Starting phenix.real_space_refine on Sun Aug 24 16:16:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4i_41883/08_2025/8u4i_41883_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4i_41883/08_2025/8u4i_41883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u4i_41883/08_2025/8u4i_41883_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4i_41883/08_2025/8u4i_41883_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u4i_41883/08_2025/8u4i_41883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4i_41883/08_2025/8u4i_41883.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.034 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: 5 Type Number sf(0) Gaussians S 132 5.16 5 C 6679 2.51 5 N 1795 2.21 5 O 2235 1.98 5 H 9593 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20434 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 9093 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 2 Chain: "B" Number of atoms: 9088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 9088 Classifications: {'peptide': 600} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 572} Chain breaks: 2 Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 768 Classifications: {'peptide': 50} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "D" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 768 Classifications: {'peptide': 50} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.62, per 1000 atoms: 0.23 Number of scatterers: 20434 At special positions: 0 Unit cell: (85.17, 147.795, 137.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 O 2235 8.00 N 1795 7.00 C 6679 6.00 H 9593 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.13 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.05 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.02 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 229 " distance=2.01 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=2.01 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.11 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 289 " distance=2.11 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.01 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.28 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.10 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.01 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.02 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.06 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.02 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.01 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 56 " distance=2.12 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 197 " distance=2.02 Simple disulfide: pdb=" SG CYS B 193 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 221 " distance=2.04 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 229 " distance=2.15 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 238 " distance=2.01 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.20 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 258 " distance=2.08 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 289 " distance=2.02 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 304 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 330 " distance=2.02 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.05 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 496 " distance=2.04 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 512 " distance=1.79 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 552 " distance=2.02 Simple disulfide: pdb=" SG CYS B 555 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 577 " distance=2.04 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 589 " distance=2.05 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 625 " distance=2.02 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 633 " distance=2.08 Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 210 " distance=2.13 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 221 " distance=2.02 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 190 " - pdb=" SG CYS D 210 " distance=2.04 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 221 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 701 " - " ASN A 495 " " NAG B 701 " - " ASN B 495 " " NAG E 1 " - " ASN A 548 " " NAG F 1 " - " ASN A 576 " " NAG G 1 " - " ASN A 473 " " NAG H 1 " - " ASN A 253 " " NAG I 1 " - " ASN A 358 " " NAG J 1 " - " ASN A 410 " " NAG K 1 " - " ASN A 138 " " NAG L 1 " - " ASN B 138 " " NAG M 1 " - " ASN B 253 " " NAG N 1 " - " ASN B 358 " " NAG O 1 " - " ASN B 410 " " NAG P 1 " - " ASN B 473 " " NAG Q 1 " - " ASN B 548 " " NAG R 1 " - " ASN B 576 " Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 580.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 34 sheets defined 17.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.626A pdb=" N SER A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.814A pdb=" N ILE A 161 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.672A pdb=" N CYS A 229 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.937A pdb=" N ILE A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.152A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.607A pdb=" N HIS A 470 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 573 through 577 removed outlier: 4.069A pdb=" N CYS A 577 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 54 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.646A pdb=" N SER B 79 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.673A pdb=" N ILE B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.777A pdb=" N MET B 343 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.014A pdb=" N THR B 394 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.549A pdb=" N HIS B 470 " --> pdb=" O CYS B 467 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 472 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 629 through 633 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.955A pdb=" N CYS C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.099A pdb=" N SER A 38 " --> pdb=" O CYS C 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 5.602A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A 147 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.761A pdb=" N ALA A 248 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY A 237 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N CYS A 246 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA7, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.949A pdb=" N GLN A 274 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.575A pdb=" N VAL A 298 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AB2, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.397A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 366 through 368 removed outlier: 4.621A pdb=" N LEU A 432 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N TYR A 459 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 434 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR A 461 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 436 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.881A pdb=" N ILE A 531 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 545 through 548 Processing sheet with id=AB6, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AB7, first strand: chain 'A' and resid 606 through 608 Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 39 removed outlier: 4.343A pdb=" N ARG D 207 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.470A pdb=" N GLY B 146 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 117 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AC2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AC3, first strand: chain 'B' and resid 235 through 238 removed outlier: 3.706A pdb=" N ALA B 248 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY B 237 " --> pdb=" O CYS B 246 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N CYS B 246 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AC5, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.030A pdb=" N GLN B 274 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC7, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC9, first strand: chain 'B' and resid 334 through 335 removed outlier: 7.004A pdb=" N CYS B 334 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 366 through 368 removed outlier: 6.595A pdb=" N LEU B 366 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN B 457 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ARG B 488 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 460 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AD3, first strand: chain 'B' and resid 545 through 547 Processing sheet with id=AD4, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AD5, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AD6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AD7, first strand: chain 'D' and resid 216 through 217 226 hydrogen bonds defined for protein. 405 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: 4.56 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9593 1.13 - 1.30: 1810 1.30 - 1.48: 4333 1.48 - 1.65: 4755 1.65 - 1.82: 152 Bond restraints: 20643 Sorted by residual: bond pdb=" ND2 ASN B 465 " pdb="HD22 ASN B 465 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL B 83 " pdb=" H VAL B 83 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ILE A 362 " pdb=" H ILE A 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN A 132 " pdb="HE21 GLN A 132 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ PHE B 266 " pdb=" HZ PHE B 266 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 20638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 32655 2.60 - 5.19: 2885 5.19 - 7.79: 1273 7.79 - 10.39: 24 10.39 - 12.99: 1 Bond angle restraints: 36838 Sorted by residual: angle pdb=" N CYS D 212 " pdb=" CA CYS D 212 " pdb=" C CYS D 212 " ideal model delta sigma weight residual 108.14 115.10 -6.96 1.15e+00 7.56e-01 3.67e+01 angle pdb=" N ILE A 357 " pdb=" CA ILE A 357 " pdb=" C ILE A 357 " ideal model delta sigma weight residual 110.62 116.70 -6.08 1.02e+00 9.61e-01 3.55e+01 angle pdb=" N ALA B 90 " pdb=" CA ALA B 90 " pdb=" C ALA B 90 " ideal model delta sigma weight residual 114.31 121.82 -7.51 1.29e+00 6.01e-01 3.39e+01 angle pdb=" C ARG A 525 " pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " ideal model delta sigma weight residual 117.23 109.58 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" N PHE A 120 " pdb=" CA PHE A 120 " pdb=" C PHE A 120 " ideal model delta sigma weight residual 109.07 117.02 -7.95 1.52e+00 4.33e-01 2.73e+01 ... (remaining 36833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 9881 20.69 - 41.39: 455 41.39 - 62.08: 282 62.08 - 82.77: 88 82.77 - 103.46: 56 Dihedral angle restraints: 10762 sinusoidal: 6378 harmonic: 4384 Sorted by residual: dihedral pdb=" CB CYS A 326 " pdb=" SG CYS A 326 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -44.44 -41.56 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CB CYS B 217 " pdb=" SG CYS B 217 " pdb=" SG CYS B 229 " pdb=" CB CYS B 229 " ideal model delta sinusoidal sigma weight residual -86.00 -45.35 -40.65 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA LEU B 437 " pdb=" C LEU B 437 " pdb=" N LYS B 438 " pdb=" CA LYS B 438 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 10759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1785 0.309 - 0.618: 16 0.618 - 0.926: 0 0.926 - 1.235: 0 1.235 - 1.544: 1 Chirality restraints: 1802 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.86 -1.54 2.00e-02 2.50e+03 5.96e+03 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.68e+01 ... (remaining 1799 not shown) Planarity restraints: 3125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 495 " 0.299 2.00e-02 2.50e+03 2.38e-01 8.48e+02 pdb=" CG ASN A 495 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 495 " -0.231 2.00e-02 2.50e+03 pdb=" ND2 ASN A 495 " -0.044 2.00e-02 2.50e+03 pdb="HD21 ASN A 495 " -0.309 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " 0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.204 2.00e-02 2.50e+03 1.70e-01 3.61e+02 pdb=" C7 NAG G 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.145 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.280 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 495 " -0.025 2.00e-02 2.50e+03 1.16e-01 1.68e+02 pdb=" CG ASN A 495 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 495 " 0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN A 495 " -0.187 2.00e-02 2.50e+03 pdb="HD21 ASN A 495 " 0.154 2.00e-02 2.50e+03 ... (remaining 3122 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 918 2.10 - 2.73: 29044 2.73 - 3.35: 55365 3.35 - 3.98: 73431 3.98 - 4.60: 106084 Nonbonded interactions: 264842 Sorted by model distance: nonbonded pdb=" O LYS D 187 " pdb=" HG1 THR D 188 " model vdw 1.475 2.450 nonbonded pdb=" OE1 GLN B 164 " pdb=" H GLN B 164 " model vdw 1.598 2.450 nonbonded pdb=" OE1 GLN A 623 " pdb=" H GLN A 623 " model vdw 1.612 2.450 nonbonded pdb=" OE1 GLU B 542 " pdb=" H GLU B 542 " model vdw 1.621 2.450 nonbonded pdb=" OD1 ASP B 349 " pdb=" HG SER B 351 " model vdw 1.621 2.450 ... (remaining 264837 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' and (resid 26 through 595 or resid 604 through 701)) selection = (chain 'B' and (resid 26 through 634 or resid 701)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'R' } ncs_group { reference = chain 'J' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.810 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.015 0.250 11163 Z= 0.867 Angle : 1.663 16.542 15234 Z= 1.036 Chirality : 0.094 1.544 1802 Planarity : 0.010 0.170 1874 Dihedral : 16.961 103.463 4949 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.35 % Allowed : 0.26 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.22), residues: 1281 helix: -3.11 (0.39), residues: 96 sheet: -1.20 (0.35), residues: 172 loop : 0.30 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 544 TYR 0.114 0.010 TYR A 157 PHE 0.063 0.003 PHE D 189 TRP 0.077 0.006 TRP B 407 HIS 0.009 0.001 HIS A 582 Details of bonding type rmsd covalent geometry : bond 0.01390 (11050) covalent geometry : angle 1.55932 (14951) SS BOND : bond 0.06253 ( 56) SS BOND : angle 3.35608 ( 112) hydrogen bonds : bond 0.22343 ( 226) hydrogen bonds : angle 7.93235 ( 405) link_ALPHA1-3 : bond 0.02910 ( 7) link_ALPHA1-3 : angle 4.66522 ( 21) link_ALPHA1-6 : bond 0.02561 ( 8) link_ALPHA1-6 : angle 3.82452 ( 24) link_BETA1-4 : bond 0.03022 ( 26) link_BETA1-4 : angle 5.66692 ( 78) link_NAG-ASN : bond 0.05396 ( 16) link_NAG-ASN : angle 4.97145 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 LYS cc_start: 0.8573 (pttt) cc_final: 0.8362 (tptp) REVERT: D 217 THR cc_start: 0.8635 (t) cc_final: 0.8425 (p) outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.2959 time to fit residues: 68.8654 Evaluate side-chains 75 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.156214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101547 restraints weight = 48794.696| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.08 r_work: 0.3429 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11163 Z= 0.169 Angle : 0.775 8.395 15234 Z= 0.385 Chirality : 0.050 0.271 1802 Planarity : 0.005 0.064 1874 Dihedral : 15.025 82.694 2549 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.95 % Allowed : 4.77 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.23), residues: 1281 helix: -2.55 (0.43), residues: 102 sheet: -1.47 (0.34), residues: 182 loop : -0.02 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 95 TYR 0.012 0.002 TYR B 148 PHE 0.017 0.001 PHE D 189 TRP 0.010 0.001 TRP B 407 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00385 (11050) covalent geometry : angle 0.72092 (14951) SS BOND : bond 0.00424 ( 56) SS BOND : angle 1.40126 ( 112) hydrogen bonds : bond 0.05193 ( 226) hydrogen bonds : angle 6.43299 ( 405) link_ALPHA1-3 : bond 0.01135 ( 7) link_ALPHA1-3 : angle 2.18288 ( 21) link_ALPHA1-6 : bond 0.00744 ( 8) link_ALPHA1-6 : angle 1.59248 ( 24) link_BETA1-4 : bond 0.00850 ( 26) link_BETA1-4 : angle 3.15836 ( 78) link_NAG-ASN : bond 0.00953 ( 16) link_NAG-ASN : angle 2.19695 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.8651 (p0) cc_final: 0.8382 (p0) REVERT: B 222 TYR cc_start: 0.6786 (p90) cc_final: 0.6369 (p90) REVERT: B 232 ARG cc_start: 0.7945 (tpt90) cc_final: 0.7699 (tpt90) REVERT: D 217 THR cc_start: 0.8196 (t) cc_final: 0.7808 (p) outliers start: 11 outliers final: 7 residues processed: 81 average time/residue: 0.3112 time to fit residues: 33.6298 Evaluate side-chains 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.158851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.102818 restraints weight = 46902.423| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.15 r_work: 0.3375 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11163 Z= 0.134 Angle : 0.643 7.060 15234 Z= 0.317 Chirality : 0.048 0.231 1802 Planarity : 0.004 0.039 1874 Dihedral : 11.661 73.934 2549 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.78 % Allowed : 5.37 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.23), residues: 1281 helix: -2.26 (0.44), residues: 104 sheet: -1.57 (0.35), residues: 182 loop : -0.18 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 124 TYR 0.009 0.001 TYR B 148 PHE 0.009 0.001 PHE B 94 TRP 0.008 0.001 TRP B 407 HIS 0.005 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00304 (11050) covalent geometry : angle 0.60896 (14951) SS BOND : bond 0.00377 ( 56) SS BOND : angle 0.92466 ( 112) hydrogen bonds : bond 0.04052 ( 226) hydrogen bonds : angle 5.86530 ( 405) link_ALPHA1-3 : bond 0.01119 ( 7) link_ALPHA1-3 : angle 1.68009 ( 21) link_ALPHA1-6 : bond 0.00857 ( 8) link_ALPHA1-6 : angle 1.55077 ( 24) link_BETA1-4 : bond 0.00748 ( 26) link_BETA1-4 : angle 2.26730 ( 78) link_NAG-ASN : bond 0.00524 ( 16) link_NAG-ASN : angle 1.66650 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 ASP cc_start: 0.8619 (p0) cc_final: 0.8364 (p0) REVERT: B 222 TYR cc_start: 0.6634 (p90) cc_final: 0.6260 (p90) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.2969 time to fit residues: 29.5329 Evaluate side-chains 66 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.157777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101610 restraints weight = 47117.695| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 4.15 r_work: 0.3360 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11163 Z= 0.126 Angle : 0.597 6.071 15234 Z= 0.296 Chirality : 0.046 0.238 1802 Planarity : 0.004 0.079 1874 Dihedral : 9.350 60.277 2549 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.87 % Allowed : 5.63 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.23), residues: 1281 helix: -2.06 (0.46), residues: 105 sheet: -1.38 (0.37), residues: 170 loop : -0.25 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 488 TYR 0.013 0.001 TYR D 208 PHE 0.009 0.001 PHE D 197 TRP 0.009 0.001 TRP B 198 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00288 (11050) covalent geometry : angle 0.56687 (14951) SS BOND : bond 0.00570 ( 56) SS BOND : angle 0.93119 ( 112) hydrogen bonds : bond 0.03702 ( 226) hydrogen bonds : angle 5.55843 ( 405) link_ALPHA1-3 : bond 0.00976 ( 7) link_ALPHA1-3 : angle 1.77665 ( 21) link_ALPHA1-6 : bond 0.00954 ( 8) link_ALPHA1-6 : angle 1.43759 ( 24) link_BETA1-4 : bond 0.00590 ( 26) link_BETA1-4 : angle 1.93262 ( 78) link_NAG-ASN : bond 0.00431 ( 16) link_NAG-ASN : angle 1.57762 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: A 71 ASN cc_start: 0.8326 (t0) cc_final: 0.7953 (t0) REVERT: A 251 ASN cc_start: 0.8336 (m110) cc_final: 0.8064 (m110) REVERT: A 413 ASP cc_start: 0.8634 (p0) cc_final: 0.8310 (p0) REVERT: B 222 TYR cc_start: 0.6736 (p90) cc_final: 0.6356 (p90) REVERT: B 322 MET cc_start: 0.7642 (mtt) cc_final: 0.7318 (mpp) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 0.2592 time to fit residues: 25.0792 Evaluate side-chains 68 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.156962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.103471 restraints weight = 46930.387| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.68 r_work: 0.3339 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11163 Z= 0.128 Angle : 0.574 5.383 15234 Z= 0.284 Chirality : 0.045 0.235 1802 Planarity : 0.004 0.036 1874 Dihedral : 8.010 59.644 2549 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.78 % Allowed : 5.63 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.23), residues: 1281 helix: -1.91 (0.48), residues: 105 sheet: -1.61 (0.36), residues: 182 loop : -0.35 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 188 TYR 0.008 0.001 TYR B 148 PHE 0.009 0.001 PHE B 94 TRP 0.008 0.001 TRP B 198 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00296 (11050) covalent geometry : angle 0.54541 (14951) SS BOND : bond 0.00427 ( 56) SS BOND : angle 0.87429 ( 112) hydrogen bonds : bond 0.03413 ( 226) hydrogen bonds : angle 5.44274 ( 405) link_ALPHA1-3 : bond 0.01024 ( 7) link_ALPHA1-3 : angle 1.70248 ( 21) link_ALPHA1-6 : bond 0.00962 ( 8) link_ALPHA1-6 : angle 1.71710 ( 24) link_BETA1-4 : bond 0.00593 ( 26) link_BETA1-4 : angle 1.72236 ( 78) link_NAG-ASN : bond 0.00377 ( 16) link_NAG-ASN : angle 1.56908 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8348 (t0) cc_final: 0.7958 (t0) REVERT: A 251 ASN cc_start: 0.8294 (m110) cc_final: 0.8013 (m110) REVERT: A 413 ASP cc_start: 0.8584 (p0) cc_final: 0.8312 (p0) REVERT: B 222 TYR cc_start: 0.6699 (p90) cc_final: 0.6296 (p90) REVERT: B 232 ARG cc_start: 0.7899 (tpt90) cc_final: 0.7575 (tpt90) REVERT: B 322 MET cc_start: 0.7640 (mtt) cc_final: 0.7371 (mpp) REVERT: C 215 GLU cc_start: 0.7954 (mp0) cc_final: 0.7670 (tt0) REVERT: D 219 ASP cc_start: 0.7904 (p0) cc_final: 0.6755 (t0) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.2342 time to fit residues: 22.0683 Evaluate side-chains 65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 490 ASN D 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.154597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101264 restraints weight = 47073.542| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.35 r_work: 0.3306 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11163 Z= 0.165 Angle : 0.591 5.282 15234 Z= 0.298 Chirality : 0.045 0.228 1802 Planarity : 0.004 0.038 1874 Dihedral : 7.334 59.381 2549 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.21 % Allowed : 5.63 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.23), residues: 1281 helix: -2.05 (0.47), residues: 105 sheet: -1.75 (0.37), residues: 172 loop : -0.50 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 168 TYR 0.011 0.001 TYR A 123 PHE 0.015 0.001 PHE B 368 TRP 0.016 0.002 TRP B 198 HIS 0.003 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00387 (11050) covalent geometry : angle 0.56565 (14951) SS BOND : bond 0.00478 ( 56) SS BOND : angle 0.89536 ( 112) hydrogen bonds : bond 0.03730 ( 226) hydrogen bonds : angle 5.47512 ( 405) link_ALPHA1-3 : bond 0.00911 ( 7) link_ALPHA1-3 : angle 1.79576 ( 21) link_ALPHA1-6 : bond 0.00904 ( 8) link_ALPHA1-6 : angle 1.48439 ( 24) link_BETA1-4 : bond 0.00560 ( 26) link_BETA1-4 : angle 1.59828 ( 78) link_NAG-ASN : bond 0.00310 ( 16) link_NAG-ASN : angle 1.59835 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8263 (t0) cc_final: 0.7946 (t0) REVERT: A 251 ASN cc_start: 0.8382 (m110) cc_final: 0.8100 (m110) REVERT: A 413 ASP cc_start: 0.8578 (p0) cc_final: 0.8331 (p0) REVERT: B 222 TYR cc_start: 0.6671 (p90) cc_final: 0.6224 (p90) REVERT: B 232 ARG cc_start: 0.7935 (tpt90) cc_final: 0.7602 (tpt90) REVERT: B 322 MET cc_start: 0.7673 (mtt) cc_final: 0.7432 (mpp) REVERT: B 411 MET cc_start: 0.6352 (mtp) cc_final: 0.6089 (mtm) REVERT: C 215 GLU cc_start: 0.7981 (mp0) cc_final: 0.7692 (tt0) REVERT: D 219 ASP cc_start: 0.7934 (p0) cc_final: 0.6922 (t0) outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.2206 time to fit residues: 23.7722 Evaluate side-chains 66 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 570 HIS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.153951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097623 restraints weight = 47321.949| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.11 r_work: 0.3296 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11163 Z= 0.171 Angle : 0.594 7.184 15234 Z= 0.301 Chirality : 0.045 0.222 1802 Planarity : 0.004 0.038 1874 Dihedral : 6.919 59.380 2549 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.04 % Allowed : 6.33 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.23), residues: 1281 helix: -2.36 (0.45), residues: 105 sheet: -1.70 (0.39), residues: 162 loop : -0.58 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 188 TYR 0.019 0.001 TYR A 468 PHE 0.015 0.001 PHE B 368 TRP 0.018 0.002 TRP B 198 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00406 (11050) covalent geometry : angle 0.56425 (14951) SS BOND : bond 0.00457 ( 56) SS BOND : angle 1.31425 ( 112) hydrogen bonds : bond 0.03809 ( 226) hydrogen bonds : angle 5.57820 ( 405) link_ALPHA1-3 : bond 0.00850 ( 7) link_ALPHA1-3 : angle 1.75391 ( 21) link_ALPHA1-6 : bond 0.00844 ( 8) link_ALPHA1-6 : angle 1.44028 ( 24) link_BETA1-4 : bond 0.00555 ( 26) link_BETA1-4 : angle 1.51844 ( 78) link_NAG-ASN : bond 0.00330 ( 16) link_NAG-ASN : angle 1.66183 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8322 (t0) cc_final: 0.7977 (t0) REVERT: A 174 ASN cc_start: 0.4486 (OUTLIER) cc_final: 0.4222 (t0) REVERT: A 251 ASN cc_start: 0.8407 (m110) cc_final: 0.8118 (m110) REVERT: B 222 TYR cc_start: 0.6673 (p90) cc_final: 0.6241 (p90) REVERT: B 232 ARG cc_start: 0.7903 (tpt90) cc_final: 0.7567 (tpt90) REVERT: B 322 MET cc_start: 0.7674 (mtt) cc_final: 0.7456 (mpp) REVERT: B 411 MET cc_start: 0.6279 (mtp) cc_final: 0.6036 (mtm) REVERT: C 214 ASN cc_start: 0.8731 (m-40) cc_final: 0.8367 (t0) REVERT: C 215 GLU cc_start: 0.8047 (mp0) cc_final: 0.7801 (tt0) REVERT: D 219 ASP cc_start: 0.7950 (p0) cc_final: 0.6981 (t0) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.2471 time to fit residues: 23.3148 Evaluate side-chains 65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 186 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN A 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.155260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099082 restraints weight = 47396.104| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.13 r_work: 0.3320 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11163 Z= 0.104 Angle : 0.549 6.165 15234 Z= 0.276 Chirality : 0.044 0.208 1802 Planarity : 0.004 0.039 1874 Dihedral : 6.694 59.611 2549 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.95 % Allowed : 6.76 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.23), residues: 1281 helix: -2.27 (0.45), residues: 105 sheet: -1.69 (0.39), residues: 162 loop : -0.53 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 188 TYR 0.008 0.001 TYR B 148 PHE 0.009 0.001 PHE B 120 TRP 0.012 0.001 TRP B 198 HIS 0.002 0.000 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00239 (11050) covalent geometry : angle 0.52036 (14951) SS BOND : bond 0.00358 ( 56) SS BOND : angle 1.06753 ( 112) hydrogen bonds : bond 0.03317 ( 226) hydrogen bonds : angle 5.46966 ( 405) link_ALPHA1-3 : bond 0.00811 ( 7) link_ALPHA1-3 : angle 1.73988 ( 21) link_ALPHA1-6 : bond 0.00828 ( 8) link_ALPHA1-6 : angle 1.42338 ( 24) link_BETA1-4 : bond 0.00515 ( 26) link_BETA1-4 : angle 1.48440 ( 78) link_NAG-ASN : bond 0.00313 ( 16) link_NAG-ASN : angle 1.62969 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8300 (t0) cc_final: 0.7977 (t0) REVERT: A 174 ASN cc_start: 0.4623 (OUTLIER) cc_final: 0.4268 (t0) REVERT: A 251 ASN cc_start: 0.8336 (m110) cc_final: 0.8047 (m110) REVERT: B 222 TYR cc_start: 0.6682 (p90) cc_final: 0.6251 (p90) REVERT: B 232 ARG cc_start: 0.7880 (tpt90) cc_final: 0.7308 (tpt90) REVERT: B 322 MET cc_start: 0.7672 (mtt) cc_final: 0.7455 (mpp) REVERT: C 214 ASN cc_start: 0.8753 (m-40) cc_final: 0.8499 (t0) REVERT: C 215 GLU cc_start: 0.8055 (mp0) cc_final: 0.7820 (tt0) REVERT: D 219 ASP cc_start: 0.7925 (p0) cc_final: 0.7023 (t0) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.2494 time to fit residues: 23.8035 Evaluate side-chains 65 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.155249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099203 restraints weight = 47567.307| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 4.14 r_work: 0.3325 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 11163 Z= 0.112 Angle : 0.559 10.905 15234 Z= 0.282 Chirality : 0.044 0.207 1802 Planarity : 0.004 0.042 1874 Dihedral : 6.587 57.177 2549 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.04 % Allowed : 6.59 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.23), residues: 1281 helix: -2.32 (0.45), residues: 105 sheet: -1.68 (0.39), residues: 162 loop : -0.52 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 188 TYR 0.012 0.001 TYR A 469 PHE 0.011 0.001 PHE A 401 TRP 0.011 0.001 TRP B 198 HIS 0.001 0.000 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00268 (11050) covalent geometry : angle 0.52609 (14951) SS BOND : bond 0.00333 ( 56) SS BOND : angle 1.32594 ( 112) hydrogen bonds : bond 0.03476 ( 226) hydrogen bonds : angle 5.58550 ( 405) link_ALPHA1-3 : bond 0.00767 ( 7) link_ALPHA1-3 : angle 1.72312 ( 21) link_ALPHA1-6 : bond 0.00806 ( 8) link_ALPHA1-6 : angle 1.43585 ( 24) link_BETA1-4 : bond 0.00505 ( 26) link_BETA1-4 : angle 1.46590 ( 78) link_NAG-ASN : bond 0.00309 ( 16) link_NAG-ASN : angle 1.70077 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8296 (t0) cc_final: 0.7970 (t0) REVERT: A 251 ASN cc_start: 0.8285 (m110) cc_final: 0.7999 (m110) REVERT: B 222 TYR cc_start: 0.6687 (p90) cc_final: 0.6250 (p90) REVERT: B 322 MET cc_start: 0.7701 (mtt) cc_final: 0.7487 (mpp) REVERT: C 214 ASN cc_start: 0.8785 (m-40) cc_final: 0.8513 (t0) REVERT: C 215 GLU cc_start: 0.8047 (mp0) cc_final: 0.7811 (tt0) REVERT: D 219 ASP cc_start: 0.7852 (p0) cc_final: 0.7009 (t0) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.2085 time to fit residues: 19.8367 Evaluate side-chains 63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 19 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.156005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.100284 restraints weight = 47284.215| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 4.14 r_work: 0.3344 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 11163 Z= 0.093 Angle : 0.528 9.009 15234 Z= 0.264 Chirality : 0.043 0.202 1802 Planarity : 0.004 0.082 1874 Dihedral : 6.313 54.179 2549 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.52 % Allowed : 7.02 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.24), residues: 1281 helix: -2.24 (0.46), residues: 105 sheet: -1.52 (0.39), residues: 172 loop : -0.46 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 188 TYR 0.009 0.001 TYR D 208 PHE 0.012 0.001 PHE B 94 TRP 0.013 0.001 TRP B 198 HIS 0.001 0.000 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00218 (11050) covalent geometry : angle 0.49777 (14951) SS BOND : bond 0.00291 ( 56) SS BOND : angle 1.12019 ( 112) hydrogen bonds : bond 0.03090 ( 226) hydrogen bonds : angle 5.41019 ( 405) link_ALPHA1-3 : bond 0.00729 ( 7) link_ALPHA1-3 : angle 1.67431 ( 21) link_ALPHA1-6 : bond 0.00801 ( 8) link_ALPHA1-6 : angle 1.43270 ( 24) link_BETA1-4 : bond 0.00502 ( 26) link_BETA1-4 : angle 1.43554 ( 78) link_NAG-ASN : bond 0.00320 ( 16) link_NAG-ASN : angle 1.69811 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8257 (t0) cc_final: 0.7943 (t0) REVERT: A 251 ASN cc_start: 0.8192 (m110) cc_final: 0.7911 (m110) REVERT: B 222 TYR cc_start: 0.6694 (p90) cc_final: 0.6241 (p90) REVERT: C 214 ASN cc_start: 0.8818 (m-40) cc_final: 0.8564 (t0) REVERT: C 215 GLU cc_start: 0.8056 (mp0) cc_final: 0.7856 (tt0) REVERT: D 219 ASP cc_start: 0.7781 (p0) cc_final: 0.7135 (t0) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.1837 time to fit residues: 17.5400 Evaluate side-chains 60 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 513 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 26 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.156017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100233 restraints weight = 47561.485| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.14 r_work: 0.3337 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11163 Z= 0.098 Angle : 0.526 7.551 15234 Z= 0.263 Chirality : 0.043 0.205 1802 Planarity : 0.004 0.057 1874 Dihedral : 6.223 53.697 2549 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.61 % Allowed : 7.11 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.24), residues: 1281 helix: -2.25 (0.45), residues: 112 sheet: -1.55 (0.39), residues: 172 loop : -0.43 (0.21), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 95 TYR 0.007 0.001 TYR D 208 PHE 0.008 0.001 PHE A 94 TRP 0.017 0.001 TRP B 198 HIS 0.002 0.000 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00230 (11050) covalent geometry : angle 0.49705 (14951) SS BOND : bond 0.00330 ( 56) SS BOND : angle 1.03976 ( 112) hydrogen bonds : bond 0.03102 ( 226) hydrogen bonds : angle 5.32224 ( 405) link_ALPHA1-3 : bond 0.00718 ( 7) link_ALPHA1-3 : angle 1.65945 ( 21) link_ALPHA1-6 : bond 0.00770 ( 8) link_ALPHA1-6 : angle 1.42745 ( 24) link_BETA1-4 : bond 0.00500 ( 26) link_BETA1-4 : angle 1.42480 ( 78) link_NAG-ASN : bond 0.00298 ( 16) link_NAG-ASN : angle 1.66749 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5246.35 seconds wall clock time: 89 minutes 45.64 seconds (5385.64 seconds total)