Starting phenix.real_space_refine on Sun Nov 17 05:29:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/11_2024/8on7_16981.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/11_2024/8on7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/11_2024/8on7_16981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/11_2024/8on7_16981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/11_2024/8on7_16981.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8on7_16981/11_2024/8on7_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-5513/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: 8.07, per 1000 atoms: 0.62 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: 3.81 Conformation dependent library (CDL) restraints added in 1.7 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: 1.42 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: 4.49 Time building geometry restraints manager: 4.36 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: 0.540 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.400 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.630 ------------------------------------------------------------------------------- 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 0.035 13359 Z= 0.248 Angle : 0.714 8.648 18090 Z= 0.390 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 *********************** 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 : 1.381 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: 1.6136 time to fit residues: 797.9740 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 : 1.522 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13359 Z= 0.190 Angle : 0.600 12.570 18090 Z= 0.315 Chirality : 0.044 0.226 1986 Planarity : 0.005 0.049 2325 Dihedral : 5.284 36.544 2172 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.84 % Allowed : 11.66 % 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: 1.71 (0.21), residues: 1569 helix: 1.56 (0.20), residues: 690 sheet: 1.42 (0.29), residues: 267 loop : 0.66 (0.26), 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 *********************** 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 427 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 387 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 7 MET cc_start: 0.6940 (mmm) cc_final: 0.6725 (mmp) REVERT: A 16 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7418 (mtt) REVERT: A 21 LYS cc_start: 0.6652 (mmtp) cc_final: 0.6286 (mttm) REVERT: A 29 MET cc_start: 0.6891 (mmm) cc_final: 0.6522 (mmm) REVERT: A 31 ARG cc_start: 0.6539 (ttm170) cc_final: 0.6209 (ttm170) REVERT: A 50 SER cc_start: 0.7482 (t) cc_final: 0.7040 (p) REVERT: A 66 GLU cc_start: 0.8324 (pt0) cc_final: 0.7991 (pt0) REVERT: A 95 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7579 (mtt-85) REVERT: A 125 TYR cc_start: 0.8101 (m-80) cc_final: 0.7876 (m-80) REVERT: A 138 GLU cc_start: 0.7406 (mp0) cc_final: 0.7061 (mp0) REVERT: A 216 GLU cc_start: 0.7855 (mp0) cc_final: 0.7634 (mp0) REVERT: A 271 GLU cc_start: 0.7714 (pt0) cc_final: 0.7308 (pt0) REVERT: A 273 TYR cc_start: 0.8430 (m-80) cc_final: 0.8163 (m-80) REVERT: A 302 ASP cc_start: 0.7644 (t0) cc_final: 0.7136 (t0) REVERT: A 303 LYS cc_start: 0.8165 (ptmm) cc_final: 0.7624 (ptpp) REVERT: A 347 ILE cc_start: 0.7646 (mt) cc_final: 0.7235 (tp) REVERT: A 353 ASP cc_start: 0.7432 (p0) cc_final: 0.7212 (p0) REVERT: A 359 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 380 LYS cc_start: 0.7187 (mtmt) cc_final: 0.6874 (mtpp) REVERT: A 391 LYS cc_start: 0.8013 (mptt) cc_final: 0.7771 (mmtm) REVERT: A 409 SER cc_start: 0.8529 (t) cc_final: 0.8243 (m) REVERT: A 425 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 448 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7131 (m) REVERT: A 465 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 16 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7056 (mtm) REVERT: B 21 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6349 (mttt) REVERT: B 31 ARG cc_start: 0.6479 (ttm-80) cc_final: 0.6212 (ttm-80) REVERT: B 50 SER cc_start: 0.7800 (t) cc_final: 0.7313 (p) REVERT: B 51 GLU cc_start: 0.7213 (mt-10) cc_final: 0.7003 (mt-10) REVERT: B 120 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7872 (ttmm) REVERT: B 121 LYS cc_start: 0.7973 (mtpp) cc_final: 0.7490 (tttm) REVERT: B 138 GLU cc_start: 0.7381 (mp0) cc_final: 0.6964 (mp0) REVERT: B 141 GLN cc_start: 0.8025 (mm110) cc_final: 0.7796 (mm-40) REVERT: B 164 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7821 (mm-40) REVERT: B 178 ARG cc_start: 0.7989 (ttm170) cc_final: 0.7739 (ttm170) REVERT: B 213 GLU cc_start: 0.7677 (pt0) cc_final: 0.7406 (pt0) REVERT: B 244 GLU cc_start: 0.7951 (tp30) cc_final: 0.7731 (tp30) REVERT: B 293 ILE cc_start: 0.7909 (mm) cc_final: 0.7663 (mt) REVERT: B 302 ASP cc_start: 0.7565 (t0) cc_final: 0.7076 (t0) REVERT: B 303 LYS cc_start: 0.8286 (ptmm) cc_final: 0.7722 (ptpp) REVERT: B 326 TYR cc_start: 0.7660 (m-80) cc_final: 0.7222 (m-80) REVERT: B 347 ILE cc_start: 0.7845 (mt) cc_final: 0.7441 (tp) REVERT: B 362 PHE cc_start: 0.7960 (m-80) cc_final: 0.7748 (m-80) REVERT: B 388 LYS cc_start: 0.7380 (mtmt) cc_final: 0.7096 (mtmm) REVERT: B 391 LYS cc_start: 0.7573 (mptt) cc_final: 0.7307 (mmtp) REVERT: B 407 GLU cc_start: 0.7793 (tt0) cc_final: 0.7256 (tt0) REVERT: B 425 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6994 (mt-10) REVERT: B 427 ASP cc_start: 0.7592 (m-30) cc_final: 0.7391 (m-30) REVERT: C 29 MET cc_start: 0.7071 (mmm) cc_final: 0.6695 (mmm) REVERT: C 44 MET cc_start: 0.7269 (mmm) cc_final: 0.6882 (mmm) REVERT: C 49 MET cc_start: 0.7426 (mmm) cc_final: 0.7187 (mmm) REVERT: C 120 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7416 (ttmm) REVERT: C 213 GLU cc_start: 0.7635 (pt0) cc_final: 0.7239 (pt0) REVERT: C 273 TYR cc_start: 0.8496 (m-80) cc_final: 0.8130 (m-80) REVERT: C 288 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7582 (mtp85) REVERT: C 326 TYR cc_start: 0.7514 (m-80) cc_final: 0.7067 (m-80) REVERT: C 359 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6561 (mt-10) REVERT: C 363 THR cc_start: 0.7848 (m) cc_final: 0.7386 (p) REVERT: C 386 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7815 (ttpt) REVERT: C 391 LYS cc_start: 0.7935 (mptt) cc_final: 0.7678 (mmtp) REVERT: C 396 MET cc_start: 0.7796 (mmp) cc_final: 0.7537 (mmm) REVERT: C 399 CYS cc_start: 0.6769 (m) cc_final: 0.6219 (m) REVERT: C 407 GLU cc_start: 0.7683 (tt0) cc_final: 0.7426 (tt0) REVERT: C 411 ASP cc_start: 0.7934 (m-30) cc_final: 0.7721 (m-30) REVERT: C 468 MET cc_start: 0.8470 (mmm) cc_final: 0.8236 (mmm) REVERT: C 480 ASP cc_start: 0.7003 (m-30) cc_final: 0.6728 (m-30) REVERT: C 489 SER cc_start: 0.8117 (m) cc_final: 0.7837 (m) REVERT: C 518 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6362 (mm-30) outliers start: 40 outliers final: 7 residues processed: 405 average time/residue: 1.6594 time to fit residues: 717.5358 Evaluate side-chains 378 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 365 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 120 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 386 LYS 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 78 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 0.0070 chunk 140 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 106 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 482 ASN C 106 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13359 Z= 0.201 Angle : 0.590 12.533 18090 Z= 0.307 Chirality : 0.044 0.231 1986 Planarity : 0.005 0.050 2325 Dihedral : 5.174 31.753 2172 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.91 % Allowed : 13.22 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.68 (0.20), residues: 690 sheet: 1.30 (0.29), residues: 270 loop : 0.50 (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 260 PHE 0.014 0.001 PHE B 443 TYR 0.014 0.001 TYR C 118 ARG 0.005 0.000 ARG A 288 *********************** 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 405 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 364 time to evaluate : 1.552 Fit side-chains REVERT: A 7 MET cc_start: 0.6979 (mmm) cc_final: 0.6768 (mmp) REVERT: A 16 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7448 (mtt) REVERT: A 29 MET cc_start: 0.6907 (mmm) cc_final: 0.6527 (mmm) REVERT: A 31 ARG cc_start: 0.6550 (ttm170) cc_final: 0.6233 (ttm170) REVERT: A 50 SER cc_start: 0.7510 (t) cc_final: 0.7083 (p) REVERT: A 66 GLU cc_start: 0.8295 (pt0) cc_final: 0.7983 (pt0) REVERT: A 95 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7676 (mtt-85) REVERT: A 119 MET cc_start: 0.8234 (mmt) cc_final: 0.7864 (mmt) REVERT: A 125 TYR cc_start: 0.8128 (m-80) cc_final: 0.7881 (m-80) REVERT: A 216 GLU cc_start: 0.7866 (mp0) cc_final: 0.7640 (mp0) REVERT: A 271 GLU cc_start: 0.7645 (pt0) cc_final: 0.7240 (pt0) REVERT: A 273 TYR cc_start: 0.8461 (m-80) cc_final: 0.8203 (m-80) REVERT: A 293 ILE cc_start: 0.7618 (mm) cc_final: 0.7404 (mm) REVERT: A 302 ASP cc_start: 0.7646 (t0) cc_final: 0.7144 (t0) REVERT: A 303 LYS cc_start: 0.8164 (ptmm) cc_final: 0.7659 (ptpp) REVERT: A 347 ILE cc_start: 0.7705 (mt) cc_final: 0.7256 (tp) REVERT: A 359 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 373 MET cc_start: 0.6926 (mmm) cc_final: 0.6725 (mmp) REVERT: A 391 LYS cc_start: 0.7981 (mptt) cc_final: 0.7732 (mmtp) REVERT: A 409 SER cc_start: 0.8523 (t) cc_final: 0.7984 (p) REVERT: A 425 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6941 (mt-10) REVERT: A 448 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.7157 (m) REVERT: A 465 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 490 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 16 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7104 (mtm) REVERT: B 50 SER cc_start: 0.7828 (t) cc_final: 0.7402 (p) REVERT: B 51 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6957 (mt-10) REVERT: B 120 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7846 (ttmm) REVERT: B 121 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7484 (tttm) REVERT: B 138 GLU cc_start: 0.7395 (mp0) cc_final: 0.6976 (mp0) REVERT: B 164 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7822 (mm-40) REVERT: B 213 GLU cc_start: 0.7784 (pt0) cc_final: 0.7513 (pt0) REVERT: B 302 ASP cc_start: 0.7554 (t0) cc_final: 0.7051 (t0) REVERT: B 303 LYS cc_start: 0.8305 (ptmm) cc_final: 0.7722 (ptpp) REVERT: B 326 TYR cc_start: 0.7610 (m-80) cc_final: 0.7232 (m-80) REVERT: B 347 ILE cc_start: 0.7897 (mt) cc_final: 0.7500 (tp) REVERT: B 362 PHE cc_start: 0.7943 (m-80) cc_final: 0.7709 (m-80) REVERT: B 388 LYS cc_start: 0.7365 (mtmt) cc_final: 0.7155 (mtmm) REVERT: B 391 LYS cc_start: 0.7622 (mptt) cc_final: 0.7269 (mmtp) REVERT: B 399 CYS cc_start: 0.6952 (m) cc_final: 0.6568 (m) REVERT: B 407 GLU cc_start: 0.7804 (tt0) cc_final: 0.7260 (tt0) REVERT: B 425 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 518 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6376 (mm-30) REVERT: C 29 MET cc_start: 0.7054 (mmm) cc_final: 0.6706 (mmm) REVERT: C 44 MET cc_start: 0.7277 (mmm) cc_final: 0.6855 (mmm) REVERT: C 49 MET cc_start: 0.7442 (mmm) cc_final: 0.7146 (mmm) REVERT: C 120 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7433 (ttmm) REVERT: C 142 GLU cc_start: 0.7586 (tp30) cc_final: 0.7342 (tt0) REVERT: C 156 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7337 (mm-30) REVERT: C 203 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 234 ASP cc_start: 0.7951 (p0) cc_final: 0.7744 (p0) REVERT: C 235 GLU cc_start: 0.8052 (pt0) cc_final: 0.7241 (pm20) REVERT: C 273 TYR cc_start: 0.8554 (m-80) cc_final: 0.8178 (m-80) REVERT: C 288 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7570 (mtp85) REVERT: C 293 ILE cc_start: 0.7921 (mm) cc_final: 0.7331 (mt) REVERT: C 326 TYR cc_start: 0.7492 (m-80) cc_final: 0.7034 (m-80) REVERT: C 359 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6253 (tp30) REVERT: C 363 THR cc_start: 0.7872 (m) cc_final: 0.7173 (p) REVERT: C 386 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7850 (ttpt) REVERT: C 391 LYS cc_start: 0.7917 (mptt) cc_final: 0.7648 (mmtp) REVERT: C 396 MET cc_start: 0.7802 (mmp) cc_final: 0.7519 (mmm) REVERT: C 399 CYS cc_start: 0.6728 (m) cc_final: 0.6193 (m) REVERT: C 409 SER cc_start: 0.8429 (m) cc_final: 0.8174 (p) REVERT: C 453 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7415 (mt-10) REVERT: C 465 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7842 (tp30) REVERT: C 468 MET cc_start: 0.8541 (mmm) cc_final: 0.8317 (mmm) REVERT: C 480 ASP cc_start: 0.7032 (m-30) cc_final: 0.6791 (m-30) REVERT: C 489 SER cc_start: 0.8163 (m) cc_final: 0.7865 (m) outliers start: 41 outliers final: 17 residues processed: 379 average time/residue: 1.6490 time to fit residues: 667.6165 Evaluate side-chains 366 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 344 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 520 LEU 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 381 CYS Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 490 GLU 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 140 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN C 482 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13359 Z= 0.197 Angle : 0.562 7.002 18090 Z= 0.291 Chirality : 0.043 0.189 1986 Planarity : 0.005 0.049 2325 Dihedral : 4.865 30.702 2172 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.06 % Allowed : 13.57 % Favored : 83.37 % 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: 1.76 (0.20), residues: 690 sheet: 1.29 (0.29), residues: 270 loop : 0.40 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 PHE 0.023 0.001 PHE A 10 TYR 0.014 0.001 TYR C 118 ARG 0.006 0.000 ARG A 288 *********************** 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 392 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 349 time to evaluate : 1.788 Fit side-chains REVERT: A 7 MET cc_start: 0.7016 (mmm) cc_final: 0.6803 (mmp) REVERT: A 21 LYS cc_start: 0.6502 (mttt) cc_final: 0.6287 (mttm) REVERT: A 29 MET cc_start: 0.6980 (mmm) cc_final: 0.6564 (mmm) REVERT: A 31 ARG cc_start: 0.6469 (ttm170) cc_final: 0.6166 (ttm170) REVERT: A 49 MET cc_start: 0.7394 (mmp) cc_final: 0.7171 (mmm) REVERT: A 50 SER cc_start: 0.7517 (t) cc_final: 0.7089 (p) REVERT: A 66 GLU cc_start: 0.8311 (pt0) cc_final: 0.8046 (pt0) REVERT: A 95 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7689 (mtt-85) REVERT: A 119 MET cc_start: 0.8335 (mmt) cc_final: 0.7910 (mmm) REVERT: A 125 TYR cc_start: 0.8108 (m-80) cc_final: 0.7872 (m-80) REVERT: A 141 GLN cc_start: 0.7870 (mm110) cc_final: 0.7641 (mm110) REVERT: A 216 GLU cc_start: 0.7844 (mp0) cc_final: 0.7638 (mp0) REVERT: A 271 GLU cc_start: 0.7603 (pt0) cc_final: 0.7198 (pt0) REVERT: A 273 TYR cc_start: 0.8469 (m-80) cc_final: 0.8241 (m-80) REVERT: A 289 ARG cc_start: 0.7844 (ttt-90) cc_final: 0.7621 (ttt-90) REVERT: A 293 ILE cc_start: 0.7613 (mm) cc_final: 0.7313 (mp) REVERT: A 302 ASP cc_start: 0.7676 (t0) cc_final: 0.7157 (t0) REVERT: A 303 LYS cc_start: 0.8109 (ptmm) cc_final: 0.7589 (ptpp) REVERT: A 347 ILE cc_start: 0.7690 (mt) cc_final: 0.7254 (tp) REVERT: A 359 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6675 (mt-10) REVERT: A 380 LYS cc_start: 0.7208 (mtmt) cc_final: 0.6892 (mtpp) REVERT: A 391 LYS cc_start: 0.7987 (mptt) cc_final: 0.7782 (mppt) REVERT: A 409 SER cc_start: 0.8533 (t) cc_final: 0.8039 (p) REVERT: A 425 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6948 (mt-10) REVERT: A 438 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7848 (mtpp) REVERT: A 465 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7710 (mm-30) REVERT: A 490 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 16 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7118 (mtm) REVERT: B 50 SER cc_start: 0.7820 (t) cc_final: 0.7410 (p) REVERT: B 57 PHE cc_start: 0.7432 (m-80) cc_final: 0.7153 (m-80) REVERT: B 120 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7879 (ttmm) REVERT: B 121 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7484 (tttm) REVERT: B 138 GLU cc_start: 0.7411 (mp0) cc_final: 0.6977 (mp0) REVERT: B 213 GLU cc_start: 0.7855 (pt0) cc_final: 0.7545 (pt0) REVERT: B 293 ILE cc_start: 0.7929 (mm) cc_final: 0.7723 (mt) REVERT: B 302 ASP cc_start: 0.7633 (t0) cc_final: 0.7183 (t0) REVERT: B 303 LYS cc_start: 0.8307 (ptmm) cc_final: 0.7729 (ptpp) REVERT: B 326 TYR cc_start: 0.7588 (m-80) cc_final: 0.7104 (m-80) REVERT: B 347 ILE cc_start: 0.7964 (mt) cc_final: 0.7576 (tp) REVERT: B 362 PHE cc_start: 0.7933 (m-80) cc_final: 0.7712 (m-80) REVERT: B 370 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6905 (mm-40) REVERT: B 380 LYS cc_start: 0.7139 (mtmt) cc_final: 0.6906 (mtmt) REVERT: B 388 LYS cc_start: 0.7397 (mtmt) cc_final: 0.7164 (mtmm) REVERT: B 391 LYS cc_start: 0.7592 (mptt) cc_final: 0.7238 (mmtp) REVERT: B 399 CYS cc_start: 0.7021 (m) cc_final: 0.6614 (m) REVERT: B 407 GLU cc_start: 0.7813 (tt0) cc_final: 0.7255 (tt0) REVERT: B 425 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6881 (mt-10) REVERT: B 518 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6612 (mm-30) REVERT: C 29 MET cc_start: 0.7122 (mmm) cc_final: 0.6763 (mmm) REVERT: C 44 MET cc_start: 0.7284 (mmm) cc_final: 0.6843 (mmm) REVERT: C 49 MET cc_start: 0.7389 (mmm) cc_final: 0.7012 (mmm) REVERT: C 120 LYS cc_start: 0.7703 (mtmt) cc_final: 0.7430 (ttmm) REVERT: C 156 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7284 (mm-30) REVERT: C 203 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 234 ASP cc_start: 0.7961 (p0) cc_final: 0.7724 (p0) REVERT: C 235 GLU cc_start: 0.8031 (pt0) cc_final: 0.7199 (pm20) REVERT: C 273 TYR cc_start: 0.8568 (m-80) cc_final: 0.8145 (m-80) REVERT: C 326 TYR cc_start: 0.7413 (m-80) cc_final: 0.6974 (m-80) REVERT: C 359 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6338 (tp30) REVERT: C 363 THR cc_start: 0.7998 (m) cc_final: 0.7273 (p) REVERT: C 386 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7895 (ttpt) REVERT: C 391 LYS cc_start: 0.7896 (mptt) cc_final: 0.7629 (mmtp) REVERT: C 396 MET cc_start: 0.7798 (mmp) cc_final: 0.7522 (mmm) REVERT: C 399 CYS cc_start: 0.6770 (m) cc_final: 0.6318 (m) REVERT: C 437 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7346 (tm-30) REVERT: C 453 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 465 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7863 (tp30) REVERT: C 468 MET cc_start: 0.8574 (mmm) cc_final: 0.8290 (mmm) REVERT: C 480 ASP cc_start: 0.7051 (m-30) cc_final: 0.6807 (m-30) REVERT: C 489 SER cc_start: 0.8170 (m) cc_final: 0.7884 (m) outliers start: 43 outliers final: 16 residues processed: 365 average time/residue: 1.6839 time to fit residues: 656.2710 Evaluate side-chains 360 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 340 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 200 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 438 LYS 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 16 MET Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 511 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 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.7980 chunk 85 optimal weight: 0.0020 chunk 2 optimal weight: 0.0170 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.5226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 475 ASN A 482 ASN B 108 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13359 Z= 0.166 Angle : 0.541 7.307 18090 Z= 0.279 Chirality : 0.042 0.165 1986 Planarity : 0.004 0.047 2325 Dihedral : 4.660 30.009 2172 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.13 % Allowed : 14.50 % Favored : 82.37 % 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: 1.87 (0.20), residues: 690 sheet: 1.25 (0.30), residues: 273 loop : 0.25 (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 C 376 PHE 0.011 0.001 PHE C 443 TYR 0.013 0.001 TYR B 118 ARG 0.004 0.000 ARG A 288 *********************** 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 400 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 356 time to evaluate : 1.573 Fit side-chains REVERT: A 7 MET cc_start: 0.7094 (mmm) cc_final: 0.6889 (mmp) REVERT: A 29 MET cc_start: 0.7025 (mmm) cc_final: 0.6601 (mmm) REVERT: A 31 ARG cc_start: 0.6549 (ttm170) cc_final: 0.6216 (ttm170) REVERT: A 49 MET cc_start: 0.7461 (mmp) cc_final: 0.7234 (mmm) REVERT: A 50 SER cc_start: 0.7577 (t) cc_final: 0.7197 (p) REVERT: A 66 GLU cc_start: 0.8304 (pt0) cc_final: 0.8036 (pt0) REVERT: A 86 ASP cc_start: 0.7629 (t0) cc_final: 0.7299 (t0) REVERT: A 95 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7688 (mtt-85) REVERT: A 119 MET cc_start: 0.8335 (mmt) cc_final: 0.7930 (mmt) REVERT: A 125 TYR cc_start: 0.8130 (m-80) cc_final: 0.7899 (m-80) REVERT: A 141 GLN cc_start: 0.7840 (mm110) cc_final: 0.7615 (mm-40) REVERT: A 216 GLU cc_start: 0.7843 (mp0) cc_final: 0.7631 (mp0) REVERT: A 271 GLU cc_start: 0.7525 (pt0) cc_final: 0.7106 (pt0) REVERT: A 273 TYR cc_start: 0.8468 (m-80) cc_final: 0.8244 (m-80) REVERT: A 289 ARG cc_start: 0.7853 (ttt-90) cc_final: 0.7648 (ttt-90) REVERT: A 302 ASP cc_start: 0.7702 (t0) cc_final: 0.7154 (t0) REVERT: A 303 LYS cc_start: 0.8118 (ptmm) cc_final: 0.7573 (ptpp) REVERT: A 347 ILE cc_start: 0.7676 (mt) cc_final: 0.7263 (tp) REVERT: A 353 ASP cc_start: 0.7383 (p0) cc_final: 0.7151 (p0) REVERT: A 359 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6669 (mt-10) REVERT: A 391 LYS cc_start: 0.8000 (mptt) cc_final: 0.7783 (mmtm) REVERT: A 409 SER cc_start: 0.8564 (t) cc_final: 0.8089 (p) REVERT: A 425 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6930 (mt-10) REVERT: A 465 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 16 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7077 (mtm) REVERT: B 50 SER cc_start: 0.7802 (t) cc_final: 0.7377 (p) REVERT: B 82 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: B 111 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7423 (mm-30) REVERT: B 113 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6768 (mm-30) REVERT: B 120 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7894 (ttmm) REVERT: B 121 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7526 (tttm) REVERT: B 138 GLU cc_start: 0.7427 (mp0) cc_final: 0.7028 (mp0) REVERT: B 156 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7111 (mm-30) REVERT: B 246 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7827 (mtt180) REVERT: B 293 ILE cc_start: 0.7950 (mm) cc_final: 0.7460 (mt) REVERT: B 302 ASP cc_start: 0.7631 (t0) cc_final: 0.7164 (t0) REVERT: B 303 LYS cc_start: 0.8310 (ptmm) cc_final: 0.7731 (ptpp) REVERT: B 326 TYR cc_start: 0.7554 (m-80) cc_final: 0.7033 (m-80) REVERT: B 347 ILE cc_start: 0.7884 (mt) cc_final: 0.7532 (tp) REVERT: B 362 PHE cc_start: 0.7922 (m-80) cc_final: 0.7645 (m-80) REVERT: B 370 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6873 (mm-40) REVERT: B 380 LYS cc_start: 0.7085 (mtmt) cc_final: 0.6850 (mtmt) REVERT: B 391 LYS cc_start: 0.7578 (mptt) cc_final: 0.7217 (mmtp) REVERT: B 399 CYS cc_start: 0.7051 (m) cc_final: 0.6618 (m) REVERT: B 407 GLU cc_start: 0.7828 (tt0) cc_final: 0.7556 (tt0) REVERT: B 425 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 437 GLU cc_start: 0.7709 (tp30) cc_final: 0.7112 (tm-30) REVERT: B 466 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7196 (mm-30) REVERT: C 29 MET cc_start: 0.7076 (mmm) cc_final: 0.6719 (mmm) REVERT: C 44 MET cc_start: 0.7295 (mmm) cc_final: 0.6810 (mmm) REVERT: C 49 MET cc_start: 0.7461 (mmm) cc_final: 0.7177 (mmm) REVERT: C 120 LYS cc_start: 0.7700 (mtmt) cc_final: 0.7434 (ttmm) REVERT: C 156 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7287 (mm-30) REVERT: C 203 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7400 (mm-30) REVERT: C 235 GLU cc_start: 0.8010 (pt0) cc_final: 0.7723 (pt0) REVERT: C 273 TYR cc_start: 0.8568 (m-80) cc_final: 0.8136 (m-80) REVERT: C 326 TYR cc_start: 0.7490 (m-80) cc_final: 0.7000 (m-80) REVERT: C 359 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6358 (tp30) REVERT: C 363 THR cc_start: 0.7887 (m) cc_final: 0.7194 (p) REVERT: C 386 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7777 (ttmt) REVERT: C 391 LYS cc_start: 0.7860 (mptt) cc_final: 0.7595 (mmtp) REVERT: C 396 MET cc_start: 0.7793 (mmp) cc_final: 0.7490 (mmm) REVERT: C 399 CYS cc_start: 0.6791 (m) cc_final: 0.6417 (m) REVERT: C 437 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7301 (tm-30) REVERT: C 453 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 465 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7860 (tp30) REVERT: C 468 MET cc_start: 0.8563 (mmm) cc_final: 0.8294 (mmm) REVERT: C 480 ASP cc_start: 0.7050 (m-30) cc_final: 0.6813 (m-30) REVERT: C 489 SER cc_start: 0.7981 (m) cc_final: 0.7691 (m) outliers start: 44 outliers final: 18 residues processed: 372 average time/residue: 1.6443 time to fit residues: 654.6318 Evaluate side-chains 367 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 345 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 200 LYS 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 82 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS 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 50 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 475 ASN A 482 ASN B 108 ASN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13359 Z= 0.209 Angle : 0.562 7.980 18090 Z= 0.288 Chirality : 0.043 0.170 1986 Planarity : 0.004 0.046 2325 Dihedral : 4.603 29.391 2172 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.62 % Allowed : 14.50 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.21), residues: 1569 helix: 1.89 (0.20), residues: 690 sheet: 1.28 (0.30), residues: 273 loop : 0.19 (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 B 177 PHE 0.025 0.001 PHE A 10 TYR 0.015 0.001 TYR C 118 ARG 0.006 0.000 ARG A 288 *********************** 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 397 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 346 time to evaluate : 1.673 Fit side-chains REVERT: A 21 LYS cc_start: 0.6391 (mttt) cc_final: 0.6107 (mttt) REVERT: A 29 MET cc_start: 0.7014 (mmm) cc_final: 0.6587 (mmm) REVERT: A 31 ARG cc_start: 0.6548 (ttm170) cc_final: 0.6201 (ttm170) REVERT: A 49 MET cc_start: 0.7451 (mmp) cc_final: 0.7223 (mmm) REVERT: A 50 SER cc_start: 0.7569 (t) cc_final: 0.7206 (p) REVERT: A 66 GLU cc_start: 0.8300 (pt0) cc_final: 0.8021 (pt0) REVERT: A 86 ASP cc_start: 0.7634 (t0) cc_final: 0.7297 (t0) REVERT: A 95 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7537 (mtt-85) REVERT: A 119 MET cc_start: 0.8348 (mmt) cc_final: 0.7930 (mmt) REVERT: A 125 TYR cc_start: 0.8132 (m-80) cc_final: 0.7881 (m-80) REVERT: A 141 GLN cc_start: 0.7850 (mm110) cc_final: 0.7606 (mm-40) REVERT: A 216 GLU cc_start: 0.7852 (mp0) cc_final: 0.7647 (mp0) REVERT: A 244 GLU cc_start: 0.7776 (tp30) cc_final: 0.7337 (tp30) REVERT: A 271 GLU cc_start: 0.7536 (pt0) cc_final: 0.7118 (pt0) REVERT: A 273 TYR cc_start: 0.8470 (m-80) cc_final: 0.8249 (m-80) REVERT: A 293 ILE cc_start: 0.7536 (mm) cc_final: 0.6958 (OUTLIER) REVERT: A 302 ASP cc_start: 0.7707 (t0) cc_final: 0.7165 (t0) REVERT: A 303 LYS cc_start: 0.8129 (ptmm) cc_final: 0.7604 (ptpp) REVERT: A 347 ILE cc_start: 0.7664 (mt) cc_final: 0.7259 (tp) REVERT: A 359 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6665 (mt-10) REVERT: A 391 LYS cc_start: 0.8023 (mptt) cc_final: 0.7809 (mmtm) REVERT: A 409 SER cc_start: 0.8565 (t) cc_final: 0.8093 (p) REVERT: A 425 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 438 LYS cc_start: 0.8096 (mttp) cc_final: 0.7839 (mtpp) REVERT: A 465 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 16 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7117 (mtm) REVERT: B 50 SER cc_start: 0.7777 (t) cc_final: 0.7380 (p) REVERT: B 57 PHE cc_start: 0.7482 (m-80) cc_final: 0.7225 (m-80) REVERT: B 82 MET cc_start: 0.8784 (mtm) cc_final: 0.8533 (mtt) REVERT: B 86 ASP cc_start: 0.7638 (t0) cc_final: 0.7364 (t0) REVERT: B 111 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7426 (mm-30) REVERT: B 113 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6774 (mm-30) REVERT: B 120 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7882 (ttmm) REVERT: B 121 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7500 (tttm) REVERT: B 131 ASN cc_start: 0.7932 (m-40) cc_final: 0.7541 (m-40) REVERT: B 138 GLU cc_start: 0.7439 (mp0) cc_final: 0.7045 (mp0) REVERT: B 156 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7116 (mm-30) REVERT: B 293 ILE cc_start: 0.7876 (mm) cc_final: 0.7645 (mt) REVERT: B 302 ASP cc_start: 0.7570 (t0) cc_final: 0.7127 (t0) REVERT: B 303 LYS cc_start: 0.8301 (ptmm) cc_final: 0.7729 (ptpp) REVERT: B 326 TYR cc_start: 0.7553 (m-80) cc_final: 0.7058 (m-80) REVERT: B 347 ILE cc_start: 0.7891 (mt) cc_final: 0.7563 (tp) REVERT: B 362 PHE cc_start: 0.7896 (m-80) cc_final: 0.7657 (m-80) REVERT: B 370 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6883 (mm-40) REVERT: B 388 LYS cc_start: 0.7607 (mtpp) cc_final: 0.7295 (mtpt) REVERT: B 391 LYS cc_start: 0.7556 (mptt) cc_final: 0.7185 (mmtp) REVERT: B 399 CYS cc_start: 0.7048 (m) cc_final: 0.6624 (m) REVERT: B 407 GLU cc_start: 0.7839 (tt0) cc_final: 0.7557 (tt0) REVERT: B 425 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6958 (mt-10) REVERT: B 437 GLU cc_start: 0.7692 (tp30) cc_final: 0.7112 (tm-30) REVERT: B 438 LYS cc_start: 0.8320 (mmtp) cc_final: 0.8034 (mmtp) REVERT: B 448 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6726 (p) REVERT: B 453 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7264 (mt-10) REVERT: B 466 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7236 (mm-30) REVERT: C 7 MET cc_start: 0.6801 (mmm) cc_final: 0.6529 (mpm) REVERT: C 29 MET cc_start: 0.7034 (mmm) cc_final: 0.6680 (mmm) REVERT: C 44 MET cc_start: 0.7313 (mmm) cc_final: 0.6788 (mmm) REVERT: C 49 MET cc_start: 0.7397 (mmm) cc_final: 0.7109 (mmm) REVERT: C 120 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7436 (ttmm) REVERT: C 156 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7292 (mm-30) REVERT: C 203 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 235 GLU cc_start: 0.8003 (pt0) cc_final: 0.7782 (pt0) REVERT: C 273 TYR cc_start: 0.8580 (m-80) cc_final: 0.8160 (m-80) REVERT: C 293 ILE cc_start: 0.7732 (mm) cc_final: 0.7506 (mt) REVERT: C 319 GLN cc_start: 0.7352 (mt0) cc_final: 0.7133 (mt0) REVERT: C 326 TYR cc_start: 0.7448 (m-80) cc_final: 0.6963 (m-80) REVERT: C 355 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.6931 (p0) REVERT: C 359 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6420 (tp30) REVERT: C 363 THR cc_start: 0.7985 (m) cc_final: 0.7329 (p) REVERT: C 386 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7822 (ttmt) REVERT: C 391 LYS cc_start: 0.7875 (mptt) cc_final: 0.7591 (mmtm) REVERT: C 396 MET cc_start: 0.7797 (mmp) cc_final: 0.7496 (mmm) REVERT: C 399 CYS cc_start: 0.6810 (m) cc_final: 0.6347 (m) REVERT: C 437 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7299 (tm-30) REVERT: C 453 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 465 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7866 (tp30) REVERT: C 468 MET cc_start: 0.8639 (mmm) cc_final: 0.8390 (mmm) REVERT: C 480 ASP cc_start: 0.7049 (m-30) cc_final: 0.6809 (m-30) REVERT: C 489 SER cc_start: 0.8160 (m) cc_final: 0.7881 (m) outliers start: 51 outliers final: 25 residues processed: 366 average time/residue: 1.6083 time to fit residues: 630.2542 Evaluate side-chains 368 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 339 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 200 LYS 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 99 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 441 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.0170 chunk 110 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 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 319 GLN A 376 HIS A 475 ASN A 482 ASN B 108 ASN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13359 Z= 0.175 Angle : 0.561 8.119 18090 Z= 0.286 Chirality : 0.042 0.170 1986 Planarity : 0.004 0.045 2325 Dihedral : 4.536 29.070 2172 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.34 % Allowed : 15.85 % Favored : 80.81 % 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: 1.72 (0.21), residues: 1569 helix: 1.98 (0.20), residues: 687 sheet: 1.24 (0.30), residues: 273 loop : 0.20 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 349 HIS 0.003 0.001 HIS B 177 PHE 0.011 0.001 PHE B 188 TYR 0.013 0.001 TYR A 118 ARG 0.006 0.000 ARG A 187 *********************** 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 396 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 349 time to evaluate : 1.628 Fit side-chains REVERT: A 29 MET cc_start: 0.7003 (mmm) cc_final: 0.6578 (mmm) REVERT: A 31 ARG cc_start: 0.6544 (ttm170) cc_final: 0.6193 (ttm170) REVERT: A 49 MET cc_start: 0.7440 (mmp) cc_final: 0.7227 (mmm) REVERT: A 50 SER cc_start: 0.7579 (t) cc_final: 0.7341 (p) REVERT: A 66 GLU cc_start: 0.8302 (pt0) cc_final: 0.8040 (pt0) REVERT: A 86 ASP cc_start: 0.7623 (t0) cc_final: 0.7295 (t0) REVERT: A 95 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7538 (mtt-85) REVERT: A 119 MET cc_start: 0.8336 (mmt) cc_final: 0.7958 (mmt) REVERT: A 141 GLN cc_start: 0.7822 (mm110) cc_final: 0.7587 (mm-40) REVERT: A 216 GLU cc_start: 0.7845 (mp0) cc_final: 0.7635 (mp0) REVERT: A 271 GLU cc_start: 0.7507 (pt0) cc_final: 0.7095 (pt0) REVERT: A 273 TYR cc_start: 0.8463 (m-80) cc_final: 0.8241 (m-80) REVERT: A 302 ASP cc_start: 0.7694 (t0) cc_final: 0.7169 (t0) REVERT: A 303 LYS cc_start: 0.8086 (ptmm) cc_final: 0.7562 (ptpp) REVERT: A 347 ILE cc_start: 0.7645 (mt) cc_final: 0.7264 (tp) REVERT: A 359 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6679 (mt-10) REVERT: A 391 LYS cc_start: 0.8069 (mptt) cc_final: 0.7788 (mmtp) REVERT: A 409 SER cc_start: 0.8566 (t) cc_final: 0.8101 (p) REVERT: A 425 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 438 LYS cc_start: 0.8091 (mttp) cc_final: 0.7847 (mttp) REVERT: A 465 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 16 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7128 (mtm) REVERT: B 50 SER cc_start: 0.7786 (t) cc_final: 0.7393 (p) REVERT: B 57 PHE cc_start: 0.7499 (m-80) cc_final: 0.7208 (m-80) REVERT: B 82 MET cc_start: 0.8785 (mtm) cc_final: 0.8487 (mtm) REVERT: B 86 ASP cc_start: 0.7632 (t0) cc_final: 0.7339 (t0) REVERT: B 113 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6719 (mm-30) REVERT: B 120 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7881 (ttmm) REVERT: B 121 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7473 (tttm) REVERT: B 131 ASN cc_start: 0.7888 (m-40) cc_final: 0.7505 (m-40) REVERT: B 156 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7117 (mm-30) REVERT: B 293 ILE cc_start: 0.7867 (mm) cc_final: 0.7638 (mt) REVERT: B 302 ASP cc_start: 0.7627 (t0) cc_final: 0.7163 (t0) REVERT: B 303 LYS cc_start: 0.8285 (ptmm) cc_final: 0.7732 (ptpp) REVERT: B 326 TYR cc_start: 0.7539 (m-80) cc_final: 0.7027 (m-80) REVERT: B 347 ILE cc_start: 0.7891 (mt) cc_final: 0.7587 (tp) REVERT: B 362 PHE cc_start: 0.7887 (m-80) cc_final: 0.7672 (m-80) REVERT: B 370 GLN cc_start: 0.7072 (mm-40) cc_final: 0.6830 (mm-40) REVERT: B 391 LYS cc_start: 0.7538 (mptt) cc_final: 0.7252 (mmtp) REVERT: B 399 CYS cc_start: 0.7042 (m) cc_final: 0.6625 (m) REVERT: B 407 GLU cc_start: 0.7836 (tt0) cc_final: 0.7584 (tt0) REVERT: B 425 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6916 (mt-10) REVERT: B 437 GLU cc_start: 0.7691 (tp30) cc_final: 0.7108 (tm-30) REVERT: B 448 THR cc_start: 0.7181 (OUTLIER) cc_final: 0.6701 (p) REVERT: B 453 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7234 (mt-10) REVERT: B 466 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7254 (mm-30) REVERT: B 490 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: B 518 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6569 (mm-30) REVERT: C 7 MET cc_start: 0.6802 (mmm) cc_final: 0.6561 (mpm) REVERT: C 29 MET cc_start: 0.7006 (mmm) cc_final: 0.6634 (mmm) REVERT: C 44 MET cc_start: 0.7304 (mmm) cc_final: 0.6797 (mmm) REVERT: C 49 MET cc_start: 0.7424 (mmm) cc_final: 0.7073 (mmm) REVERT: C 120 LYS cc_start: 0.7698 (mtmt) cc_final: 0.7433 (ttmm) REVERT: C 156 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7354 (mm-30) REVERT: C 235 GLU cc_start: 0.7959 (pt0) cc_final: 0.7735 (pt0) REVERT: C 273 TYR cc_start: 0.8571 (m-80) cc_final: 0.8141 (m-80) REVERT: C 293 ILE cc_start: 0.7752 (mm) cc_final: 0.7521 (mt) REVERT: C 326 TYR cc_start: 0.7423 (m-80) cc_final: 0.6895 (m-80) REVERT: C 355 ASN cc_start: 0.7401 (OUTLIER) cc_final: 0.6941 (p0) REVERT: C 359 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6431 (tp30) REVERT: C 363 THR cc_start: 0.7872 (m) cc_final: 0.7232 (p) REVERT: C 386 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7855 (ttmt) REVERT: C 391 LYS cc_start: 0.7862 (mptt) cc_final: 0.7574 (mmtp) REVERT: C 396 MET cc_start: 0.7799 (mmp) cc_final: 0.7505 (mmm) REVERT: C 399 CYS cc_start: 0.6814 (m) cc_final: 0.6348 (m) REVERT: C 437 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 468 MET cc_start: 0.8636 (mmm) cc_final: 0.8384 (mmm) REVERT: C 480 ASP cc_start: 0.7046 (m-30) cc_final: 0.6806 (m-30) REVERT: C 489 SER cc_start: 0.8116 (m) cc_final: 0.7853 (m) outliers start: 47 outliers final: 24 residues processed: 372 average time/residue: 1.6023 time to fit residues: 638.1505 Evaluate side-chains 372 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 342 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 200 LYS Chi-restraints excluded: chain A residue 293 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 16 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 120 LYS 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 490 GLU Chi-restraints excluded: chain B residue 494 ARG 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 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 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 475 ASN A 482 ASN B 108 ASN B 133 GLN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13359 Z= 0.209 Angle : 0.575 8.795 18090 Z= 0.294 Chirality : 0.043 0.203 1986 Planarity : 0.005 0.046 2325 Dihedral : 4.526 28.493 2172 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.06 % Allowed : 17.13 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1569 helix: 1.93 (0.20), residues: 687 sheet: 1.24 (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 0.004 0.001 HIS A 297 PHE 0.028 0.001 PHE A 10 TYR 0.014 0.001 TYR C 118 ARG 0.010 0.000 ARG C 494 *********************** 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 395 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 1.637 Fit side-chains REVERT: A 16 MET cc_start: 0.7308 (mtp) cc_final: 0.7000 (mtt) REVERT: A 29 MET cc_start: 0.7003 (mmm) cc_final: 0.6574 (mmm) REVERT: A 31 ARG cc_start: 0.6555 (ttm170) cc_final: 0.6203 (ttm170) REVERT: A 49 MET cc_start: 0.7450 (mmp) cc_final: 0.7237 (mmm) REVERT: A 50 SER cc_start: 0.7577 (t) cc_final: 0.7344 (p) REVERT: A 66 GLU cc_start: 0.8301 (pt0) cc_final: 0.8034 (pt0) REVERT: A 86 ASP cc_start: 0.7606 (t0) cc_final: 0.7272 (t0) REVERT: A 95 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7550 (mtt-85) REVERT: A 111 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 119 MET cc_start: 0.8322 (mmt) cc_final: 0.7943 (mmt) REVERT: A 216 GLU cc_start: 0.7845 (mp0) cc_final: 0.7620 (mp0) REVERT: A 271 GLU cc_start: 0.7531 (pt0) cc_final: 0.7108 (pt0) REVERT: A 273 TYR cc_start: 0.8440 (m-80) cc_final: 0.8217 (m-80) REVERT: A 293 ILE cc_start: 0.7451 (mm) cc_final: 0.7138 (mp) REVERT: A 302 ASP cc_start: 0.7713 (t0) cc_final: 0.7196 (t0) REVERT: A 303 LYS cc_start: 0.8101 (ptmm) cc_final: 0.7565 (ptpp) REVERT: A 347 ILE cc_start: 0.7635 (mt) cc_final: 0.7258 (tp) REVERT: A 359 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6681 (mt-10) REVERT: A 391 LYS cc_start: 0.8073 (mptt) cc_final: 0.7800 (mmtp) REVERT: A 409 SER cc_start: 0.8567 (t) cc_final: 0.8101 (p) REVERT: A 425 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 438 LYS cc_start: 0.8098 (mttp) cc_final: 0.7846 (mttp) REVERT: A 465 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7723 (mm-30) REVERT: B 16 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7125 (mtm) REVERT: B 50 SER cc_start: 0.7764 (t) cc_final: 0.7376 (p) REVERT: B 57 PHE cc_start: 0.7525 (m-80) cc_final: 0.7213 (m-80) REVERT: B 86 ASP cc_start: 0.7643 (t0) cc_final: 0.7311 (t0) REVERT: B 113 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6727 (mm-30) REVERT: B 120 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7873 (ttmm) REVERT: B 121 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7451 (tttm) REVERT: B 131 ASN cc_start: 0.7920 (m-40) cc_final: 0.7535 (m-40) REVERT: B 138 GLU cc_start: 0.7433 (mp0) cc_final: 0.7032 (mp0) REVERT: B 156 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7136 (mm-30) REVERT: B 293 ILE cc_start: 0.7875 (mm) cc_final: 0.7649 (mt) REVERT: B 302 ASP cc_start: 0.7636 (t0) cc_final: 0.7175 (t0) REVERT: B 303 LYS cc_start: 0.8287 (ptmm) cc_final: 0.7734 (ptpp) REVERT: B 326 TYR cc_start: 0.7510 (m-80) cc_final: 0.7019 (m-80) REVERT: B 347 ILE cc_start: 0.7900 (mt) cc_final: 0.7614 (tp) REVERT: B 362 PHE cc_start: 0.7888 (m-80) cc_final: 0.7663 (m-80) REVERT: B 370 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6852 (mm-40) REVERT: B 391 LYS cc_start: 0.7536 (mptt) cc_final: 0.7242 (mmtp) REVERT: B 399 CYS cc_start: 0.7060 (m) cc_final: 0.6639 (m) REVERT: B 407 GLU cc_start: 0.7827 (tt0) cc_final: 0.7575 (tt0) REVERT: B 425 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6945 (mt-10) REVERT: B 437 GLU cc_start: 0.7686 (tp30) cc_final: 0.7090 (tm-30) REVERT: B 448 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6682 (p) REVERT: B 453 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 466 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7247 (mm-30) REVERT: C 7 MET cc_start: 0.6826 (mmm) cc_final: 0.6572 (mpm) REVERT: C 29 MET cc_start: 0.7014 (mmm) cc_final: 0.6641 (mmm) REVERT: C 44 MET cc_start: 0.7312 (mmm) cc_final: 0.6807 (mmm) REVERT: C 49 MET cc_start: 0.7366 (mmm) cc_final: 0.7060 (mmm) REVERT: C 120 LYS cc_start: 0.7717 (mtmt) cc_final: 0.7449 (ttmm) REVERT: C 156 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7354 (mm-30) REVERT: C 235 GLU cc_start: 0.8015 (pt0) cc_final: 0.7804 (pt0) REVERT: C 273 TYR cc_start: 0.8567 (m-80) cc_final: 0.8117 (m-80) REVERT: C 319 GLN cc_start: 0.7318 (mt0) cc_final: 0.7110 (mt0) REVERT: C 326 TYR cc_start: 0.7446 (m-80) cc_final: 0.6914 (m-80) REVERT: C 355 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6987 (p0) REVERT: C 359 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6448 (tp30) REVERT: C 363 THR cc_start: 0.7894 (m) cc_final: 0.7270 (p) REVERT: C 386 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7899 (ttpt) REVERT: C 391 LYS cc_start: 0.7866 (mptt) cc_final: 0.7574 (mmtp) REVERT: C 396 MET cc_start: 0.7794 (mmp) cc_final: 0.7495 (mmm) REVERT: C 399 CYS cc_start: 0.6824 (m) cc_final: 0.6356 (m) REVERT: C 437 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7297 (tm-30) REVERT: C 468 MET cc_start: 0.8633 (mmm) cc_final: 0.8392 (mmm) REVERT: C 480 ASP cc_start: 0.7036 (m-30) cc_final: 0.6786 (m-30) REVERT: C 489 SER cc_start: 0.8112 (m) cc_final: 0.7864 (m) outliers start: 43 outliers final: 20 residues processed: 373 average time/residue: 1.5902 time to fit residues: 637.2007 Evaluate side-chains 362 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 337 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 200 LYS 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 67 VAL Chi-restraints excluded: chain B residue 120 LYS 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 200 LYS Chi-restraints excluded: chain C residue 215 ILE 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 386 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 108 ASN B 133 GLN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS C 152 ASN C 475 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13359 Z= 0.213 Angle : 0.582 9.652 18090 Z= 0.298 Chirality : 0.043 0.202 1986 Planarity : 0.005 0.054 2325 Dihedral : 4.521 28.075 2172 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.63 % Allowed : 17.77 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1569 helix: 1.92 (0.20), residues: 687 sheet: 1.21 (0.30), residues: 273 loop : 0.16 (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 376 PHE 0.015 0.001 PHE C 443 TYR 0.015 0.001 TYR A 118 ARG 0.013 0.001 ARG C 494 *********************** 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 383 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 346 time to evaluate : 1.479 Fit side-chains REVERT: A 29 MET cc_start: 0.6953 (mmm) cc_final: 0.6530 (mmm) REVERT: A 31 ARG cc_start: 0.6561 (ttm170) cc_final: 0.6238 (ttm170) REVERT: A 49 MET cc_start: 0.7452 (mmp) cc_final: 0.7235 (mmm) REVERT: A 50 SER cc_start: 0.7570 (t) cc_final: 0.7345 (p) REVERT: A 57 PHE cc_start: 0.7486 (m-80) cc_final: 0.7266 (m-80) REVERT: A 66 GLU cc_start: 0.8300 (pt0) cc_final: 0.8028 (pt0) REVERT: A 86 ASP cc_start: 0.7601 (t0) cc_final: 0.7262 (t0) REVERT: A 95 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7556 (mtt-85) REVERT: A 111 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 119 MET cc_start: 0.8325 (mmt) cc_final: 0.7936 (mmt) REVERT: A 216 GLU cc_start: 0.7844 (mp0) cc_final: 0.7623 (mp0) REVERT: A 271 GLU cc_start: 0.7540 (pt0) cc_final: 0.7162 (pt0) REVERT: A 273 TYR cc_start: 0.8436 (m-80) cc_final: 0.8225 (m-80) REVERT: A 293 ILE cc_start: 0.7496 (mm) cc_final: 0.7208 (OUTLIER) REVERT: A 302 ASP cc_start: 0.7716 (t0) cc_final: 0.7203 (t0) REVERT: A 303 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7581 (ptpp) REVERT: A 347 ILE cc_start: 0.7623 (mt) cc_final: 0.7255 (tp) REVERT: A 359 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6679 (mt-10) REVERT: A 391 LYS cc_start: 0.8063 (mptt) cc_final: 0.7781 (mmtp) REVERT: A 409 SER cc_start: 0.8568 (t) cc_final: 0.8101 (p) REVERT: A 425 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6931 (mt-10) REVERT: A 438 LYS cc_start: 0.8105 (mttp) cc_final: 0.7859 (mttp) REVERT: A 465 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 16 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7091 (mtm) REVERT: B 50 SER cc_start: 0.7787 (t) cc_final: 0.7393 (p) REVERT: B 86 ASP cc_start: 0.7641 (t0) cc_final: 0.7258 (t0) REVERT: B 113 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6871 (mm-30) REVERT: B 120 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7893 (ttmm) REVERT: B 131 ASN cc_start: 0.7867 (m-40) cc_final: 0.7494 (m-40) REVERT: B 138 GLU cc_start: 0.7417 (mp0) cc_final: 0.6959 (mp0) REVERT: B 213 GLU cc_start: 0.7827 (pt0) cc_final: 0.7569 (pt0) REVERT: B 302 ASP cc_start: 0.7637 (t0) cc_final: 0.7179 (t0) REVERT: B 303 LYS cc_start: 0.8286 (ptmm) cc_final: 0.7739 (ptpp) REVERT: B 326 TYR cc_start: 0.7542 (m-80) cc_final: 0.7041 (m-80) REVERT: B 347 ILE cc_start: 0.7896 (mt) cc_final: 0.7624 (tp) REVERT: B 360 CYS cc_start: 0.7065 (t) cc_final: 0.6799 (m) REVERT: B 362 PHE cc_start: 0.7886 (m-80) cc_final: 0.7663 (m-80) REVERT: B 370 GLN cc_start: 0.7143 (mm-40) cc_final: 0.6874 (mm-40) REVERT: B 388 LYS cc_start: 0.7583 (mtpp) cc_final: 0.7273 (mtpt) REVERT: B 391 LYS cc_start: 0.7538 (mptt) cc_final: 0.7242 (mmtp) REVERT: B 399 CYS cc_start: 0.7053 (m) cc_final: 0.6631 (m) REVERT: B 425 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6910 (mt-10) REVERT: B 448 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6672 (p) REVERT: B 488 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7840 (mt-10) REVERT: B 490 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: C 7 MET cc_start: 0.6827 (mmm) cc_final: 0.6586 (mpm) REVERT: C 29 MET cc_start: 0.6995 (mmm) cc_final: 0.6629 (mmm) REVERT: C 44 MET cc_start: 0.7316 (mmm) cc_final: 0.6775 (mmm) REVERT: C 49 MET cc_start: 0.7366 (mmm) cc_final: 0.7018 (mmm) REVERT: C 120 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7430 (ttmm) REVERT: C 156 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7358 (mm-30) REVERT: C 203 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7457 (mm-30) REVERT: C 235 GLU cc_start: 0.8014 (pt0) cc_final: 0.7800 (pt0) REVERT: C 273 TYR cc_start: 0.8563 (m-80) cc_final: 0.8117 (m-80) REVERT: C 293 ILE cc_start: 0.7772 (mm) cc_final: 0.7536 (mt) REVERT: C 326 TYR cc_start: 0.7441 (m-80) cc_final: 0.6908 (m-80) REVERT: C 355 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7032 (p0) REVERT: C 359 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6406 (tp30) REVERT: C 363 THR cc_start: 0.7908 (m) cc_final: 0.7262 (p) REVERT: C 380 LYS cc_start: 0.7297 (mttt) cc_final: 0.7059 (mttt) REVERT: C 386 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7929 (mtpt) REVERT: C 391 LYS cc_start: 0.7867 (mptt) cc_final: 0.7573 (mmtp) REVERT: C 396 MET cc_start: 0.7785 (mmp) cc_final: 0.7484 (mmm) REVERT: C 399 CYS cc_start: 0.6830 (m) cc_final: 0.6364 (m) REVERT: C 437 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7299 (tm-30) REVERT: C 468 MET cc_start: 0.8627 (mmm) cc_final: 0.8391 (mmm) REVERT: C 480 ASP cc_start: 0.7040 (m-30) cc_final: 0.6799 (m-30) REVERT: C 489 SER cc_start: 0.8115 (m) cc_final: 0.7854 (m) outliers start: 37 outliers final: 24 residues processed: 363 average time/residue: 1.6701 time to fit residues: 648.1644 Evaluate side-chains 364 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 335 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 200 LYS 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 16 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 405 CYS Chi-restraints excluded: chain B residue 448 THR 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 200 LYS Chi-restraints excluded: chain C residue 215 ILE 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 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13359 Z= 0.190 Angle : 0.569 10.037 18090 Z= 0.290 Chirality : 0.042 0.184 1986 Planarity : 0.004 0.049 2325 Dihedral : 4.468 27.837 2172 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.27 % Allowed : 18.62 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1569 helix: 2.00 (0.20), residues: 687 sheet: 1.19 (0.30), residues: 273 loop : 0.18 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 349 HIS 0.004 0.001 HIS B 297 PHE 0.029 0.001 PHE A 10 TYR 0.014 0.001 TYR A 118 ARG 0.012 0.000 ARG C 494 ********************** 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 370 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 338 time to evaluate : 1.534 Fit side-chains REVERT: A 29 MET cc_start: 0.6939 (mmm) cc_final: 0.6519 (mmm) REVERT: A 31 ARG cc_start: 0.6560 (ttm170) cc_final: 0.6203 (ttm170) REVERT: A 49 MET cc_start: 0.7381 (mmp) cc_final: 0.7148 (mmm) REVERT: A 50 SER cc_start: 0.7600 (t) cc_final: 0.7372 (p) REVERT: A 57 PHE cc_start: 0.7512 (m-80) cc_final: 0.7291 (m-80) REVERT: A 66 GLU cc_start: 0.8298 (pt0) cc_final: 0.8034 (pt0) REVERT: A 86 ASP cc_start: 0.7591 (t0) cc_final: 0.7266 (t0) REVERT: A 95 ARG cc_start: 0.7899 (mtt180) cc_final: 0.7542 (mtt-85) REVERT: A 111 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7531 (mt-10) REVERT: A 216 GLU cc_start: 0.7838 (mp0) cc_final: 0.7612 (mp0) REVERT: A 271 GLU cc_start: 0.7543 (pt0) cc_final: 0.7206 (pt0) REVERT: A 273 TYR cc_start: 0.8437 (m-80) cc_final: 0.8193 (m-80) REVERT: A 293 ILE cc_start: 0.7497 (mm) cc_final: 0.7242 (OUTLIER) REVERT: A 302 ASP cc_start: 0.7700 (t0) cc_final: 0.7186 (t0) REVERT: A 303 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7546 (ptpp) REVERT: A 347 ILE cc_start: 0.7614 (mt) cc_final: 0.7254 (tp) REVERT: A 359 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6789 (mt-10) REVERT: A 391 LYS cc_start: 0.8058 (mptt) cc_final: 0.7782 (mmtp) REVERT: A 409 SER cc_start: 0.8543 (t) cc_final: 0.8090 (p) REVERT: A 425 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6924 (mt-10) REVERT: A 438 LYS cc_start: 0.8102 (mttp) cc_final: 0.7858 (mttp) REVERT: A 465 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 16 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7087 (mtm) REVERT: B 50 SER cc_start: 0.7741 (t) cc_final: 0.7355 (p) REVERT: B 86 ASP cc_start: 0.7615 (t0) cc_final: 0.7203 (t0) REVERT: B 113 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6677 (mm-30) REVERT: B 120 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7897 (ttmm) REVERT: B 131 ASN cc_start: 0.7854 (m-40) cc_final: 0.7479 (m-40) REVERT: B 156 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7143 (mm-30) REVERT: B 302 ASP cc_start: 0.7633 (t0) cc_final: 0.7177 (t0) REVERT: B 303 LYS cc_start: 0.8285 (ptmm) cc_final: 0.7739 (ptpp) REVERT: B 326 TYR cc_start: 0.7511 (m-80) cc_final: 0.7009 (m-80) REVERT: B 347 ILE cc_start: 0.7898 (mt) cc_final: 0.7622 (tp) REVERT: B 360 CYS cc_start: 0.7038 (t) cc_final: 0.6793 (m) REVERT: B 362 PHE cc_start: 0.7897 (m-80) cc_final: 0.7636 (m-80) REVERT: B 370 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6853 (mm-40) REVERT: B 381 CYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5213 (t) REVERT: B 388 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7290 (mtpt) REVERT: B 391 LYS cc_start: 0.7533 (mptt) cc_final: 0.7158 (mmtp) REVERT: B 399 CYS cc_start: 0.7008 (m) cc_final: 0.6571 (m) REVERT: B 425 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6917 (mt-10) REVERT: B 437 GLU cc_start: 0.7643 (tp30) cc_final: 0.7012 (tm-30) REVERT: B 448 THR cc_start: 0.7138 (OUTLIER) cc_final: 0.6659 (p) REVERT: B 453 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 466 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7256 (mm-30) REVERT: B 490 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: C 7 MET cc_start: 0.6857 (mmm) cc_final: 0.6642 (mpm) REVERT: C 29 MET cc_start: 0.6990 (mmm) cc_final: 0.6622 (mmm) REVERT: C 44 MET cc_start: 0.7313 (mmm) cc_final: 0.6774 (mmm) REVERT: C 49 MET cc_start: 0.7359 (mmm) cc_final: 0.7017 (mmm) REVERT: C 120 LYS cc_start: 0.7698 (mtmt) cc_final: 0.7442 (ttmm) REVERT: C 121 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7359 (tttm) REVERT: C 156 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7357 (mm-30) REVERT: C 203 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7455 (mm-30) REVERT: C 235 GLU cc_start: 0.8000 (pt0) cc_final: 0.7782 (pt0) REVERT: C 273 TYR cc_start: 0.8567 (m-80) cc_final: 0.8124 (m-80) REVERT: C 289 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7546 (ttt90) REVERT: C 293 ILE cc_start: 0.7791 (mm) cc_final: 0.7553 (OUTLIER) REVERT: C 326 TYR cc_start: 0.7419 (m-80) cc_final: 0.6891 (m-80) REVERT: C 355 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7025 (p0) REVERT: C 359 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6400 (tp30) REVERT: C 363 THR cc_start: 0.7903 (m) cc_final: 0.7259 (p) REVERT: C 386 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7933 (mtpt) REVERT: C 391 LYS cc_start: 0.7861 (mptt) cc_final: 0.7570 (mmtp) REVERT: C 396 MET cc_start: 0.7792 (mmp) cc_final: 0.7491 (mmm) REVERT: C 399 CYS cc_start: 0.6832 (m) cc_final: 0.6367 (m) REVERT: C 437 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 468 MET cc_start: 0.8627 (mmm) cc_final: 0.8395 (mmm) REVERT: C 480 ASP cc_start: 0.7055 (m-30) cc_final: 0.6786 (m-30) REVERT: C 489 SER cc_start: 0.8146 (m) cc_final: 0.7875 (m) outliers start: 32 outliers final: 24 residues processed: 351 average time/residue: 1.5859 time to fit residues: 595.8572 Evaluate side-chains 361 residues out of total 1407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 200 LYS 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 16 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 405 CYS Chi-restraints excluded: chain B residue 448 THR 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 215 ILE 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 386 LYS Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN A 482 ASN B 108 ASN B 133 GLN B 141 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116384 restraints weight = 17124.172| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.71 r_work: 0.3481 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13359 Z= 0.216 Angle : 0.585 9.808 18090 Z= 0.299 Chirality : 0.043 0.205 1986 Planarity : 0.004 0.044 2325 Dihedral : 4.462 27.405 2172 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.42 % Allowed : 18.34 % Favored : 79.25 % 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: 1.67 (0.21), residues: 1569 helix: 1.95 (0.20), residues: 687 sheet: 1.17 (0.30), residues: 273 loop : 0.18 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 349 HIS 0.005 0.001 HIS C 376 PHE 0.013 0.001 PHE C 443 TYR 0.016 0.001 TYR A 118 ARG 0.010 0.000 ARG C 494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8647.69 seconds wall clock time: 153 minutes 41.57 seconds (9221.57 seconds total)