Starting phenix.real_space_refine on Wed Jun 18 12:15:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4i_41883/06_2025/8u4i_41883_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4i_41883/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4i_41883/06_2025/8u4i_41883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4i_41883/06_2025/8u4i_41883.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4i_41883/06_2025/8u4i_41883_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4i_41883/06_2025/8u4i_41883_trim.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.85, per 1000 atoms: 0.53 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: 5.93 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2.14 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: 7.70 Time building geometry restraints manager: 6.93 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 634 or resid 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: 3.860 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: 0.350 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 46.700 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (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 TRP 0.077 0.006 TRP B 407 HIS 0.009 0.001 HIS A 582 PHE 0.063 0.003 PHE D 189 TYR 0.114 0.010 TYR A 157 ARG 0.006 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.05396 ( 16) link_NAG-ASN : angle 4.97145 ( 48) 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_ALPHA1-3 : bond 0.02910 ( 7) link_ALPHA1-3 : angle 4.66522 ( 21) hydrogen bonds : bond 0.22343 ( 226) hydrogen bonds : angle 7.93235 ( 405) SS BOND : bond 0.06253 ( 56) SS BOND : angle 3.35608 ( 112) covalent geometry : bond 0.01390 (11050) covalent geometry : angle 1.55932 (14951) *********************** 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 : 1.638 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: 0.8422 (p) outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.5796 time to fit residues: 136.3627 Evaluate side-chains 74 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 109 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 B 264 GLN B 295 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.156086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101540 restraints weight = 48705.009| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 4.08 r_work: 0.3434 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11163 Z= 0.164 Angle : 0.774 8.521 15234 Z= 0.384 Chirality : 0.049 0.270 1802 Planarity : 0.005 0.061 1874 Dihedral : 15.110 82.690 2549 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1281 helix: -2.55 (0.43), residues: 102 sheet: -1.46 (0.34), residues: 182 loop : -0.01 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 407 HIS 0.005 0.001 HIS B 295 PHE 0.017 0.001 PHE D 189 TYR 0.012 0.002 TYR B 148 ARG 0.010 0.001 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 16) link_NAG-ASN : angle 2.23922 ( 48) link_ALPHA1-6 : bond 0.00788 ( 8) link_ALPHA1-6 : angle 1.60972 ( 24) link_BETA1-4 : bond 0.00877 ( 26) link_BETA1-4 : angle 3.17484 ( 78) link_ALPHA1-3 : bond 0.01199 ( 7) link_ALPHA1-3 : angle 2.11340 ( 21) hydrogen bonds : bond 0.05277 ( 226) hydrogen bonds : angle 6.44505 ( 405) SS BOND : bond 0.00427 ( 56) SS BOND : angle 1.38442 ( 112) covalent geometry : bond 0.00373 (11050) covalent geometry : angle 0.71880 (14951) *********************** 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 83 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.572 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: 0.8652 (p0) cc_final: 0.8380 (p0) REVERT: B 222 TYR cc_start: 0.6796 (p90) cc_final: 0.6380 (p90) REVERT: B 232 ARG cc_start: 0.7951 (tpt90) cc_final: 0.7721 (tpt90) REVERT: D 217 THR cc_start: 0.8200 (t) cc_final: 0.7814 (p) outliers start: 11 outliers final: 7 residues processed: 80 average time/residue: 0.5749 time to fit residues: 62.9895 Evaluate side-chains 68 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.155347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098954 restraints weight = 46944.876| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.12 r_work: 0.3317 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11163 Z= 0.190 Angle : 0.685 9.699 15234 Z= 0.344 Chirality : 0.049 0.241 1802 Planarity : 0.005 0.052 1874 Dihedral : 11.123 64.997 2549 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.87 % Allowed : 5.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1281 helix: -2.41 (0.44), residues: 105 sheet: -1.53 (0.37), residues: 160 loop : -0.39 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 407 HIS 0.006 0.001 HIS B 162 PHE 0.015 0.002 PHE B 94 TYR 0.011 0.002 TYR B 148 ARG 0.008 0.001 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 16) link_NAG-ASN : angle 1.61966 ( 48) link_ALPHA1-6 : bond 0.00888 ( 8) link_ALPHA1-6 : angle 1.48708 ( 24) link_BETA1-4 : bond 0.00760 ( 26) link_BETA1-4 : angle 2.09532 ( 78) link_ALPHA1-3 : bond 0.01124 ( 7) link_ALPHA1-3 : angle 1.64892 ( 21) hydrogen bonds : bond 0.04342 ( 226) hydrogen bonds : angle 5.81781 ( 405) SS BOND : bond 0.00519 ( 56) SS BOND : angle 1.19225 ( 112) covalent geometry : bond 0.00445 (11050) covalent geometry : angle 0.65527 (14951) *********************** 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 72 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 1.727 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: A 71 ASN cc_start: 0.8364 (t0) cc_final: 0.7996 (t0) REVERT: A 413 ASP cc_start: 0.8667 (p0) cc_final: 0.8449 (p0) REVERT: B 222 TYR cc_start: 0.6659 (p90) cc_final: 0.6228 (p90) REVERT: B 322 MET cc_start: 0.7756 (mtt) cc_final: 0.7413 (mpp) REVERT: C 208 TYR cc_start: 0.8356 (m-80) cc_final: 0.8065 (m-10) outliers start: 10 outliers final: 8 residues processed: 71 average time/residue: 0.5514 time to fit residues: 55.1237 Evaluate side-chains 64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.156358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.102597 restraints weight = 47204.713| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.58 r_work: 0.3328 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3627 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= 0.122 Angle : 0.610 6.262 15234 Z= 0.301 Chirality : 0.047 0.239 1802 Planarity : 0.004 0.058 1874 Dihedral : 9.600 58.201 2549 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.95 % Allowed : 5.63 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1281 helix: -2.19 (0.46), residues: 105 sheet: -1.61 (0.37), residues: 160 loop : -0.38 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 198 HIS 0.003 0.001 HIS A 505 PHE 0.013 0.001 PHE D 197 TYR 0.009 0.001 TYR B 148 ARG 0.006 0.001 ARG B 396 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 16) link_NAG-ASN : angle 1.59679 ( 48) link_ALPHA1-6 : bond 0.00914 ( 8) link_ALPHA1-6 : angle 1.46052 ( 24) link_BETA1-4 : bond 0.00576 ( 26) link_BETA1-4 : angle 1.94247 ( 78) link_ALPHA1-3 : bond 0.01003 ( 7) link_ALPHA1-3 : angle 1.84127 ( 21) hydrogen bonds : bond 0.03749 ( 226) hydrogen bonds : angle 5.61317 ( 405) SS BOND : bond 0.00460 ( 56) SS BOND : angle 0.97012 ( 112) covalent geometry : bond 0.00279 (11050) covalent geometry : angle 0.58022 (14951) *********************** 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 71 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 1.655 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: A 64 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: A 69 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7910 (mt-10) REVERT: A 71 ASN cc_start: 0.8350 (t0) cc_final: 0.7959 (t0) REVERT: A 251 ASN cc_start: 0.8405 (m110) cc_final: 0.8155 (m110) REVERT: A 413 ASP cc_start: 0.8625 (p0) cc_final: 0.8374 (p0) REVERT: B 222 TYR cc_start: 0.6657 (p90) cc_final: 0.6212 (p90) REVERT: B 322 MET cc_start: 0.7731 (mtt) cc_final: 0.7398 (mpp) REVERT: C 208 TYR cc_start: 0.8337 (m-80) cc_final: 0.8126 (m-10) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.5064 time to fit residues: 51.0693 Evaluate side-chains 63 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 C residue 186 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 79 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.154914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101327 restraints weight = 47303.375| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.56 r_work: 0.3310 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11163 Z= 0.143 Angle : 0.592 5.904 15234 Z= 0.295 Chirality : 0.046 0.232 1802 Planarity : 0.004 0.036 1874 Dihedral : 7.946 59.078 2549 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.21 % Allowed : 5.46 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1281 helix: -2.07 (0.48), residues: 105 sheet: -1.83 (0.36), residues: 172 loop : -0.54 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 198 HIS 0.004 0.001 HIS B 162 PHE 0.013 0.001 PHE D 189 TYR 0.010 0.001 TYR B 148 ARG 0.009 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 16) link_NAG-ASN : angle 1.59354 ( 48) link_ALPHA1-6 : bond 0.01009 ( 8) link_ALPHA1-6 : angle 1.85943 ( 24) link_BETA1-4 : bond 0.00591 ( 26) link_BETA1-4 : angle 1.70411 ( 78) link_ALPHA1-3 : bond 0.01041 ( 7) link_ALPHA1-3 : angle 1.68179 ( 21) hydrogen bonds : bond 0.03623 ( 226) hydrogen bonds : angle 5.48190 ( 405) SS BOND : bond 0.00441 ( 56) SS BOND : angle 0.94206 ( 112) covalent geometry : bond 0.00334 (11050) covalent geometry : angle 0.56407 (14951) *********************** 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 76 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 1.514 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: A 71 ASN cc_start: 0.8310 (t0) cc_final: 0.7995 (t0) REVERT: A 251 ASN cc_start: 0.8379 (m110) cc_final: 0.8112 (m110) REVERT: A 413 ASP cc_start: 0.8591 (p0) cc_final: 0.8340 (p0) REVERT: B 222 TYR cc_start: 0.6639 (p90) cc_final: 0.6162 (p90) REVERT: B 232 ARG cc_start: 0.7937 (tpt90) cc_final: 0.7642 (tpt90) REVERT: B 322 MET cc_start: 0.7719 (mtt) cc_final: 0.7465 (mpp) REVERT: D 219 ASP cc_start: 0.7937 (p0) cc_final: 0.6851 (t0) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.5142 time to fit residues: 55.7332 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 : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 506 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.154763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098588 restraints weight = 47099.389| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 4.11 r_work: 0.3313 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11163 Z= 0.130 Angle : 0.572 5.499 15234 Z= 0.287 Chirality : 0.045 0.217 1802 Planarity : 0.004 0.051 1874 Dihedral : 7.354 58.504 2549 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.04 % Allowed : 6.15 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1281 helix: -2.31 (0.45), residues: 105 sheet: -1.73 (0.38), residues: 162 loop : -0.55 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 198 HIS 0.002 0.001 HIS B 470 PHE 0.010 0.001 PHE B 368 TYR 0.016 0.001 TYR A 468 ARG 0.007 0.000 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 16) link_NAG-ASN : angle 1.62198 ( 48) link_ALPHA1-6 : bond 0.00922 ( 8) link_ALPHA1-6 : angle 1.45264 ( 24) link_BETA1-4 : bond 0.00542 ( 26) link_BETA1-4 : angle 1.57853 ( 78) link_ALPHA1-3 : bond 0.00875 ( 7) link_ALPHA1-3 : angle 1.81277 ( 21) hydrogen bonds : bond 0.03547 ( 226) hydrogen bonds : angle 5.48378 ( 405) SS BOND : bond 0.00397 ( 56) SS BOND : angle 1.09231 ( 112) covalent geometry : bond 0.00305 (11050) covalent geometry : angle 0.54280 (14951) *********************** 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 69 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.624 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: A 71 ASN cc_start: 0.8301 (t0) cc_final: 0.7989 (t0) REVERT: A 251 ASN cc_start: 0.8333 (m110) cc_final: 0.8054 (m110) REVERT: A 413 ASP cc_start: 0.8598 (p0) cc_final: 0.8348 (p0) REVERT: B 222 TYR cc_start: 0.6611 (p90) cc_final: 0.6148 (p90) REVERT: B 232 ARG cc_start: 0.7911 (tpt90) cc_final: 0.7585 (tpt90) REVERT: B 322 MET cc_start: 0.7699 (mtt) cc_final: 0.7450 (mpp) REVERT: B 411 MET cc_start: 0.6312 (mtp) cc_final: 0.6069 (mtm) REVERT: B 462 ASP cc_start: 0.7378 (m-30) cc_final: 0.7161 (m-30) REVERT: D 219 ASP cc_start: 0.7894 (p0) cc_final: 0.6898 (t0) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.5248 time to fit residues: 51.0359 Evaluate side-chains 67 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 506 LEU 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 513 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 chunk 119 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.156125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.103016 restraints weight = 46716.003| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 4.63 r_work: 0.3331 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11163 Z= 0.092 Angle : 0.526 5.927 15234 Z= 0.262 Chirality : 0.043 0.200 1802 Planarity : 0.004 0.040 1874 Dihedral : 6.611 58.260 2549 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.78 % Allowed : 6.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.23), residues: 1281 helix: -2.15 (0.47), residues: 105 sheet: -1.54 (0.38), residues: 172 loop : -0.47 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 198 HIS 0.002 0.000 HIS A 470 PHE 0.007 0.001 PHE A 583 TYR 0.007 0.001 TYR B 148 ARG 0.004 0.000 ARG A 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 16) link_NAG-ASN : angle 1.59172 ( 48) link_ALPHA1-6 : bond 0.00868 ( 8) link_ALPHA1-6 : angle 1.38587 ( 24) link_BETA1-4 : bond 0.00554 ( 26) link_BETA1-4 : angle 1.48868 ( 78) link_ALPHA1-3 : bond 0.00905 ( 7) link_ALPHA1-3 : angle 1.71982 ( 21) hydrogen bonds : bond 0.02981 ( 226) hydrogen bonds : angle 5.31077 ( 405) SS BOND : bond 0.00389 ( 56) SS BOND : angle 0.93106 ( 112) covalent geometry : bond 0.00207 (11050) covalent geometry : angle 0.49831 (14951) *********************** 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 72 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 2.044 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 71 ASN cc_start: 0.8317 (t0) cc_final: 0.7963 (t0) REVERT: A 251 ASN cc_start: 0.8215 (m110) cc_final: 0.7935 (m110) REVERT: A 413 ASP cc_start: 0.8594 (p0) cc_final: 0.8251 (p0) REVERT: B 222 TYR cc_start: 0.6675 (p90) cc_final: 0.6216 (p90) REVERT: B 232 ARG cc_start: 0.7907 (tpt90) cc_final: 0.7316 (tpt90) REVERT: C 214 ASN cc_start: 0.8759 (m-40) cc_final: 0.8461 (t0) REVERT: D 219 ASP cc_start: 0.7863 (p0) cc_final: 0.7103 (t0) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.6408 time to fit residues: 64.2550 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 : 1.773 ------------------------------------------------------------------------------- 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 365 ASN Chi-restraints excluded: chain A residue 506 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.154035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.098255 restraints weight = 47322.642| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.07 r_work: 0.3303 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11163 Z= 0.165 Angle : 0.576 8.753 15234 Z= 0.292 Chirality : 0.044 0.222 1802 Planarity : 0.004 0.071 1874 Dihedral : 6.597 57.890 2549 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.13 % Allowed : 6.76 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.23), residues: 1281 helix: -2.34 (0.45), residues: 105 sheet: -1.50 (0.41), residues: 153 loop : -0.58 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 513 HIS 0.002 0.001 HIS C 178 PHE 0.013 0.001 PHE B 368 TYR 0.010 0.001 TYR A 469 ARG 0.008 0.000 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 16) link_NAG-ASN : angle 1.65255 ( 48) link_ALPHA1-6 : bond 0.00793 ( 8) link_ALPHA1-6 : angle 1.46493 ( 24) link_BETA1-4 : bond 0.00530 ( 26) link_BETA1-4 : angle 1.47852 ( 78) link_ALPHA1-3 : bond 0.00784 ( 7) link_ALPHA1-3 : angle 1.74918 ( 21) hydrogen bonds : bond 0.03744 ( 226) hydrogen bonds : angle 5.51793 ( 405) SS BOND : bond 0.00407 ( 56) SS BOND : angle 1.20408 ( 112) covalent geometry : bond 0.00396 (11050) covalent geometry : angle 0.54657 (14951) *********************** 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: 13 poor density : 56 time to evaluate : 1.556 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: 0.8303 (t0) cc_final: 0.7978 (t0) REVERT: A 174 ASN cc_start: 0.4555 (OUTLIER) cc_final: 0.4309 (t0) REVERT: A 251 ASN cc_start: 0.8303 (m110) cc_final: 0.8004 (m110) REVERT: A 413 ASP cc_start: 0.8600 (p0) cc_final: 0.8355 (p0) REVERT: B 222 TYR cc_start: 0.6660 (p90) cc_final: 0.6167 (p90) REVERT: B 322 MET cc_start: 0.7645 (mtm) cc_final: 0.7104 (mpp) REVERT: C 214 ASN cc_start: 0.8812 (m-40) cc_final: 0.8402 (t0) REVERT: D 219 ASP cc_start: 0.7889 (p0) cc_final: 0.7191 (t0) outliers start: 13 outliers final: 9 residues processed: 67 average time/residue: 0.5649 time to fit residues: 53.1650 Evaluate side-chains 62 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 A residue 347 THR Chi-restraints excluded: chain A residue 506 LEU 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 44 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4263 r_free = 0.4263 target = 0.154948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101798 restraints weight = 47048.910| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 4.55 r_work: 0.3319 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11163 Z= 0.109 Angle : 0.543 8.914 15234 Z= 0.273 Chirality : 0.043 0.209 1802 Planarity : 0.004 0.057 1874 Dihedral : 6.493 56.708 2549 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.87 % Allowed : 7.11 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1281 helix: -2.34 (0.45), residues: 105 sheet: -1.49 (0.41), residues: 153 loop : -0.55 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 198 HIS 0.002 0.000 HIS A 231 PHE 0.008 0.001 PHE B 94 TYR 0.008 0.001 TYR A 469 ARG 0.010 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 16) link_NAG-ASN : angle 1.63914 ( 48) link_ALPHA1-6 : bond 0.00810 ( 8) link_ALPHA1-6 : angle 1.44246 ( 24) link_BETA1-4 : bond 0.00505 ( 26) link_BETA1-4 : angle 1.45994 ( 78) link_ALPHA1-3 : bond 0.00769 ( 7) link_ALPHA1-3 : angle 1.71884 ( 21) hydrogen bonds : bond 0.03323 ( 226) hydrogen bonds : angle 5.45913 ( 405) SS BOND : bond 0.00334 ( 56) SS BOND : angle 1.11687 ( 112) covalent geometry : bond 0.00257 (11050) covalent geometry : angle 0.51403 (14951) *********************** 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 66 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.476 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: 0.8306 (t0) cc_final: 0.7986 (t0) REVERT: A 251 ASN cc_start: 0.8249 (m110) cc_final: 0.7958 (m110) REVERT: A 413 ASP cc_start: 0.8614 (p0) cc_final: 0.8335 (p0) REVERT: B 222 TYR cc_start: 0.6691 (p90) cc_final: 0.6188 (p90) REVERT: B 322 MET cc_start: 0.7702 (mtm) cc_final: 0.7160 (mpp) REVERT: C 214 ASN cc_start: 0.8798 (m-40) cc_final: 0.8520 (t0) REVERT: D 219 ASP cc_start: 0.7845 (p0) cc_final: 0.7188 (t0) outliers start: 10 outliers final: 9 residues processed: 65 average time/residue: 0.4427 time to fit residues: 42.8355 Evaluate side-chains 64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 506 LEU 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 8 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.154879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.102035 restraints weight = 46889.639| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.56 r_work: 0.3315 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11163 Z= 0.109 Angle : 0.534 7.523 15234 Z= 0.268 Chirality : 0.043 0.206 1802 Planarity : 0.004 0.051 1874 Dihedral : 6.331 54.859 2549 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.78 % Allowed : 7.19 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1281 helix: -2.23 (0.46), residues: 105 sheet: -1.46 (0.41), residues: 156 loop : -0.54 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 198 HIS 0.002 0.000 HIS A 231 PHE 0.009 0.001 PHE A 401 TYR 0.010 0.001 TYR D 208 ARG 0.010 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 16) link_NAG-ASN : angle 1.65320 ( 48) link_ALPHA1-6 : bond 0.00780 ( 8) link_ALPHA1-6 : angle 1.43772 ( 24) link_BETA1-4 : bond 0.00501 ( 26) link_BETA1-4 : angle 1.43107 ( 78) link_ALPHA1-3 : bond 0.00731 ( 7) link_ALPHA1-3 : angle 1.68115 ( 21) hydrogen bonds : bond 0.03204 ( 226) hydrogen bonds : angle 5.38490 ( 405) SS BOND : bond 0.00316 ( 56) SS BOND : angle 1.00708 ( 112) covalent geometry : bond 0.00257 (11050) covalent geometry : angle 0.50636 (14951) ********************** 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 66 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 1.510 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: 0.8280 (t0) cc_final: 0.7958 (t0) REVERT: A 251 ASN cc_start: 0.8194 (m110) cc_final: 0.7908 (m110) REVERT: A 413 ASP cc_start: 0.8636 (p0) cc_final: 0.8360 (p0) REVERT: B 64 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: B 222 TYR cc_start: 0.6653 (p90) cc_final: 0.6143 (p90) REVERT: B 322 MET cc_start: 0.7741 (mtm) cc_final: 0.7194 (mpp) REVERT: C 214 ASN cc_start: 0.8811 (m-40) cc_final: 0.8415 (t0) REVERT: D 219 ASP cc_start: 0.7806 (p0) cc_final: 0.7196 (t0) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.4558 time to fit residues: 44.0883 Evaluate side-chains 64 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 64 GLU 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 70 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 10 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.153399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097540 restraints weight = 47572.298| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.07 r_work: 0.3300 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11163 Z= 0.161 Angle : 0.570 7.722 15234 Z= 0.289 Chirality : 0.044 0.219 1802 Planarity : 0.004 0.058 1874 Dihedral : 6.426 54.953 2549 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.95 % Allowed : 7.28 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.24), residues: 1281 helix: -2.34 (0.46), residues: 105 sheet: -1.51 (0.42), residues: 151 loop : -0.64 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.004 0.001 HIS B 162 PHE 0.013 0.001 PHE B 368 TYR 0.011 0.001 TYR A 123 ARG 0.011 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 16) link_NAG-ASN : angle 1.70923 ( 48) link_ALPHA1-6 : bond 0.00743 ( 8) link_ALPHA1-6 : angle 1.45852 ( 24) link_BETA1-4 : bond 0.00496 ( 26) link_BETA1-4 : angle 1.43083 ( 78) link_ALPHA1-3 : bond 0.00705 ( 7) link_ALPHA1-3 : angle 1.68554 ( 21) hydrogen bonds : bond 0.03676 ( 226) hydrogen bonds : angle 5.44952 ( 405) SS BOND : bond 0.00406 ( 56) SS BOND : angle 1.13176 ( 112) covalent geometry : bond 0.00385 (11050) covalent geometry : angle 0.54231 (14951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10058.43 seconds wall clock time: 173 minutes 13.59 seconds (10393.59 seconds total)