00 1.00e+00 1.33e+01 ... (remaining 18085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 7632 17.56 - 35.12: 540 35.12 - 52.67: 102 52.67 - 70.23: 36 70.23 - 87.79: 15 Dihedral angle restraints: 8325 sinusoidal: 3678 harmonic: 4647 Sorted by residual: dihedral pdb=" CA GLY B 294 " pdb=" C GLY B 294 " pdb=" N PRO B 295 " pdb=" CA PRO B 295 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY C 294 " pdb=" C GLY C 294 " pdb=" N PRO C 295 " pdb=" CA PRO C 295 " ideal model delta harmonic sigma weight residual -180.00 -160.79 -19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY A 294 " pdb=" C GLY A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 8322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1392 0.040 - 0.080: 388 0.080 - 0.120: 182 0.120 - 0.160: 18 0.160 - 0.200: 6 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CA MET A 229 " pdb=" N MET A 229 " pdb=" C MET A 229 " pdb=" CB MET A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA MET C 229 " pdb=" N MET C 229 " pdb=" C MET C 229 " pdb=" CB MET C 229 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET B 229 " pdb=" N MET B 229 " pdb=" C MET B 229 " pdb=" CB MET B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 1983 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 342 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C PRO A 342 " -0.051 2.00e-02 2.50e+03 pdb=" O PRO A 342 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 343 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 342 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C PRO C 342 " -0.050 2.00e-02 2.50e+03 pdb=" O PRO C 342 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 343 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 342 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C PRO B 342 " -0.050 2.00e-02 2.50e+03 pdb=" O PRO B 342 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 343 " 0.017 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 127 2.68 - 3.23: 12279 3.23 - 3.79: 20203 3.79 - 4.34: 28672 4.34 - 4.90: 46440 Nonbonded interactions: 107721 Sorted by model distance: nonbonded pdb=" O ASP C 302 " pdb=" OD1 ASP C 302 " model vdw 2.122 3.040 nonbonded pdb=" O ASP A 302 " pdb=" OD1 ASP A 302 " model vdw 2.123 3.040 nonbonded pdb=" O ASP B 302 " pdb=" OD1 ASP B 302 " model vdw 2.123 3.040 nonbonded pdb=" O ASP A 308 " pdb=" OD1 ASP A 308 " model vdw 2.191 3.040 nonbonded pdb=" O ASP C 308 " pdb=" OD1 ASP C 308 " model vdw 2.191 3.040 ... (remaining 107716 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.160 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 13407 Z= 0.264 Angle : 0.735 9.082 18201 Z= 0.394 Chirality : 0.045 0.200 1986 Planarity : 0.005 0.044 2325 Dihedral : 13.287 87.791 5253 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.21 % Allowed : 4.48 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.21), residues: 1569 helix: 1.27 (0.20), residues: 666 sheet: 1.70 (0.29), residues: 267 loop : 0.51 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 34 HIS 0.006 0.001 HIS C 376 PHE 0.023 0.002 PHE C 10 TYR 0.018 0.001 TYR B 118 ARG 0.005 0.001 ARG E 611 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 15) link_NAG-ASN : angle 3.39080 ( 45) link_BETA1-4 : bond 0.00599 ( 6) link_BETA1-4 : angle 1.62149 ( 18) hydrogen bonds : bond 0.15082 ( 661) hydrogen bonds : angle 6.37183 ( 1911) SS BOND : bond 0.00215 ( 24) SS BOND : angle 1.02601 ( 48) covalent geometry : bond 0.00385 (13359) covalent geometry : angle 0.71384 (18090) Misc. bond : bond 0.10909 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 462 time to evaluate : 1.592 Fit side-chains REVERT: A 31 ARG cc_start: 0.6652 (ttm170) cc_final: 0.6353 (ttm170) REVERT: A 50 SER cc_start: 0.7408 (t) cc_final: 0.6962 (p) REVERT: A 66 GLU cc_start: 0.8248 (pt0) cc_final: 0.7900 (pt0) REVERT: A 111 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 120 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7673 (mtmt) REVERT: A 125 TYR cc_start: 0.8118 (m-80) cc_final: 0.7865 (m-80) REVERT: A 200 LYS cc_start: 0.8133 (mttt) cc_final: 0.7894 (mmtp) REVERT: A 216 GLU cc_start: 0.7817 (mp0) cc_final: 0.7615 (mp0) REVERT: A 273 TYR cc_start: 0.8314 (m-80) cc_final: 0.7994 (m-80) REVERT: A 302 ASP cc_start: 0.7463 (t0) cc_final: 0.7189 (t0) REVERT: A 347 ILE cc_start: 0.7612 (mt) cc_final: 0.7214 (tp) REVERT: A 353 ASP cc_start: 0.7400 (p0) cc_final: 0.7138 (p0) REVERT: A 359 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6670 (mt-10) REVERT: A 388 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7409 (mtmm) REVERT: A 391 LYS cc_start: 0.8040 (mptt) cc_final: 0.7746 (mmtm) REVERT: A 425 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 438 LYS cc_start: 0.8124 (mttp) cc_final: 0.7920 (mttp) REVERT: A 445 LYS cc_start: 0.6808 (mtmt) cc_final: 0.6605 (mtmm) REVERT: B 16 MET cc_start: 0.7691 (mtp) cc_final: 0.7480 (mtm) REVERT: B 50 SER cc_start: 0.7790 (t) cc_final: 0.7247 (p) REVERT: B 51 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7048 (mt-10) REVERT: B 82 MET cc_start: 0.8625 (mtt) cc_final: 0.8263 (mtm) REVERT: B 111 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7485 (mt-10) REVERT: B 138 GLU cc_start: 0.7322 (mp0) cc_final: 0.6951 (mp0) REVERT: B 141 GLN cc_start: 0.8015 (mm110) cc_final: 0.7665 (mm-40) REVERT: B 235 GLU cc_start: 0.7934 (pt0) cc_final: 0.7696 (pt0) REVERT: B 326 TYR cc_start: 0.7648 (m-80) cc_final: 0.7176 (m-80) REVERT: B 347 ILE cc_start: 0.7773 (mt) cc_final: 0.7422 (tp) REVERT: B 360 CYS cc_start: 0.6970 (m) cc_final: 0.6707 (m) REVERT: B 362 PHE cc_start: 0.7976 (m-80) cc_final: 0.7754 (m-80) REVERT: B 388 LYS cc_start: 0.7449 (mtmt) cc_final: 0.7149 (mtmm) REVERT: B 391 LYS cc_start: 0.7650 (mptt) cc_final: 0.7352 (mmtp) REVERT: B 407 GLU cc_start: 0.7597 (tt0) cc_final: 0.7236 (tt0) REVERT: B 425 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 427 ASP cc_start: 0.7643 (m-30) cc_final: 0.7416 (m-30) REVERT: C 16 MET cc_start: 0.7647 (mtp) cc_final: 0.7365 (mtm) REVERT: C 29 MET cc_start: 0.7060 (mmm) cc_final: 0.6671 (mmm) REVERT: C 51 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6975 (mt-10) REVERT: C 66 GLU cc_start: 0.8010 (pt0) cc_final: 0.7758 (pt0) REVERT: C 120 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7423 (ttmm) REVERT: C 125 TYR cc_start: 0.7916 (m-80) cc_final: 0.7612 (m-80) REVERT: C 131 ASN cc_start: 0.8183 (m-40) cc_final: 0.7969 (m-40) REVERT: C 273 TYR cc_start: 0.8415 (m-80) cc_final: 0.8021 (m-80) REVERT: C 288 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7422 (mtp85) REVERT: C 301 SER cc_start: 0.7616 (t) cc_final: 0.7234 (p) REVERT: C 326 TYR cc_start: 0.7532 (m-80) cc_final: 0.7026 (m-80) REVERT: C 353 ASP cc_start: 0.7460 (p0) cc_final: 0.7089 (p0) REVERT: C 355 ASN cc_start: 0.7312 (m110) cc_final: 0.7106 (m110) REVERT: C 363 THR cc_start: 0.7910 (m) cc_final: 0.7468 (p) REVERT: C 380 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7401 (mtmm) REVERT: C 391 LYS cc_start: 0.8025 (mptt) cc_final: 0.7749 (mmtp) REVERT: C 396 MET cc_start: 0.7841 (mmp) cc_final: 0.7616 (mmm) REVERT: C 399 CYS cc_start: 0.6685 (m) cc_final: 0.6110 (m) REVERT: C 409 SER cc_start: 0.8032 (m) cc_final: 0.7603 (p) REVERT: C 411 ASP cc_start: 0.7836 (m-30) cc_final: 0.7588 (m-30) REVERT: C 418 LYS cc_start: 0.8500 (tttm) cc_final: 0.8292 (tttm) REVERT: C 448 THR cc_start: 0.7353 (m) cc_final: 0.7077 (t) REVERT: C 457 LYS cc_start: 0.7892 (mtpp) cc_final: 0.7676 (mtpp) REVERT: C 468 MET cc_start: 0.8417 (mmm) cc_final: 0.8216 (mmm) REVERT: C 480 ASP cc_start: 0.7009 (m-30) cc_final: 0.6726 (m-30) outliers start: 3 outliers final: 0 residues processed: 462 average time/residue: 1.4608 time to fit residues: 722.9535 Evaluate side-chains 359 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.0770 chunk 141 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 108 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 106 ASN B 108 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN C 106 ASN C 141 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 449 GLN C 463 ASN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115260 restraints weight = 17245.727| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.73 r_work: 0.3459 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13407 Z= 0.146 Angle : 0.634 13.371 18201 Z= 0.328 Chirality : 0.044 0.226 1986 Planarity : 0.005 0.049 2325 Dihedral : 5.310 36.698 2172 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.13 % Allowed : 11.37 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1569 helix: 1.52 (0.20), residues: 690 sheet: 1.41 (0.29), residues: 267 loop : 0.64 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 349 HIS 0.005 0.001 HIS A 17 PHE 0.018 0.001 PHE A 10 TYR 0.014 0.001 TYR C 118 ARG 0.006 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 15) link_NAG-ASN : angle 2.32043 ( 45) link_BETA1-4 : bond 0.00660 ( 6) link_BETA1-4 : angle 1.37923 ( 18) hydrogen bonds : bond 0.04616 ( 661) hydrogen bonds : angle 4.90231 ( 1911) SS BOND : bond 0.00938 ( 24) SS BOND : angle 2.46008 ( 48) covalent geometry : bond 0.00332 (13359) covalent geometry : angle 0.61060 (18090) Misc. bond : bond 0.00020 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7276 (mmm) cc_final: 0.7076 (mmm) REVERT: A 116 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7999 (mtm180) REVERT: A 138 GLU cc_start: 0.7782 (mp0) cc_final: 0.7575 (mp0) REVERT: A 216 GLU cc_start: 0.7765 (mp0) cc_final: 0.7561 (mp0) REVERT: A 271 GLU cc_start: 0.7798 (pt0) cc_final: 0.7576 (pt0) REVERT: A 273 TYR cc_start: 0.8480 (m-80) cc_final: 0.8256 (m-80) REVERT: A 302 ASP cc_start: 0.8124 (t0) cc_final: 0.7695 (t0) REVERT: A 347 ILE cc_start: 0.8228 (mt) cc_final: 0.8022 (tp) REVERT: A 353 ASP cc_start: 0.7696 (p0) cc_final: 0.7377 (p0) REVERT: A 465 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 21 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8169 (mttp) REVERT: B 121 LYS cc_start: 0.8310 (mtpp) cc_final: 0.8090 (tttm) REVERT: B 138 GLU cc_start: 0.7806 (mp0) cc_final: 0.7564 (mp0) REVERT: B 164 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8043 (mm-40) REVERT: B 256 ARG cc_start: 0.8554 (tpt170) cc_final: 0.8316 (tpt170) REVERT: B 293 ILE cc_start: 0.8573 (mm) cc_final: 0.8336 (mt) REVERT: B 302 ASP cc_start: 0.7918 (t0) cc_final: 0.7522 (t0) REVERT: B 326 TYR cc_start: 0.8851 (m-80) cc_final: 0.8588 (m-80) REVERT: B 360 CYS cc_start: 0.7220 (m) cc_final: 0.6986 (m) REVERT: C 213 GLU cc_start: 0.7742 (pt0) cc_final: 0.7480 (pt0) REVERT: C 273 TYR cc_start: 0.8552 (m-80) cc_final: 0.8302 (m-80) REVERT: C 326 TYR cc_start: 0.8695 (m-80) cc_final: 0.8453 (m-80) REVERT: C 363 THR cc_start: 0.8745 (m) cc_final: 0.8490 (p) REVERT: C 399 CYS cc_start: 0.7414 (m) cc_final: 0.7196 (m) REVERT: C 468 MET cc_start: 0.8818 (mmm) cc_final: 0.8577 (mmm) outliers start: 44 outliers final: 7 residues processed: 416 average time/residue: 1.5532 time to fit residues: 690.4330 Evaluate side-chains 354 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 345 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 482 ASN C 106 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS C 449 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.125594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113999 restraints weight = 17335.103| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.69 r_work: 0.3444 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13407 Z= 0.188 Angle : 0.660 13.571 18201 Z= 0.337 Chirality : 0.046 0.252 1986 Planarity : 0.005 0.051 2325 Dihedral : 5.287 31.451 2172 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.84 % Allowed : 14.36 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.54 (0.21), residues: 1569 helix: 1.55 (0.20), residues: 690 sheet: 1.36 (0.29), residues: 267 loop : 0.39 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 349 HIS 0.005 0.001 HIS A 260 PHE 0.017 0.002 PHE C 443 TYR 0.015 0.001 TYR C 118 ARG 0.005 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 15) link_NAG-ASN : angle 2.52854 ( 45) link_BETA1-4 : bond 0.00679 ( 6) link_BETA1-4 : angle 1.37070 ( 18) hydrogen bonds : bond 0.04694 ( 661) hydrogen bonds : angle 4.56271 ( 1911) SS BOND : bond 0.00638 ( 24) SS BOND : angle 2.62261 ( 48) covalent geometry : bond 0.00446 (13359) covalent geometry : angle 0.63396 (18090) Misc. bond : bond 0.00045 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 338 time to evaluate : 1.561 Fit side-chains REVERT: A 29 MET cc_start: 0.7272 (mmm) cc_final: 0.7056 (mmm) REVERT: A 116 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8035 (mtm180) REVERT: A 302 ASP cc_start: 0.8181 (t0) cc_final: 0.7767 (t0) REVERT: A 303 LYS cc_start: 0.8695 (ptmm) cc_final: 0.8381 (ptpp) REVERT: A 347 ILE cc_start: 0.8246 (mt) cc_final: 0.8046 (tp) REVERT: A 409 SER cc_start: 0.8783 (m) cc_final: 0.8568 (p) REVERT: A 465 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 121 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8029 (tttm) REVERT: B 293 ILE cc_start: 0.8592 (mm) cc_final: 0.8378 (mt) REVERT: B 302 ASP cc_start: 0.8033 (t0) cc_final: 0.7638 (t0) REVERT: B 360 CYS cc_start: 0.7280 (m) cc_final: 0.7049 (m) REVERT: C 203 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7524 (mm-30) REVERT: C 273 TYR cc_start: 0.8600 (m-80) cc_final: 0.8344 (m-80) REVERT: C 293 ILE cc_start: 0.8528 (mm) cc_final: 0.8261 (OUTLIER) REVERT: C 326 TYR cc_start: 0.8709 (m-80) cc_final: 0.8404 (m-80) REVERT: C 359 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: C 363 THR cc_start: 0.8787 (m) cc_final: 0.8454 (p) REVERT: C 468 MET cc_start: 0.8832 (mmm) cc_final: 0.8554 (mmm) outliers start: 40 outliers final: 19 residues processed: 353 average time/residue: 1.5235 time to fit residues: 574.6967 Evaluate side-chains 355 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 335 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 105 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 57 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 324 GLN A 475 ASN A 482 ASN B 106 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116524 restraints weight = 17401.118| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.71 r_work: 0.3483 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13407 Z= 0.111 Angle : 0.576 7.668 18201 Z= 0.293 Chirality : 0.042 0.170 1986 Planarity : 0.005 0.050 2325 Dihedral : 4.884 30.866 2172 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.77 % Allowed : 15.35 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1569 helix: 1.77 (0.20), residues: 690 sheet: 1.28 (0.30), residues: 270 loop : 0.37 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.003 0.001 HIS C 376 PHE 0.023 0.001 PHE A 10 TYR 0.012 0.001 TYR B 118 ARG 0.006 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 15) link_NAG-ASN : angle 2.16753 ( 45) link_BETA1-4 : bond 0.00480 ( 6) link_BETA1-4 : angle 1.10971 ( 18) hydrogen bonds : bond 0.03787 ( 661) hydrogen bonds : angle 4.26782 ( 1911) SS BOND : bond 0.00573 ( 24) SS BOND : angle 2.06050 ( 48) covalent geometry : bond 0.00241 (13359) covalent geometry : angle 0.55637 (18090) Misc. bond : bond 0.00017 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 346 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.7240 (mmm) cc_final: 0.7036 (mmm) REVERT: A 95 ARG cc_start: 0.8638 (mtt-85) cc_final: 0.8395 (mtt-85) REVERT: A 119 MET cc_start: 0.8735 (mmt) cc_final: 0.8284 (mmt) REVERT: A 293 ILE cc_start: 0.8301 (mm) cc_final: 0.7931 (mm) REVERT: A 302 ASP cc_start: 0.8133 (t0) cc_final: 0.7695 (t0) REVERT: A 303 LYS cc_start: 0.8691 (ptmm) cc_final: 0.8367 (ptpp) REVERT: A 353 ASP cc_start: 0.7578 (p0) cc_final: 0.7326 (p0) REVERT: A 465 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 57 PHE cc_start: 0.8164 (m-80) cc_final: 0.7888 (m-80) REVERT: B 121 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8010 (tttp) REVERT: B 293 ILE cc_start: 0.8623 (mm) cc_final: 0.8371 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8003 (t0) cc_final: 0.7598 (t0) REVERT: B 326 TYR cc_start: 0.8733 (m-80) cc_final: 0.8518 (m-80) REVERT: B 437 GLU cc_start: 0.7921 (tp30) cc_final: 0.7534 (tm-30) REVERT: B 518 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7365 (mm-30) REVERT: C 273 TYR cc_start: 0.8571 (m-80) cc_final: 0.8287 (m-80) REVERT: C 293 ILE cc_start: 0.8430 (mm) cc_final: 0.8203 (mt) REVERT: C 326 TYR cc_start: 0.8652 (m-80) cc_final: 0.8345 (m-80) REVERT: C 359 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7524 (tp30) REVERT: C 363 THR cc_start: 0.8739 (m) cc_final: 0.8410 (p) REVERT: C 468 MET cc_start: 0.8845 (mmm) cc_final: 0.8586 (mmm) outliers start: 39 outliers final: 14 residues processed: 362 average time/residue: 1.4935 time to fit residues: 579.0604 Evaluate side-chains 336 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 323 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 482 ASN B 108 ASN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115047 restraints weight = 17518.338| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.73 r_work: 0.3461 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13407 Z= 0.141 Angle : 0.586 7.659 18201 Z= 0.297 Chirality : 0.043 0.174 1986 Planarity : 0.005 0.048 2325 Dihedral : 4.688 29.759 2172 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.20 % Allowed : 16.20 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1569 helix: 1.83 (0.20), residues: 690 sheet: 1.20 (0.30), residues: 273 loop : 0.24 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 PHE 0.013 0.001 PHE C 443 TYR 0.014 0.001 TYR C 118 ARG 0.005 0.000 ARG C 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 15) link_NAG-ASN : angle 2.33510 ( 45) link_BETA1-4 : bond 0.00486 ( 6) link_BETA1-4 : angle 1.09615 ( 18) hydrogen bonds : bond 0.03989 ( 661) hydrogen bonds : angle 4.23609 ( 1911) SS BOND : bond 0.00520 ( 24) SS BOND : angle 2.02245 ( 48) covalent geometry : bond 0.00332 (13359) covalent geometry : angle 0.56545 (18090) Misc. bond : bond 0.00034 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 1.526 Fit side-chains REVERT: A 29 MET cc_start: 0.7301 (mmm) cc_final: 0.7078 (mmm) REVERT: A 293 ILE cc_start: 0.8385 (mm) cc_final: 0.8171 (mm) REVERT: A 302 ASP cc_start: 0.8175 (t0) cc_final: 0.7749 (t0) REVERT: A 303 LYS cc_start: 0.8726 (ptmm) cc_final: 0.8431 (ptpp) REVERT: A 465 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 53 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8035 (mp) REVERT: B 121 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7988 (tttm) REVERT: B 249 VAL cc_start: 0.8386 (m) cc_final: 0.8053 (p) REVERT: B 293 ILE cc_start: 0.8567 (mm) cc_final: 0.8296 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8048 (t0) cc_final: 0.7656 (t0) REVERT: B 326 TYR cc_start: 0.8752 (m-80) cc_final: 0.8473 (m-80) REVERT: B 437 GLU cc_start: 0.7918 (tp30) cc_final: 0.7505 (tm-30) REVERT: B 518 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7378 (mm-30) REVERT: C 21 LYS cc_start: 0.8055 (mttt) cc_final: 0.7688 (mttt) REVERT: C 273 TYR cc_start: 0.8621 (m-80) cc_final: 0.8345 (m-80) REVERT: C 293 ILE cc_start: 0.8440 (mm) cc_final: 0.8232 (mt) REVERT: C 326 TYR cc_start: 0.8681 (m-80) cc_final: 0.8383 (m-80) REVERT: C 359 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7564 (tp30) REVERT: C 363 THR cc_start: 0.8776 (m) cc_final: 0.8454 (p) REVERT: C 468 MET cc_start: 0.8835 (mmm) cc_final: 0.8595 (mmm) outliers start: 45 outliers final: 22 residues processed: 353 average time/residue: 1.5088 time to fit residues: 570.5724 Evaluate side-chains 347 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 325 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 376 HIS A 475 ASN A 482 ASN B 108 ASN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS C 475 ASN C 482 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.115697 restraints weight = 17620.567| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.75 r_work: 0.3473 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13407 Z= 0.122 Angle : 0.582 7.876 18201 Z= 0.293 Chirality : 0.042 0.158 1986 Planarity : 0.004 0.046 2325 Dihedral : 4.585 29.436 2172 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.27 % Allowed : 16.13 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1569 helix: 1.93 (0.20), residues: 687 sheet: 1.21 (0.30), residues: 273 loop : 0.23 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 PHE 0.024 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.006 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 15) link_NAG-ASN : angle 2.20393 ( 45) link_BETA1-4 : bond 0.00533 ( 6) link_BETA1-4 : angle 1.06176 ( 18) hydrogen bonds : bond 0.03794 ( 661) hydrogen bonds : angle 4.19337 ( 1911) SS BOND : bond 0.00471 ( 24) SS BOND : angle 2.08917 ( 48) covalent geometry : bond 0.00280 (13359) covalent geometry : angle 0.56205 (18090) Misc. bond : bond 0.00024 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 330 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.7889 (mmp) cc_final: 0.7569 (mmp) REVERT: A 21 LYS cc_start: 0.8111 (mttt) cc_final: 0.7899 (mttt) REVERT: A 29 MET cc_start: 0.7345 (mmm) cc_final: 0.7117 (mmm) REVERT: A 293 ILE cc_start: 0.8335 (mm) cc_final: 0.7860 (mm) REVERT: A 302 ASP cc_start: 0.8179 (t0) cc_final: 0.7740 (t0) REVERT: A 303 LYS cc_start: 0.8737 (ptmm) cc_final: 0.8430 (ptpp) REVERT: A 352 ASP cc_start: 0.8210 (t70) cc_final: 0.8004 (t0) REVERT: A 465 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 57 PHE cc_start: 0.8228 (m-80) cc_final: 0.7953 (m-80) REVERT: B 121 LYS cc_start: 0.8364 (mtpp) cc_final: 0.7971 (tttm) REVERT: B 131 ASN cc_start: 0.8480 (m-40) cc_final: 0.8259 (m-40) REVERT: B 249 VAL cc_start: 0.8389 (m) cc_final: 0.8045 (p) REVERT: B 293 ILE cc_start: 0.8542 (mm) cc_final: 0.8311 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8068 (t0) cc_final: 0.7676 (t0) REVERT: B 326 TYR cc_start: 0.8708 (m-80) cc_final: 0.8483 (m-80) REVERT: B 437 GLU cc_start: 0.7910 (tp30) cc_final: 0.7485 (tm-30) REVERT: B 448 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7558 (p) REVERT: C 273 TYR cc_start: 0.8604 (m-80) cc_final: 0.8312 (m-80) REVERT: C 293 ILE cc_start: 0.8427 (mm) cc_final: 0.8210 (mt) REVERT: C 326 TYR cc_start: 0.8658 (m-80) cc_final: 0.8330 (m-80) REVERT: C 359 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: C 363 THR cc_start: 0.8774 (m) cc_final: 0.8483 (p) REVERT: C 468 MET cc_start: 0.8831 (mmm) cc_final: 0.8569 (mmm) REVERT: C 518 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7703 (mm-30) outliers start: 46 outliers final: 22 residues processed: 353 average time/residue: 1.4862 time to fit residues: 562.6473 Evaluate side-chains 347 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 324 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 405 CYS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS A 475 ASN A 482 ASN B 108 ASN B 133 GLN B 141 GLN B 152 ASN C 141 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.115829 restraints weight = 17437.386| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.73 r_work: 0.3472 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13407 Z= 0.134 Angle : 0.596 8.241 18201 Z= 0.301 Chirality : 0.042 0.189 1986 Planarity : 0.004 0.045 2325 Dihedral : 4.555 28.820 2172 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.70 % Allowed : 17.20 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1569 helix: 1.89 (0.20), residues: 690 sheet: 1.22 (0.30), residues: 273 loop : 0.19 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 PHE 0.021 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.008 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 15) link_NAG-ASN : angle 2.25617 ( 45) link_BETA1-4 : bond 0.00511 ( 6) link_BETA1-4 : angle 1.04059 ( 18) hydrogen bonds : bond 0.03848 ( 661) hydrogen bonds : angle 4.21483 ( 1911) SS BOND : bond 0.00505 ( 24) SS BOND : angle 2.31104 ( 48) covalent geometry : bond 0.00313 (13359) covalent geometry : angle 0.57443 (18090) Misc. bond : bond 0.00029 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 325 time to evaluate : 1.448 Fit side-chains REVERT: A 7 MET cc_start: 0.7925 (mmp) cc_final: 0.7652 (mmp) REVERT: A 29 MET cc_start: 0.7333 (mmm) cc_final: 0.7105 (mmm) REVERT: A 119 MET cc_start: 0.8688 (mmt) cc_final: 0.8311 (mmt) REVERT: A 293 ILE cc_start: 0.8309 (mm) cc_final: 0.7914 (mm) REVERT: A 302 ASP cc_start: 0.8138 (t0) cc_final: 0.7710 (t0) REVERT: A 373 MET cc_start: 0.8079 (mmp) cc_final: 0.7862 (mmm) REVERT: A 465 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 57 PHE cc_start: 0.8261 (m-80) cc_final: 0.7955 (m-80) REVERT: B 131 ASN cc_start: 0.8479 (m-40) cc_final: 0.8258 (m-40) REVERT: B 249 VAL cc_start: 0.8374 (m) cc_final: 0.8036 (p) REVERT: B 293 ILE cc_start: 0.8547 (mm) cc_final: 0.8318 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8039 (t0) cc_final: 0.7655 (t0) REVERT: B 326 TYR cc_start: 0.8707 (m-80) cc_final: 0.8454 (m-80) REVERT: B 359 GLU cc_start: 0.7518 (tp30) cc_final: 0.7193 (mm-30) REVERT: B 437 GLU cc_start: 0.7898 (tp30) cc_final: 0.7477 (tm-30) REVERT: B 448 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7527 (p) REVERT: B 518 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7792 (mm-30) REVERT: C 273 TYR cc_start: 0.8615 (m-80) cc_final: 0.8309 (m-80) REVERT: C 293 ILE cc_start: 0.8423 (mm) cc_final: 0.8201 (mt) REVERT: C 326 TYR cc_start: 0.8649 (m-80) cc_final: 0.8296 (m-80) REVERT: C 359 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: C 363 THR cc_start: 0.8781 (m) cc_final: 0.8498 (p) REVERT: C 468 MET cc_start: 0.8838 (mmm) cc_final: 0.8583 (mmm) outliers start: 38 outliers final: 20 residues processed: 346 average time/residue: 1.5650 time to fit residues: 579.2602 Evaluate side-chains 334 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 313 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 115 optimal weight: 0.0970 chunk 153 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 108 ASN B 133 GLN B 141 GLN B 376 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116868 restraints weight = 17466.774| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.72 r_work: 0.3486 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13407 Z= 0.117 Angle : 0.587 8.916 18201 Z= 0.294 Chirality : 0.042 0.184 1986 Planarity : 0.004 0.045 2325 Dihedral : 4.465 28.216 2172 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.63 % Allowed : 17.13 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1569 helix: 1.97 (0.20), residues: 687 sheet: 1.19 (0.30), residues: 273 loop : 0.22 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 349 HIS 0.003 0.001 HIS A 177 PHE 0.020 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.011 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 15) link_NAG-ASN : angle 2.14964 ( 45) link_BETA1-4 : bond 0.00518 ( 6) link_BETA1-4 : angle 0.98023 ( 18) hydrogen bonds : bond 0.03678 ( 661) hydrogen bonds : angle 4.20462 ( 1911) SS BOND : bond 0.00404 ( 24) SS BOND : angle 2.16853 ( 48) covalent geometry : bond 0.00267 (13359) covalent geometry : angle 0.56725 (18090) Misc. bond : bond 0.00021 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 1.457 Fit side-chains REVERT: A 7 MET cc_start: 0.7923 (mmp) cc_final: 0.7715 (mmp) REVERT: A 29 MET cc_start: 0.7297 (mmm) cc_final: 0.7079 (mmm) REVERT: A 57 PHE cc_start: 0.8323 (m-80) cc_final: 0.8021 (m-80) REVERT: A 119 MET cc_start: 0.8688 (mmt) cc_final: 0.8281 (mmt) REVERT: A 293 ILE cc_start: 0.8279 (mm) cc_final: 0.7890 (mm) REVERT: A 302 ASP cc_start: 0.8133 (t0) cc_final: 0.7703 (t0) REVERT: A 465 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 131 ASN cc_start: 0.8459 (m-40) cc_final: 0.8242 (m-40) REVERT: B 249 VAL cc_start: 0.8341 (m) cc_final: 0.8021 (p) REVERT: B 293 ILE cc_start: 0.8546 (mm) cc_final: 0.8307 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8037 (t0) cc_final: 0.7644 (t0) REVERT: B 326 TYR cc_start: 0.8685 (m-80) cc_final: 0.8368 (m-80) REVERT: B 359 GLU cc_start: 0.7565 (tp30) cc_final: 0.7229 (mm-30) REVERT: B 381 CYS cc_start: 0.6465 (OUTLIER) cc_final: 0.6149 (t) REVERT: B 437 GLU cc_start: 0.7866 (tp30) cc_final: 0.7381 (tm-30) REVERT: B 448 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7480 (p) REVERT: C 273 TYR cc_start: 0.8588 (m-80) cc_final: 0.8283 (m-80) REVERT: C 326 TYR cc_start: 0.8625 (m-80) cc_final: 0.8269 (m-80) REVERT: C 359 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: C 363 THR cc_start: 0.8756 (m) cc_final: 0.8496 (p) REVERT: C 468 MET cc_start: 0.8842 (mmm) cc_final: 0.8589 (mmm) outliers start: 37 outliers final: 20 residues processed: 338 average time/residue: 1.4863 time to fit residues: 539.3407 Evaluate side-chains 337 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 315 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 405 CYS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 482 ASN A 496 GLN B 108 ASN B 133 GLN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114844 restraints weight = 17393.835| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.73 r_work: 0.3461 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13407 Z= 0.170 Angle : 0.632 9.716 18201 Z= 0.318 Chirality : 0.044 0.219 1986 Planarity : 0.005 0.044 2325 Dihedral : 4.546 27.475 2172 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.20 % Allowed : 18.19 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1569 helix: 1.87 (0.20), residues: 687 sheet: 1.20 (0.30), residues: 273 loop : 0.17 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 349 HIS 0.005 0.001 HIS C 376 PHE 0.019 0.002 PHE A 10 TYR 0.016 0.001 TYR C 118 ARG 0.008 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 15) link_NAG-ASN : angle 2.32691 ( 45) link_BETA1-4 : bond 0.00467 ( 6) link_BETA1-4 : angle 0.98950 ( 18) hydrogen bonds : bond 0.04124 ( 661) hydrogen bonds : angle 4.30097 ( 1911) SS BOND : bond 0.00534 ( 24) SS BOND : angle 2.66547 ( 48) covalent geometry : bond 0.00406 (13359) covalent geometry : angle 0.60759 (18090) Misc. bond : bond 0.00047 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 1.429 Fit side-chains REVERT: A 7 MET cc_start: 0.7937 (mmp) cc_final: 0.7737 (mmp) REVERT: A 29 MET cc_start: 0.7290 (mmm) cc_final: 0.7056 (mmm) REVERT: A 119 MET cc_start: 0.8725 (mmt) cc_final: 0.8500 (mmm) REVERT: A 121 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7972 (tttm) REVERT: A 293 ILE cc_start: 0.8337 (mm) cc_final: 0.7969 (mm) REVERT: A 302 ASP cc_start: 0.8156 (t0) cc_final: 0.7738 (t0) REVERT: A 465 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 131 ASN cc_start: 0.8433 (m-40) cc_final: 0.8228 (m-40) REVERT: B 249 VAL cc_start: 0.8378 (m) cc_final: 0.8045 (p) REVERT: B 293 ILE cc_start: 0.8553 (mm) cc_final: 0.8336 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8075 (t0) cc_final: 0.7701 (t0) REVERT: B 326 TYR cc_start: 0.8731 (m-80) cc_final: 0.8446 (m-80) REVERT: B 448 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7512 (p) REVERT: C 273 TYR cc_start: 0.8624 (m-80) cc_final: 0.8335 (m-80) REVERT: C 293 ILE cc_start: 0.8466 (mm) cc_final: 0.8018 (OUTLIER) REVERT: C 326 TYR cc_start: 0.8671 (m-80) cc_final: 0.8286 (m-80) REVERT: C 359 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: C 363 THR cc_start: 0.8767 (m) cc_final: 0.8503 (p) REVERT: C 468 MET cc_start: 0.8855 (mmm) cc_final: 0.8610 (mmm) outliers start: 31 outliers final: 21 residues processed: 339 average time/residue: 1.4762 time to fit residues: 536.6869 Evaluate side-chains 340 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 101 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 96 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 482 ASN B 108 ASN B 133 GLN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.128570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116679 restraints weight = 17295.331| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.72 r_work: 0.3489 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13407 Z= 0.117 Angle : 0.612 9.764 18201 Z= 0.306 Chirality : 0.042 0.184 1986 Planarity : 0.004 0.044 2325 Dihedral : 4.484 27.522 2172 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.92 % Allowed : 18.91 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1569 helix: 1.95 (0.20), residues: 687 sheet: 1.22 (0.30), residues: 270 loop : 0.14 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 349 HIS 0.003 0.001 HIS A 177 PHE 0.019 0.001 PHE A 10 TYR 0.013 0.001 TYR B 118 ARG 0.008 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 15) link_NAG-ASN : angle 2.07597 ( 45) link_BETA1-4 : bond 0.00485 ( 6) link_BETA1-4 : angle 0.94984 ( 18) hydrogen bonds : bond 0.03674 ( 661) hydrogen bonds : angle 4.26333 ( 1911) SS BOND : bond 0.00514 ( 24) SS BOND : angle 2.57025 ( 48) covalent geometry : bond 0.00267 (13359) covalent geometry : angle 0.58922 (18090) Misc. bond : bond 0.00014 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 1.425 Fit side-chains REVERT: A 57 PHE cc_start: 0.8334 (m-80) cc_final: 0.8035 (m-80) REVERT: A 119 MET cc_start: 0.8699 (mmt) cc_final: 0.8343 (mmt) REVERT: A 121 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7908 (tttm) REVERT: A 293 ILE cc_start: 0.8245 (mm) cc_final: 0.7888 (mm) REVERT: A 302 ASP cc_start: 0.8137 (t0) cc_final: 0.7709 (t0) REVERT: A 465 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 57 PHE cc_start: 0.8261 (m-80) cc_final: 0.8022 (m-80) REVERT: B 131 ASN cc_start: 0.8388 (m-40) cc_final: 0.8177 (m-40) REVERT: B 249 VAL cc_start: 0.8350 (m) cc_final: 0.8033 (p) REVERT: B 293 ILE cc_start: 0.8533 (mm) cc_final: 0.8301 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8014 (t0) cc_final: 0.7628 (t0) REVERT: B 326 TYR cc_start: 0.8679 (m-80) cc_final: 0.8357 (m-80) REVERT: B 437 GLU cc_start: 0.7838 (tp30) cc_final: 0.7381 (tm-30) REVERT: B 448 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7442 (p) REVERT: C 273 TYR cc_start: 0.8583 (m-80) cc_final: 0.8273 (m-80) REVERT: C 326 TYR cc_start: 0.8634 (m-80) cc_final: 0.8321 (m-80) REVERT: C 359 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: C 363 THR cc_start: 0.8748 (m) cc_final: 0.8480 (p) REVERT: C 468 MET cc_start: 0.8843 (mmm) cc_final: 0.8596 (mmm) outliers start: 27 outliers final: 20 residues processed: 338 average time/residue: 1.5205 time to fit residues: 553.2319 Evaluate side-chains 339 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 317 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 85 optimal weight: 0.0470 chunk 143 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 475 ASN A 482 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN B 108 ASN B 133 GLN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 475 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116162 restraints weight = 17380.347| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.73 r_work: 0.3484 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13407 Z= 0.132 Angle : 0.616 9.533 18201 Z= 0.309 Chirality : 0.043 0.189 1986 Planarity : 0.005 0.059 2325 Dihedral : 4.464 27.065 2172 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.85 % Allowed : 19.69 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1569 helix: 1.91 (0.20), residues: 687 sheet: 1.23 (0.30), residues: 270 loop : 0.13 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 349 HIS 0.003 0.001 HIS C 376 PHE 0.018 0.001 PHE A 10 TYR 0.013 0.001 TYR C 118 ARG 0.013 0.000 ARG C 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 15) link_NAG-ASN : angle 2.12474 ( 45) link_BETA1-4 : bond 0.00477 ( 6) link_BETA1-4 : angle 0.94298 ( 18) hydrogen bonds : bond 0.03790 ( 661) hydrogen bonds : angle 4.26462 ( 1911) SS BOND : bond 0.00503 ( 24) SS BOND : angle 2.54547 ( 48) covalent geometry : bond 0.00309 (13359) covalent geometry : angle 0.59420 (18090) Misc. bond : bond 0.00032 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11794.63 seconds wall clock time: 203 minutes 1.59 seconds (12181.59 seconds total)