Starting phenix.real_space_refine on Thu Jul 31 01:28:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8on7_16981/07_2025/8on7_16981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8on7_16981/07_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_16981/07_2025/8on7_16981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8on7_16981/07_2025/8on7_16981.map" model { file = "/net/cci-nas-00/data/ceres_data/8on7_16981/07_2025/8on7_16981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8on7_16981/07_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-5711/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: 7.56, per 1000 atoms: 0.58 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: 3.12 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: 1.36 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: 4.00 Time building geometry restraints manager: 3.75 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: 0.740 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.420 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.130 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:15.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.930 ------------------------------------------------------------------------------- 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 : 1.341 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: 1.5302 time to fit residues: 757.3719 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 : 1.446 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.127127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115301 restraints weight = 17268.350| |-----------------------------------------------------------------------------| 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: 0.3313 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7285 (mmm) cc_final: 0.7084 (mmm) REVERT: A 116 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7996 (mtm180) REVERT: A 138 GLU cc_start: 0.7784 (mp0) cc_final: 0.7576 (mp0) REVERT: A 216 GLU cc_start: 0.7762 (mp0) cc_final: 0.7558 (mp0) REVERT: A 271 GLU cc_start: 0.7797 (pt0) cc_final: 0.7574 (pt0) REVERT: A 273 TYR cc_start: 0.8480 (m-80) cc_final: 0.8255 (m-80) REVERT: A 302 ASP cc_start: 0.8122 (t0) cc_final: 0.7692 (t0) REVERT: A 347 ILE cc_start: 0.8228 (mt) cc_final: 0.8023 (tp) REVERT: A 353 ASP cc_start: 0.7692 (p0) cc_final: 0.7375 (p0) REVERT: A 465 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 21 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8171 (mttp) REVERT: B 121 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8087 (tttm) REVERT: B 138 GLU cc_start: 0.7805 (mp0) cc_final: 0.7564 (mp0) REVERT: B 164 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8042 (mm-40) REVERT: B 256 ARG cc_start: 0.8553 (tpt170) cc_final: 0.8315 (tpt170) REVERT: B 293 ILE cc_start: 0.8572 (mm) cc_final: 0.8336 (mt) REVERT: B 302 ASP cc_start: 0.7916 (t0) cc_final: 0.7520 (t0) REVERT: B 326 TYR cc_start: 0.8852 (m-80) cc_final: 0.8588 (m-80) REVERT: B 360 CYS cc_start: 0.7211 (m) cc_final: 0.6977 (m) REVERT: C 213 GLU cc_start: 0.7738 (pt0) cc_final: 0.7477 (pt0) REVERT: C 273 TYR cc_start: 0.8553 (m-80) cc_final: 0.8302 (m-80) REVERT: C 326 TYR cc_start: 0.8696 (m-80) cc_final: 0.8454 (m-80) REVERT: C 363 THR cc_start: 0.8743 (m) cc_final: 0.8490 (p) REVERT: C 399 CYS cc_start: 0.7403 (m) cc_final: 0.7185 (m) REVERT: C 468 MET cc_start: 0.8817 (mmm) cc_final: 0.8576 (mmm) outliers start: 44 outliers final: 7 residues processed: 416 average time/residue: 1.7438 time to fit residues: 774.2748 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 : 1.554 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.9990 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN B 141 GLN ** 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 286 HIS C 376 HIS C 449 GLN ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113402 restraints weight = 17358.630| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.70 r_work: 0.3434 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13407 Z= 0.219 Angle : 0.679 13.789 18201 Z= 0.347 Chirality : 0.047 0.266 1986 Planarity : 0.005 0.050 2325 Dihedral : 5.325 31.228 2172 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.06 % Allowed : 14.21 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.50 (0.20), residues: 690 sheet: 1.34 (0.29), residues: 267 loop : 0.36 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 349 HIS 0.005 0.001 HIS A 260 PHE 0.019 0.002 PHE C 443 TYR 0.016 0.002 TYR C 118 ARG 0.005 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 15) link_NAG-ASN : angle 2.57255 ( 45) link_BETA1-4 : bond 0.00643 ( 6) link_BETA1-4 : angle 1.36896 ( 18) hydrogen bonds : bond 0.04858 ( 661) hydrogen bonds : angle 4.59534 ( 1911) SS BOND : bond 0.00583 ( 24) SS BOND : angle 2.81742 ( 48) covalent geometry : bond 0.00524 (13359) covalent geometry : angle 0.65102 (18090) Misc. bond : bond 0.00065 ( 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 390 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 347 time to evaluate : 1.501 Fit side-chains REVERT: A 29 MET cc_start: 0.7273 (mmm) cc_final: 0.7058 (mmm) REVERT: A 116 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8035 (mtm180) REVERT: A 302 ASP cc_start: 0.8188 (t0) cc_final: 0.7784 (t0) REVERT: A 347 ILE cc_start: 0.8243 (mt) cc_final: 0.8040 (tp) REVERT: A 409 SER cc_start: 0.8786 (m) cc_final: 0.8570 (p) REVERT: A 465 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 121 LYS cc_start: 0.8348 (mtpp) cc_final: 0.8013 (tttm) REVERT: B 138 GLU cc_start: 0.7789 (mp0) cc_final: 0.7522 (mp0) REVERT: B 141 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8259 (mm110) REVERT: B 293 ILE cc_start: 0.8588 (mm) cc_final: 0.8382 (mt) REVERT: B 302 ASP cc_start: 0.8020 (t0) cc_final: 0.7630 (t0) REVERT: B 360 CYS cc_start: 0.7280 (m) cc_final: 0.7048 (m) REVERT: B 518 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 203 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 235 GLU cc_start: 0.8228 (pt0) cc_final: 0.7996 (pm20) REVERT: C 273 TYR cc_start: 0.8594 (m-80) cc_final: 0.8322 (m-80) REVERT: C 293 ILE cc_start: 0.8535 (mm) cc_final: 0.8284 (OUTLIER) REVERT: C 326 TYR cc_start: 0.8719 (m-80) cc_final: 0.8429 (m-80) REVERT: C 359 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7534 (tp30) REVERT: C 363 THR cc_start: 0.8790 (m) cc_final: 0.8465 (p) REVERT: C 468 MET cc_start: 0.8831 (mmm) cc_final: 0.8567 (mmm) outliers start: 43 outliers final: 22 residues processed: 364 average time/residue: 1.5840 time to fit residues: 615.7230 Evaluate side-chains 358 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 334 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 39 LEU 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 489 SER 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 141 GLN 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 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: 0.8980 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.0170 chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 B 106 ASN B 108 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 = 0.3736 r_free = 0.3736 target = 0.126945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115132 restraints weight = 17330.243| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.70 r_work: 0.3466 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13407 Z= 0.128 Angle : 0.601 8.486 18201 Z= 0.306 Chirality : 0.043 0.177 1986 Planarity : 0.005 0.050 2325 Dihedral : 5.012 30.547 2172 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.84 % Allowed : 15.21 % Favored : 81.95 % 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: 1.59 (0.21), residues: 1569 helix: 1.66 (0.20), residues: 690 sheet: 1.36 (0.29), residues: 267 loop : 0.34 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 349 HIS 0.004 0.001 HIS C 376 PHE 0.022 0.001 PHE A 10 TYR 0.013 0.001 TYR B 118 ARG 0.005 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 15) link_NAG-ASN : angle 2.31182 ( 45) link_BETA1-4 : bond 0.00523 ( 6) link_BETA1-4 : angle 1.16254 ( 18) hydrogen bonds : bond 0.04111 ( 661) hydrogen bonds : angle 4.33736 ( 1911) SS BOND : bond 0.00426 ( 24) SS BOND : angle 2.32619 ( 48) covalent geometry : bond 0.00291 (13359) covalent geometry : angle 0.57839 (18090) Misc. bond : bond 0.00027 ( 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 387 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 347 time to evaluate : 1.346 Fit side-chains REVERT: A 29 MET cc_start: 0.7262 (mmm) cc_final: 0.7058 (mmm) REVERT: A 302 ASP cc_start: 0.8185 (t0) cc_final: 0.7754 (t0) REVERT: A 303 LYS cc_start: 0.8698 (ptmm) cc_final: 0.8394 (ptpp) REVERT: A 465 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 57 PHE cc_start: 0.8212 (m-80) cc_final: 0.7930 (m-80) REVERT: B 121 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7989 (tttm) REVERT: B 138 GLU cc_start: 0.7751 (mp0) cc_final: 0.7486 (mp0) REVERT: B 141 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8082 (mm110) REVERT: B 293 ILE cc_start: 0.8627 (mm) cc_final: 0.8380 (mt) REVERT: B 302 ASP cc_start: 0.8075 (t0) cc_final: 0.7698 (t0) REVERT: B 360 CYS cc_start: 0.7202 (m) cc_final: 0.6976 (m) REVERT: C 203 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 235 GLU cc_start: 0.8225 (pt0) cc_final: 0.7975 (pm20) REVERT: C 273 TYR cc_start: 0.8590 (m-80) cc_final: 0.8329 (m-80) REVERT: C 293 ILE cc_start: 0.8481 (mm) cc_final: 0.8261 (mt) REVERT: C 326 TYR cc_start: 0.8673 (m-80) cc_final: 0.8394 (m-80) REVERT: C 359 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7544 (tp30) REVERT: C 363 THR cc_start: 0.8781 (m) cc_final: 0.8448 (p) REVERT: C 468 MET cc_start: 0.8848 (mmm) cc_final: 0.8611 (mmm) REVERT: C 518 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7768 (mm-30) outliers start: 40 outliers final: 14 residues processed: 362 average time/residue: 1.6247 time to fit residues: 627.7934 Evaluate side-chains 347 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 332 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL 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 B residue 99 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 67 VAL 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 518 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: 0.8980 chunk 89 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 chunk 120 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.127085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115207 restraints weight = 17472.536| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.72 r_work: 0.3463 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13407 Z= 0.136 Angle : 0.597 8.579 18201 Z= 0.302 Chirality : 0.043 0.172 1986 Planarity : 0.005 0.048 2325 Dihedral : 4.791 29.684 2172 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.34 % Allowed : 15.42 % Favored : 81.24 % 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: 1.51 (0.21), residues: 1569 helix: 1.72 (0.20), residues: 690 sheet: 1.14 (0.29), residues: 273 loop : 0.21 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 PHE 0.014 0.001 PHE C 443 TYR 0.013 0.001 TYR B 118 ARG 0.004 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 15) link_NAG-ASN : angle 2.31273 ( 45) link_BETA1-4 : bond 0.00515 ( 6) link_BETA1-4 : angle 1.10312 ( 18) hydrogen bonds : bond 0.04054 ( 661) hydrogen bonds : angle 4.28433 ( 1911) SS BOND : bond 0.00543 ( 24) SS BOND : angle 2.27327 ( 48) covalent geometry : bond 0.00317 (13359) covalent geometry : angle 0.57508 (18090) Misc. bond : bond 0.00027 ( 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 391 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 344 time to evaluate : 1.443 Fit side-chains REVERT: A 7 MET cc_start: 0.7889 (mmp) cc_final: 0.7531 (mmp) REVERT: A 29 MET cc_start: 0.7270 (mmm) cc_final: 0.7058 (mmm) REVERT: A 302 ASP cc_start: 0.8154 (t0) cc_final: 0.7727 (t0) REVERT: A 465 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 57 PHE cc_start: 0.8261 (m-80) cc_final: 0.7928 (m-80) REVERT: B 121 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8025 (tttm) REVERT: B 131 ASN cc_start: 0.8509 (m-40) cc_final: 0.8285 (m-40) REVERT: B 138 GLU cc_start: 0.7767 (mp0) cc_final: 0.7499 (mp0) REVERT: B 293 ILE cc_start: 0.8564 (mm) cc_final: 0.8255 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8049 (t0) cc_final: 0.7668 (t0) REVERT: B 326 TYR cc_start: 0.8733 (m-80) cc_final: 0.8482 (m-80) REVERT: B 360 CYS cc_start: 0.7244 (m) cc_final: 0.7022 (m) REVERT: C 203 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 273 TYR cc_start: 0.8602 (m-80) cc_final: 0.8314 (m-80) REVERT: C 293 ILE cc_start: 0.8449 (mm) cc_final: 0.8243 (mt) REVERT: C 326 TYR cc_start: 0.8651 (m-80) cc_final: 0.8319 (m-80) REVERT: C 359 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: C 363 THR cc_start: 0.8790 (m) cc_final: 0.8468 (p) REVERT: C 468 MET cc_start: 0.8844 (mmm) cc_final: 0.8581 (mmm) outliers start: 47 outliers final: 23 residues processed: 361 average time/residue: 1.4887 time to fit residues: 575.9131 Evaluate side-chains 342 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 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 A residue 519 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 494 ARG 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 200 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 319 GLN A 475 ASN A 482 ASN B 108 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.127781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115893 restraints weight = 17585.230| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.73 r_work: 0.3473 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13407 Z= 0.125 Angle : 0.589 9.581 18201 Z= 0.296 Chirality : 0.042 0.162 1986 Planarity : 0.004 0.046 2325 Dihedral : 4.649 29.313 2172 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.91 % Allowed : 15.99 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1569 helix: 1.80 (0.20), residues: 690 sheet: 1.17 (0.30), residues: 273 loop : 0.20 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 349 HIS 0.003 0.001 HIS A 177 PHE 0.025 0.001 PHE A 10 TYR 0.013 0.001 TYR A 118 ARG 0.004 0.000 ARG A 288 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 15) link_NAG-ASN : angle 2.21958 ( 45) link_BETA1-4 : bond 0.00556 ( 6) link_BETA1-4 : angle 1.08449 ( 18) hydrogen bonds : bond 0.03831 ( 661) hydrogen bonds : angle 4.21992 ( 1911) SS BOND : bond 0.00589 ( 24) SS BOND : angle 2.12004 ( 48) covalent geometry : bond 0.00287 (13359) covalent geometry : angle 0.56923 (18090) Misc. bond : bond 0.00025 ( 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 377 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 336 time to evaluate : 1.623 Fit side-chains REVERT: A 29 MET cc_start: 0.7315 (mmm) cc_final: 0.7096 (mmm) REVERT: A 302 ASP cc_start: 0.8149 (t0) cc_final: 0.7712 (t0) REVERT: A 303 LYS cc_start: 0.8747 (ptmm) cc_final: 0.8439 (ptpp) REVERT: A 352 ASP cc_start: 0.8283 (t70) cc_final: 0.8078 (t0) REVERT: A 465 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7968 (mm-30) REVERT: B 57 PHE cc_start: 0.8281 (m-80) cc_final: 0.7904 (m-80) REVERT: B 121 LYS cc_start: 0.8380 (mtpp) cc_final: 0.7986 (tttm) REVERT: B 131 ASN cc_start: 0.8505 (m-40) cc_final: 0.8278 (m-40) REVERT: B 249 VAL cc_start: 0.8357 (m) cc_final: 0.8034 (p) REVERT: B 293 ILE cc_start: 0.8534 (mm) cc_final: 0.8288 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8012 (t0) cc_final: 0.7633 (t0) REVERT: B 326 TYR cc_start: 0.8704 (m-80) cc_final: 0.8481 (m-80) REVERT: B 360 CYS cc_start: 0.7260 (m) cc_final: 0.7058 (m) REVERT: B 393 THR cc_start: 0.8297 (p) cc_final: 0.8087 (m) REVERT: B 437 GLU cc_start: 0.7877 (tp30) cc_final: 0.7605 (tm-30) REVERT: B 448 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7489 (p) REVERT: C 203 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7515 (mm-30) REVERT: C 273 TYR cc_start: 0.8577 (m-80) cc_final: 0.8283 (m-80) REVERT: C 293 ILE cc_start: 0.8424 (mm) cc_final: 0.8206 (mt) REVERT: C 326 TYR cc_start: 0.8639 (m-80) cc_final: 0.8345 (m-80) REVERT: C 359 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7608 (tp30) REVERT: C 363 THR cc_start: 0.8762 (m) cc_final: 0.8458 (p) REVERT: C 468 MET cc_start: 0.8850 (mmm) cc_final: 0.8611 (mmm) REVERT: C 518 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7664 (mm-30) outliers start: 41 outliers final: 13 residues processed: 355 average time/residue: 1.5679 time to fit residues: 597.3693 Evaluate side-chains 336 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 321 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL 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 526 LEU 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 511 ILE 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 518 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: 0.5980 chunk 151 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 115 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 475 ASN A 482 ASN B 108 ASN B 152 ASN B 376 HIS ** 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 = 0.3746 r_free = 0.3746 target = 0.127790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115898 restraints weight = 17436.748| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.73 r_work: 0.3475 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13407 Z= 0.122 Angle : 0.598 10.602 18201 Z= 0.300 Chirality : 0.042 0.172 1986 Planarity : 0.004 0.046 2325 Dihedral : 4.555 28.663 2172 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.77 % Allowed : 17.48 % Favored : 79.74 % 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: 1.91 (0.20), residues: 687 sheet: 1.20 (0.30), residues: 273 loop : 0.20 (0.25), residues: 609 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 0.012 0.001 PHE C 443 TYR 0.013 0.001 TYR A 118 ARG 0.008 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 15) link_NAG-ASN : angle 2.20926 ( 45) link_BETA1-4 : bond 0.00511 ( 6) link_BETA1-4 : angle 1.01939 ( 18) hydrogen bonds : bond 0.03769 ( 661) hydrogen bonds : angle 4.22402 ( 1911) SS BOND : bond 0.00458 ( 24) SS BOND : angle 2.24722 ( 48) covalent geometry : bond 0.00280 (13359) covalent geometry : angle 0.57733 (18090) Misc. bond : bond 0.00020 ( 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: 39 poor density : 324 time to evaluate : 1.476 Fit side-chains REVERT: A 29 MET cc_start: 0.7290 (mmm) cc_final: 0.7074 (mmm) REVERT: A 302 ASP cc_start: 0.8140 (t0) cc_final: 0.7714 (t0) REVERT: A 353 ASP cc_start: 0.7492 (p0) cc_final: 0.7253 (p0) REVERT: A 465 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 57 PHE cc_start: 0.8275 (m-80) cc_final: 0.7883 (m-80) REVERT: B 131 ASN cc_start: 0.8425 (m-40) cc_final: 0.8222 (m-40) REVERT: B 249 VAL cc_start: 0.8358 (m) cc_final: 0.8021 (p) REVERT: B 293 ILE cc_start: 0.8546 (mm) cc_final: 0.8303 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8006 (t0) cc_final: 0.7627 (t0) REVERT: B 326 TYR cc_start: 0.8695 (m-80) cc_final: 0.8445 (m-80) REVERT: B 360 CYS cc_start: 0.7235 (m) cc_final: 0.7035 (m) REVERT: B 437 GLU cc_start: 0.7854 (tp30) cc_final: 0.7586 (tm-30) REVERT: B 448 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7500 (p) REVERT: C 273 TYR cc_start: 0.8589 (m-80) cc_final: 0.8287 (m-80) REVERT: C 326 TYR cc_start: 0.8634 (m-80) cc_final: 0.8306 (m-80) REVERT: C 359 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: C 363 THR cc_start: 0.8762 (m) cc_final: 0.8474 (p) REVERT: C 468 MET cc_start: 0.8856 (mmm) cc_final: 0.8619 (mmm) REVERT: C 518 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7724 (mm-30) outliers start: 39 outliers final: 15 residues processed: 341 average time/residue: 1.5562 time to fit residues: 568.8680 Evaluate side-chains 336 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 319 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 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 511 ILE 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 359 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 C 141 GLN ** 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 = 0.3749 r_free = 0.3749 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116045 restraints weight = 17387.609| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.73 r_work: 0.3477 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2948 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= 0.129 Angle : 0.608 11.448 18201 Z= 0.303 Chirality : 0.042 0.188 1986 Planarity : 0.004 0.045 2325 Dihedral : 4.515 27.965 2172 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.27 % Allowed : 18.76 % Favored : 78.96 % 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: 1.92 (0.20), residues: 687 sheet: 1.19 (0.30), residues: 273 loop : 0.19 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 349 HIS 0.004 0.001 HIS C 376 PHE 0.027 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.010 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 15) link_NAG-ASN : angle 2.19282 ( 45) link_BETA1-4 : bond 0.00524 ( 6) link_BETA1-4 : angle 0.99217 ( 18) hydrogen bonds : bond 0.03775 ( 661) hydrogen bonds : angle 4.23972 ( 1911) SS BOND : bond 0.00441 ( 24) SS BOND : angle 2.32430 ( 48) covalent geometry : bond 0.00301 (13359) covalent geometry : angle 0.58702 (18090) Misc. bond : bond 0.00025 ( 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 364 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 1.410 Fit side-chains REVERT: A 29 MET cc_start: 0.7261 (mmm) cc_final: 0.7046 (mmm) REVERT: A 95 ARG cc_start: 0.8643 (mtt-85) cc_final: 0.8434 (mtt-85) REVERT: A 302 ASP cc_start: 0.8117 (t0) cc_final: 0.7686 (t0) REVERT: A 353 ASP cc_start: 0.7393 (p0) cc_final: 0.7187 (p0) REVERT: A 465 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7935 (mm-30) REVERT: B 57 PHE cc_start: 0.8278 (m-80) cc_final: 0.7891 (m-80) REVERT: B 249 VAL cc_start: 0.8355 (m) cc_final: 0.8031 (p) REVERT: B 293 ILE cc_start: 0.8540 (mm) cc_final: 0.8296 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8024 (t0) cc_final: 0.7647 (t0) REVERT: B 326 TYR cc_start: 0.8695 (m-80) cc_final: 0.8435 (m-80) REVERT: B 437 GLU cc_start: 0.7840 (tp30) cc_final: 0.7521 (tm-30) REVERT: B 448 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7480 (p) REVERT: C 273 TYR cc_start: 0.8599 (m-80) cc_final: 0.8298 (m-80) REVERT: C 293 ILE cc_start: 0.8439 (mm) cc_final: 0.8019 (OUTLIER) REVERT: C 326 TYR cc_start: 0.8637 (m-80) cc_final: 0.8296 (m-80) REVERT: C 359 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: C 363 THR cc_start: 0.8749 (m) cc_final: 0.8478 (p) REVERT: C 468 MET cc_start: 0.8854 (mmm) cc_final: 0.8618 (mmm) REVERT: C 518 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7780 (mm-30) outliers start: 32 outliers final: 17 residues processed: 347 average time/residue: 1.8801 time to fit residues: 697.9404 Evaluate side-chains 346 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 67 VAL 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 511 ILE Chi-restraints excluded: chain C residue 67 VAL 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 518 GLU Chi-restraints excluded: chain C residue 519 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 29 optimal weight: 0.0030 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 376 HIS A 475 ASN A 482 ASN B 108 ASN B 131 ASN ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS B 297 HIS C 475 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116780 restraints weight = 17427.198| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.71 r_work: 0.3484 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3056 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= 0.125 Angle : 0.619 12.085 18201 Z= 0.307 Chirality : 0.043 0.196 1986 Planarity : 0.004 0.044 2325 Dihedral : 4.501 27.523 2172 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.27 % Allowed : 19.12 % Favored : 78.61 % 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: 1.68 (0.21), residues: 1569 helix: 1.95 (0.20), residues: 687 sheet: 1.20 (0.30), residues: 273 loop : 0.18 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 349 HIS 0.003 0.001 HIS A 177 PHE 0.011 0.001 PHE A 114 TYR 0.015 0.001 TYR A 118 ARG 0.008 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 15) link_NAG-ASN : angle 2.16643 ( 45) link_BETA1-4 : bond 0.00510 ( 6) link_BETA1-4 : angle 0.99188 ( 18) hydrogen bonds : bond 0.03700 ( 661) hydrogen bonds : angle 4.25578 ( 1911) SS BOND : bond 0.00507 ( 24) SS BOND : angle 2.43017 ( 48) covalent geometry : bond 0.00289 (13359) covalent geometry : angle 0.59764 (18090) Misc. bond : bond 0.00024 ( 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 355 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 323 time to evaluate : 1.481 Fit side-chains REVERT: A 7 MET cc_start: 0.7867 (mmp) cc_final: 0.7528 (mmp) REVERT: A 29 MET cc_start: 0.7269 (mmm) cc_final: 0.7050 (mmm) REVERT: A 57 PHE cc_start: 0.8316 (m-80) cc_final: 0.8014 (m-80) REVERT: A 95 ARG cc_start: 0.8648 (mtt-85) cc_final: 0.8442 (mtt-85) REVERT: A 302 ASP cc_start: 0.8119 (t0) cc_final: 0.7688 (t0) REVERT: A 465 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7925 (mm-30) REVERT: B 57 PHE cc_start: 0.8286 (m-80) cc_final: 0.7880 (m-80) REVERT: B 249 VAL cc_start: 0.8366 (m) cc_final: 0.8035 (p) REVERT: B 293 ILE cc_start: 0.8529 (mm) cc_final: 0.8278 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8007 (t0) cc_final: 0.7629 (t0) REVERT: B 326 TYR cc_start: 0.8692 (m-80) cc_final: 0.8414 (m-80) REVERT: B 437 GLU cc_start: 0.7817 (tp30) cc_final: 0.7489 (tm-30) REVERT: B 448 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7479 (p) REVERT: B 490 GLU cc_start: 0.8316 (pt0) cc_final: 0.8088 (mt-10) REVERT: C 121 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7894 (tptp) REVERT: C 273 TYR cc_start: 0.8586 (m-80) cc_final: 0.8291 (m-80) REVERT: C 293 ILE cc_start: 0.8348 (mm) cc_final: 0.8121 (OUTLIER) REVERT: C 326 TYR cc_start: 0.8625 (m-80) cc_final: 0.8276 (m-80) REVERT: C 359 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: C 363 THR cc_start: 0.8733 (m) cc_final: 0.8467 (p) REVERT: C 468 MET cc_start: 0.8850 (mmm) cc_final: 0.8609 (mmm) outliers start: 32 outliers final: 20 residues processed: 335 average time/residue: 1.5791 time to fit residues: 566.1633 Evaluate side-chains 345 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 325 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 215 ILE 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 67 VAL 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 511 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 67 VAL 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 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 101 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 108 ASN B 131 ASN B 133 GLN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN C 463 ASN C 475 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.128233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116397 restraints weight = 17262.287| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.73 r_work: 0.3477 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3109 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= 0.139 Angle : 0.639 13.032 18201 Z= 0.316 Chirality : 0.043 0.189 1986 Planarity : 0.004 0.044 2325 Dihedral : 4.491 26.883 2172 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.99 % Allowed : 19.90 % Favored : 78.11 % 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: 1.94 (0.20), residues: 687 sheet: 1.17 (0.30), residues: 273 loop : 0.14 (0.25), residues: 609 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 0.029 0.001 PHE A 10 TYR 0.018 0.001 TYR A 118 ARG 0.008 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 15) link_NAG-ASN : angle 2.17339 ( 45) link_BETA1-4 : bond 0.00477 ( 6) link_BETA1-4 : angle 0.96269 ( 18) hydrogen bonds : bond 0.03835 ( 661) hydrogen bonds : angle 4.27562 ( 1911) SS BOND : bond 0.00507 ( 24) SS BOND : angle 2.68141 ( 48) covalent geometry : bond 0.00327 (13359) covalent geometry : angle 0.61610 (18090) Misc. bond : bond 0.00030 ( 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 352 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 324 time to evaluate : 1.587 Fit side-chains REVERT: A 7 MET cc_start: 0.7912 (mmp) cc_final: 0.7594 (mmp) REVERT: A 57 PHE cc_start: 0.8351 (m-80) cc_final: 0.8061 (m-80) REVERT: A 302 ASP cc_start: 0.8151 (t0) cc_final: 0.7726 (t0) REVERT: A 465 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7935 (mm-30) REVERT: B 249 VAL cc_start: 0.8382 (m) cc_final: 0.8055 (p) REVERT: B 293 ILE cc_start: 0.8532 (mm) cc_final: 0.8288 (OUTLIER) REVERT: B 302 ASP cc_start: 0.8037 (t0) cc_final: 0.7665 (t0) REVERT: B 326 TYR cc_start: 0.8708 (m-80) cc_final: 0.8418 (m-80) REVERT: B 437 GLU cc_start: 0.7791 (tp30) cc_final: 0.7471 (tm-30) REVERT: B 448 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7447 (p) REVERT: C 273 TYR cc_start: 0.8592 (m-80) cc_final: 0.8295 (m-80) REVERT: C 326 TYR cc_start: 0.8649 (m-80) cc_final: 0.8290 (m-80) REVERT: C 359 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: C 363 THR cc_start: 0.8743 (m) cc_final: 0.8475 (p) REVERT: C 468 MET cc_start: 0.8847 (mmm) cc_final: 0.8606 (mmm) outliers start: 28 outliers final: 17 residues processed: 337 average time/residue: 1.9829 time to fit residues: 721.7594 Evaluate side-chains 342 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 324 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 215 ILE 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 67 VAL 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 C residue 67 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 376 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116674 restraints weight = 17452.140| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.72 r_work: 0.3488 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13407 Z= 0.128 Angle : 0.628 13.135 18201 Z= 0.312 Chirality : 0.043 0.193 1986 Planarity : 0.004 0.044 2325 Dihedral : 4.458 26.567 2172 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.99 % Allowed : 19.76 % Favored : 78.25 % 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: 1.96 (0.20), residues: 687 sheet: 1.16 (0.30), residues: 273 loop : 0.15 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 349 HIS 0.003 0.001 HIS A 376 PHE 0.011 0.001 PHE A 114 TYR 0.016 0.001 TYR A 118 ARG 0.007 0.000 ARG C 494 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 15) link_NAG-ASN : angle 2.09709 ( 45) link_BETA1-4 : bond 0.00482 ( 6) link_BETA1-4 : angle 0.93308 ( 18) hydrogen bonds : bond 0.03738 ( 661) hydrogen bonds : angle 4.26799 ( 1911) SS BOND : bond 0.00501 ( 24) SS BOND : angle 2.55604 ( 48) covalent geometry : bond 0.00299 (13359) covalent geometry : angle 0.60607 (18090) Misc. bond : bond 0.00026 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13370.20 seconds wall clock time: 233 minutes 16.28 seconds (13996.28 seconds total)