Starting phenix.real_space_refine on Wed May 21 09:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4j_41884/05_2025/8u4j_41884_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4j_41884/05_2025/8u4j_41884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4j_41884/05_2025/8u4j_41884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4j_41884/05_2025/8u4j_41884.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4j_41884/05_2025/8u4j_41884_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4j_41884/05_2025/8u4j_41884_trim.cif" } resolution = 3.7 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= -0.000 sd= 0.030 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 128 5.16 5 C 6691 2.51 5 N 1805 2.21 5 O 2226 1.98 5 H 9582 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20432 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 9092 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: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 762 Classifications: {'peptide': 48} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 762 Classifications: {'peptide': 48} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} 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: 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: "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: 10.39, per 1000 atoms: 0.51 Number of scatterers: 20432 At special positions: 0 Unit cell: (86.005, 142.785, 138.61, 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 128 16.00 O 2226 8.00 N 1805 7.00 C 6691 6.00 H 9582 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=2.15 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.01 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.07 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.04 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=2.03 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=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.05 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.24 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=2.16 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.02 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.06 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.04 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.03 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.04 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=2.12 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.06 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.04 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 56 " distance=2.05 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=2.01 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=2.07 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 229 " distance=2.02 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 238 " distance=2.02 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.05 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 258 " distance=2.04 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 289 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 330 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 496 " distance=2.18 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 512 " distance=2.04 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 520 " distance=2.06 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 532 " distance=2.02 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 552 " distance=2.01 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=2.00 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 614 " distance=2.08 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=2.12 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 82 " distance=2.07 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.01 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 82 " distance=2.04 Simple disulfide: pdb=" SG CYS D 77 " - pdb=" SG CYS D 93 " distance=2.02 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 104 " distance=2.02 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 N 3 " - " MAN N 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 5 " " 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: 5.87 Conformation dependent library (CDL) restraints added in 1.5 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: 2388 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 32 sheets defined 15.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.928A 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 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.403A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.942A 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 385 through 395 removed outlier: 4.242A 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 472 removed outlier: 3.598A pdb=" N HIS A 470 " --> pdb=" O CYS A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'B' and resid 41 through 54 Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.623A 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 166 removed outlier: 3.622A pdb=" N ASP B 165 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.229A 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 473 through 478 Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'D' and resid 70 through 74 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 63 through 66 removed outlier: 6.359A pdb=" N LEU A 63 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA A 90 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 65 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 149 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 238 removed outlier: 7.784A pdb=" N GLY A 237 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N CYS A 246 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.688A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 368 removed outlier: 5.511A pdb=" N ASN A 457 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 434 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ARG A 488 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 460 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 528 removed outlier: 3.758A pdb=" N ILE A 531 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 545 through 548 Processing sheet with id=AB4, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AB5, first strand: chain 'A' and resid 605 through 608 removed outlier: 4.120A pdb=" N PHE A 605 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39 removed outlier: 7.340A pdb=" N SER B 38 " --> pdb=" O CYS D 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.507A pdb=" N LEU B 63 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA B 90 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 65 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY B 146 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 117 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AC1, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.773A pdb=" N GLN B 274 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 317 Processing sheet with id=AC5, first strand: chain 'B' and resid 333 through 335 removed outlier: 6.521A pdb=" N CYS B 334 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 366 through 368 removed outlier: 4.684A pdb=" N LEU B 432 " --> pdb=" O ASN B 457 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N TYR B 459 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 434 " --> pdb=" O TYR B 459 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N THR B 461 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 436 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AC8, first strand: chain 'B' and resid 545 through 548 Processing sheet with id=AC9, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AD1, first strand: chain 'B' and resid 606 through 608 Processing sheet with id=AD2, first strand: chain 'B' and resid 624 through 625 Processing sheet with id=AD3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AD4, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AD5, first strand: chain 'D' and resid 99 through 100 227 hydrogen bonds defined for protein. 414 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: 7.14 Time building geometry restraints manager: 6.95 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: 9582 1.13 - 1.31: 1806 1.31 - 1.48: 4444 1.48 - 1.65: 4673 1.65 - 1.82: 144 Bond restraints: 20649 Sorted by residual: bond pdb=" ND2 ASN B 174 " pdb="HD22 ASN B 174 " 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 A 273 " pdb=" HZ PHE A 273 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N HIS A 204 " pdb=" H HIS A 204 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLU A 54 " pdb=" H GLU A 54 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LEU A 434 " pdb=" H LEU A 434 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 20644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 31180 1.99 - 3.99: 3364 3.99 - 5.98: 1464 5.98 - 7.98: 802 7.98 - 9.97: 12 Bond angle restraints: 36822 Sorted by residual: angle pdb=" CA ASN A 138 " pdb=" CB ASN A 138 " pdb=" CG ASN A 138 " ideal model delta sigma weight residual 112.60 119.89 -7.29 1.00e+00 1.00e+00 5.31e+01 angle pdb=" N ILE A 357 " pdb=" CA ILE A 357 " pdb=" C ILE A 357 " ideal model delta sigma weight residual 110.62 117.31 -6.69 1.14e+00 7.69e-01 3.45e+01 angle pdb=" C ARG A 525 " pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " ideal model delta sigma weight residual 117.23 109.27 7.96 1.36e+00 5.41e-01 3.42e+01 angle pdb=" N PHE A 120 " pdb=" CA PHE A 120 " pdb=" C PHE A 120 " ideal model delta sigma weight residual 108.79 117.16 -8.37 1.53e+00 4.27e-01 3.00e+01 angle pdb=" N ILE B 357 " pdb=" CA ILE B 357 " pdb=" C ILE B 357 " ideal model delta sigma weight residual 110.62 116.08 -5.46 1.02e+00 9.61e-01 2.86e+01 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 9939 21.98 - 43.97: 439 43.97 - 65.95: 269 65.95 - 87.94: 81 87.94 - 109.92: 51 Dihedral angle restraints: 10779 sinusoidal: 6383 harmonic: 4396 Sorted by residual: dihedral pdb=" CB CYS B 621 " pdb=" SG CYS B 621 " pdb=" SG CYS B 633 " pdb=" CB CYS B 633 " ideal model delta sinusoidal sigma weight residual -86.00 -167.30 81.30 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS A 614 " pdb=" CB CYS A 614 " ideal model delta sinusoidal sigma weight residual 93.00 162.52 -69.52 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB CYS D 77 " pdb=" SG CYS D 77 " pdb=" SG CYS D 93 " pdb=" CB CYS D 93 " ideal model delta sinusoidal sigma weight residual 93.00 158.06 -65.06 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 10776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1557 0.122 - 0.244: 207 0.244 - 0.366: 27 0.366 - 0.488: 7 0.488 - 0.610: 1 Chirality restraints: 1799 Sorted by residual: chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.98e+01 ... (remaining 1796 not shown) Planarity restraints: 3125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG M 1 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.321 2.00e-02 2.50e+03 2.77e-01 9.57e+02 pdb=" C7 NAG M 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.026 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.210 2.00e-02 2.50e+03 1.52e-01 3.48e+02 pdb=" CG ASN A 138 " -0.072 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " -0.039 2.00e-02 2.50e+03 pdb="HD21 ASN A 138 " -0.191 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.201 2.00e-02 2.50e+03 ... (remaining 3122 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 752 2.06 - 2.69: 25825 2.69 - 3.33: 56785 3.33 - 3.96: 74117 3.96 - 4.60: 107747 Nonbonded interactions: 265226 Sorted by model distance: nonbonded pdb=" H GLY A 364 " pdb=" HG1 THR A 399 " model vdw 1.419 2.100 nonbonded pdb=" OE2 GLU B 317 " pdb=" HZ1 LYS B 324 " model vdw 1.431 2.450 nonbonded pdb=" O TYR C 76 " pdb=" HE ARG C 103 " model vdw 1.493 2.450 nonbonded pdb=" H GLY A 364 " pdb=" OG1 THR A 399 " model vdw 1.540 2.450 nonbonded pdb=" HB3 ASN B 251 " pdb=" H PHE B 252 " model vdw 1.575 2.270 ... (remaining 265221 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 137 or (resid 138 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HB \ 2 or name HB3 or name HD21)) or resid 139 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 'N' 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 group one per residue 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: 3.830 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: 0.330 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.840 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.014 0.206 11181 Z= 0.842 Angle : 1.674 17.081 15266 Z= 1.031 Chirality : 0.087 0.610 1799 Planarity : 0.014 0.298 1878 Dihedral : 16.947 109.924 4966 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.17 % Allowed : 0.61 % Favored : 99.22 % Cbeta Deviations : 0.25 % 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: -0.45 (0.22), residues: 1281 helix: -2.74 (0.43), residues: 88 sheet: -1.36 (0.37), residues: 154 loop : 0.17 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.005 TRP B 198 HIS 0.008 0.001 HIS B 570 PHE 0.056 0.004 PHE B 154 TYR 0.102 0.006 TYR A 157 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd link_NAG-ASN : bond 0.05312 ( 16) link_NAG-ASN : angle 5.93551 ( 48) link_ALPHA1-6 : bond 0.02761 ( 8) link_ALPHA1-6 : angle 4.44575 ( 24) link_BETA1-4 : bond 0.02830 ( 26) link_BETA1-4 : angle 6.39682 ( 78) link_ALPHA1-3 : bond 0.02594 ( 8) link_ALPHA1-3 : angle 3.96482 ( 24) hydrogen bonds : bond 0.21780 ( 227) hydrogen bonds : angle 8.76697 ( 414) SS BOND : bond 0.04774 ( 56) SS BOND : angle 3.68422 ( 112) covalent geometry : bond 0.01363 (11067) covalent geometry : angle 1.53954 (14980) *********************** 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 183 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 1.909 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: 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: A 260 THR cc_start: 0.8907 (p) cc_final: 0.8668 (m) REVERT: B 251 ASN cc_start: 0.8169 (m-40) cc_final: 0.7465 (m-40) REVERT: B 331 PRO cc_start: 0.7434 (Cg_exo) cc_final: 0.6954 (Cg_endo) REVERT: D 68 ARG cc_start: 0.8468 (ttt180) cc_final: 0.7890 (tpm170) outliers start: 2 outliers final: 2 residues processed: 183 average time/residue: 0.7353 time to fit residues: 170.4385 Evaluate side-chains 97 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 410 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 631 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.137352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097100 restraints weight = 59588.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.101616 restraints weight = 29318.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104649 restraints weight = 19000.897| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11181 Z= 0.163 Angle : 0.792 13.537 15266 Z= 0.384 Chirality : 0.049 0.319 1799 Planarity : 0.005 0.061 1878 Dihedral : 15.333 88.676 2575 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.44 % Allowed : 4.53 % Favored : 95.03 % 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: -0.72 (0.23), residues: 1281 helix: -2.14 (0.49), residues: 94 sheet: -1.35 (0.35), residues: 172 loop : -0.10 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 513 HIS 0.009 0.001 HIS B 505 PHE 0.014 0.001 PHE B 154 TYR 0.013 0.001 TYR B 53 ARG 0.006 0.001 ARG B 114 Details of bonding type rmsd link_NAG-ASN : bond 0.01094 ( 16) link_NAG-ASN : angle 3.53423 ( 48) link_ALPHA1-6 : bond 0.01102 ( 8) link_ALPHA1-6 : angle 1.92523 ( 24) link_BETA1-4 : bond 0.00955 ( 26) link_BETA1-4 : angle 3.60906 ( 78) link_ALPHA1-3 : bond 0.01053 ( 8) link_ALPHA1-3 : angle 2.18062 ( 24) hydrogen bonds : bond 0.05666 ( 227) hydrogen bonds : angle 7.73421 ( 414) SS BOND : bond 0.00435 ( 56) SS BOND : angle 1.20681 ( 112) covalent geometry : bond 0.00358 (11067) covalent geometry : angle 0.71230 (14980) *********************** 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 101 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 1.792 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASN cc_start: 0.7680 (p0) cc_final: 0.7180 (p0) REVERT: B 279 PHE cc_start: 0.7788 (p90) cc_final: 0.7588 (p90) REVERT: C 110 PHE cc_start: 0.7667 (m-80) cc_final: 0.7292 (m-10) outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 0.7423 time to fit residues: 94.0813 Evaluate side-chains 82 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.141532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.097105 restraints weight = 69177.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.101994 restraints weight = 32564.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.105190 restraints weight = 20924.753| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11181 Z= 0.192 Angle : 0.706 9.798 15266 Z= 0.344 Chirality : 0.049 0.235 1799 Planarity : 0.005 0.077 1878 Dihedral : 11.793 73.029 2574 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.13 % Allowed : 5.23 % Favored : 93.64 % 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: -1.16 (0.23), residues: 1281 helix: -2.21 (0.48), residues: 95 sheet: -1.57 (0.35), residues: 162 loop : -0.49 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 474 HIS 0.006 0.001 HIS A 470 PHE 0.015 0.001 PHE B 252 TYR 0.015 0.002 TYR A 148 ARG 0.008 0.001 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 16) link_NAG-ASN : angle 2.74737 ( 48) link_ALPHA1-6 : bond 0.01208 ( 8) link_ALPHA1-6 : angle 1.84725 ( 24) link_BETA1-4 : bond 0.00791 ( 26) link_BETA1-4 : angle 2.50838 ( 78) link_ALPHA1-3 : bond 0.01116 ( 8) link_ALPHA1-3 : angle 1.60784 ( 24) hydrogen bonds : bond 0.04828 ( 227) hydrogen bonds : angle 7.16908 ( 414) SS BOND : bond 0.00376 ( 56) SS BOND : angle 0.94829 ( 112) covalent geometry : bond 0.00432 (11067) covalent geometry : angle 0.65928 (14980) *********************** 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 98 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.641 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: symmetry clash revert: symmetry clash REVERT: B 261 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8260 (tp-100) REVERT: C 110 PHE cc_start: 0.7802 (m-80) cc_final: 0.7395 (m-10) outliers start: 13 outliers final: 12 residues processed: 92 average time/residue: 0.6275 time to fit residues: 78.1839 Evaluate side-chains 79 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 91 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.141452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.103500 restraints weight = 70025.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.104787 restraints weight = 32123.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.104933 restraints weight = 22096.418| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11181 Z= 0.148 Angle : 0.644 9.335 15266 Z= 0.312 Chirality : 0.048 0.228 1799 Planarity : 0.004 0.053 1878 Dihedral : 9.899 63.901 2574 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.22 % Allowed : 6.45 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.12 (0.23), residues: 1281 helix: -1.99 (0.50), residues: 90 sheet: -1.44 (0.38), residues: 153 loop : -0.52 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 474 HIS 0.003 0.001 HIS A 470 PHE 0.011 0.001 PHE B 447 TYR 0.010 0.001 TYR B 53 ARG 0.003 0.000 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 16) link_NAG-ASN : angle 2.52054 ( 48) link_ALPHA1-6 : bond 0.01206 ( 8) link_ALPHA1-6 : angle 1.83130 ( 24) link_BETA1-4 : bond 0.00539 ( 26) link_BETA1-4 : angle 2.27342 ( 78) link_ALPHA1-3 : bond 0.00954 ( 8) link_ALPHA1-3 : angle 2.00187 ( 24) hydrogen bonds : bond 0.04084 ( 227) hydrogen bonds : angle 6.82741 ( 414) SS BOND : bond 0.00322 ( 56) SS BOND : angle 1.02407 ( 112) covalent geometry : bond 0.00338 (11067) covalent geometry : angle 0.59689 (14980) *********************** 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 85 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.729 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: A 318 ASN cc_start: 0.8029 (p0) cc_final: 0.7655 (p0) REVERT: B 53 TYR cc_start: 0.8368 (m-80) cc_final: 0.8098 (m-10) REVERT: C 110 PHE cc_start: 0.7746 (m-80) cc_final: 0.7243 (m-80) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.6193 time to fit residues: 65.4683 Evaluate side-chains 75 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.140781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.103274 restraints weight = 70196.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.104848 restraints weight = 32633.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.104893 restraints weight = 22326.354| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11181 Z= 0.128 Angle : 0.607 9.191 15266 Z= 0.294 Chirality : 0.046 0.242 1799 Planarity : 0.004 0.059 1878 Dihedral : 8.488 57.661 2574 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.05 % Allowed : 6.71 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1281 helix: -1.96 (0.51), residues: 90 sheet: -1.50 (0.38), residues: 150 loop : -0.50 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 PHE 0.010 0.001 PHE B 447 TYR 0.009 0.001 TYR A 148 ARG 0.007 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 16) link_NAG-ASN : angle 2.39071 ( 48) link_ALPHA1-6 : bond 0.01247 ( 8) link_ALPHA1-6 : angle 1.88678 ( 24) link_BETA1-4 : bond 0.00591 ( 26) link_BETA1-4 : angle 2.01839 ( 78) link_ALPHA1-3 : bond 0.01067 ( 8) link_ALPHA1-3 : angle 1.58200 ( 24) hydrogen bonds : bond 0.03714 ( 227) hydrogen bonds : angle 6.57723 ( 414) SS BOND : bond 0.00452 ( 56) SS BOND : angle 1.06857 ( 112) covalent geometry : bond 0.00290 (11067) covalent geometry : angle 0.56326 (14980) *********************** 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 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASN cc_start: 0.7997 (p0) cc_final: 0.7587 (p0) outliers start: 12 outliers final: 12 residues processed: 70 average time/residue: 0.5874 time to fit residues: 55.9399 Evaluate side-chains 72 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN A 463 ASN B 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.138061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.093565 restraints weight = 70614.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.098189 restraints weight = 33565.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.101243 restraints weight = 21744.288| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11181 Z= 0.196 Angle : 0.642 9.098 15266 Z= 0.315 Chirality : 0.047 0.215 1799 Planarity : 0.004 0.063 1878 Dihedral : 7.697 57.368 2574 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.48 % Allowed : 6.01 % Favored : 92.51 % 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: -1.43 (0.23), residues: 1281 helix: -2.00 (0.51), residues: 94 sheet: -1.67 (0.38), residues: 159 loop : -0.75 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 198 HIS 0.007 0.001 HIS B 374 PHE 0.014 0.002 PHE B 447 TYR 0.015 0.002 TYR B 53 ARG 0.004 0.001 ARG D 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 16) link_NAG-ASN : angle 2.42051 ( 48) link_ALPHA1-6 : bond 0.01192 ( 8) link_ALPHA1-6 : angle 1.57553 ( 24) link_BETA1-4 : bond 0.00484 ( 26) link_BETA1-4 : angle 1.90965 ( 78) link_ALPHA1-3 : bond 0.00832 ( 8) link_ALPHA1-3 : angle 1.77167 ( 24) hydrogen bonds : bond 0.04054 ( 227) hydrogen bonds : angle 6.59406 ( 414) SS BOND : bond 0.00405 ( 56) SS BOND : angle 1.10953 ( 112) covalent geometry : bond 0.00450 (11067) covalent geometry : angle 0.60391 (14980) *********************** 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 83 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.554 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: symmetry clash revert: symmetry clash REVERT: A 318 ASN cc_start: 0.8065 (p0) cc_final: 0.7651 (p0) outliers start: 17 outliers final: 16 residues processed: 76 average time/residue: 0.5441 time to fit residues: 58.2710 Evaluate side-chains 79 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 171 TRP Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 116 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.138551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.100602 restraints weight = 69614.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.101426 restraints weight = 33943.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.101627 restraints weight = 23390.991| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11181 Z= 0.149 Angle : 0.602 8.961 15266 Z= 0.296 Chirality : 0.046 0.201 1799 Planarity : 0.004 0.063 1878 Dihedral : 7.398 59.449 2574 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.13 % Allowed : 6.53 % Favored : 92.33 % 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: -1.34 (0.23), residues: 1281 helix: -1.96 (0.52), residues: 91 sheet: -1.56 (0.38), residues: 155 loop : -0.71 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 198 HIS 0.003 0.001 HIS A 204 PHE 0.013 0.001 PHE B 447 TYR 0.010 0.001 TYR B 53 ARG 0.004 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 16) link_NAG-ASN : angle 2.34949 ( 48) link_ALPHA1-6 : bond 0.01193 ( 8) link_ALPHA1-6 : angle 1.59513 ( 24) link_BETA1-4 : bond 0.00479 ( 26) link_BETA1-4 : angle 1.83154 ( 78) link_ALPHA1-3 : bond 0.00853 ( 8) link_ALPHA1-3 : angle 1.55248 ( 24) hydrogen bonds : bond 0.03727 ( 227) hydrogen bonds : angle 6.40986 ( 414) SS BOND : bond 0.00380 ( 56) SS BOND : angle 1.14229 ( 112) covalent geometry : bond 0.00344 (11067) covalent geometry : angle 0.56227 (14980) *********************** 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 78 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.669 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: symmetry clash REVERT: A 318 ASN cc_start: 0.8148 (p0) cc_final: 0.7731 (p0) outliers start: 13 outliers final: 13 residues processed: 73 average time/residue: 0.5304 time to fit residues: 54.5129 Evaluate side-chains 74 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.139314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.095054 restraints weight = 70027.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.099857 restraints weight = 32830.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.103038 restraints weight = 21143.725| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11181 Z= 0.107 Angle : 0.562 8.488 15266 Z= 0.275 Chirality : 0.045 0.192 1799 Planarity : 0.004 0.065 1878 Dihedral : 7.012 59.881 2574 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.13 % Allowed : 6.62 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1281 helix: -1.65 (0.54), residues: 84 sheet: -1.55 (0.37), residues: 165 loop : -0.61 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 PHE 0.010 0.001 PHE B 447 TYR 0.009 0.001 TYR A 123 ARG 0.005 0.000 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 16) link_NAG-ASN : angle 2.23705 ( 48) link_ALPHA1-6 : bond 0.01240 ( 8) link_ALPHA1-6 : angle 1.65279 ( 24) link_BETA1-4 : bond 0.00492 ( 26) link_BETA1-4 : angle 1.77795 ( 78) link_ALPHA1-3 : bond 0.00825 ( 8) link_ALPHA1-3 : angle 1.48450 ( 24) hydrogen bonds : bond 0.03344 ( 227) hydrogen bonds : angle 6.28879 ( 414) SS BOND : bond 0.00255 ( 56) SS BOND : angle 0.82584 ( 112) covalent geometry : bond 0.00247 (11067) covalent geometry : angle 0.52571 (14980) *********************** 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 77 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 1.545 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: symmetry clash revert: symmetry clash REVERT: A 318 ASN cc_start: 0.8050 (p0) cc_final: 0.7624 (p0) outliers start: 13 outliers final: 13 residues processed: 72 average time/residue: 0.5301 time to fit residues: 53.4797 Evaluate side-chains 73 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.130915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.089987 restraints weight = 65446.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.093763 restraints weight = 32540.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096360 restraints weight = 21515.377| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11181 Z= 0.188 Angle : 0.610 8.955 15266 Z= 0.301 Chirality : 0.045 0.210 1799 Planarity : 0.004 0.068 1878 Dihedral : 7.050 58.095 2574 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.13 % Allowed : 6.79 % Favored : 92.07 % 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: -1.36 (0.23), residues: 1281 helix: -1.63 (0.56), residues: 84 sheet: -1.63 (0.37), residues: 160 loop : -0.75 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.005 0.001 HIS C 75 PHE 0.014 0.001 PHE B 447 TYR 0.011 0.002 TYR B 53 ARG 0.005 0.001 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 16) link_NAG-ASN : angle 2.38677 ( 48) link_ALPHA1-6 : bond 0.01135 ( 8) link_ALPHA1-6 : angle 1.56993 ( 24) link_BETA1-4 : bond 0.00478 ( 26) link_BETA1-4 : angle 1.76189 ( 78) link_ALPHA1-3 : bond 0.00747 ( 8) link_ALPHA1-3 : angle 1.48673 ( 24) hydrogen bonds : bond 0.03951 ( 227) hydrogen bonds : angle 6.39249 ( 414) SS BOND : bond 0.00396 ( 56) SS BOND : angle 0.98770 ( 112) covalent geometry : bond 0.00432 (11067) covalent geometry : angle 0.57461 (14980) *********************** 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 76 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.830 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: A 318 ASN cc_start: 0.8053 (p0) cc_final: 0.7645 (p0) REVERT: B 41 ASP cc_start: 0.7144 (t0) cc_final: 0.6541 (m-30) outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.5528 time to fit residues: 55.5652 Evaluate side-chains 70 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.131866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.092982 restraints weight = 65796.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.094032 restraints weight = 31340.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.094541 restraints weight = 23856.826| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11181 Z= 0.097 Angle : 0.559 8.378 15266 Z= 0.274 Chirality : 0.044 0.191 1799 Planarity : 0.004 0.066 1878 Dihedral : 6.744 59.212 2574 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.05 % Allowed : 7.32 % Favored : 91.64 % 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: -1.19 (0.24), residues: 1281 helix: -1.65 (0.54), residues: 84 sheet: -1.60 (0.37), residues: 170 loop : -0.58 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 PHE 0.010 0.001 PHE B 447 TYR 0.013 0.001 TYR B 459 ARG 0.009 0.000 ARG A 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 16) link_NAG-ASN : angle 2.24870 ( 48) link_ALPHA1-6 : bond 0.01124 ( 8) link_ALPHA1-6 : angle 1.61453 ( 24) link_BETA1-4 : bond 0.00491 ( 26) link_BETA1-4 : angle 1.73379 ( 78) link_ALPHA1-3 : bond 0.00718 ( 8) link_ALPHA1-3 : angle 1.42004 ( 24) hydrogen bonds : bond 0.03295 ( 227) hydrogen bonds : angle 6.21393 ( 414) SS BOND : bond 0.00255 ( 56) SS BOND : angle 0.81605 ( 112) covalent geometry : bond 0.00219 (11067) covalent geometry : angle 0.52416 (14980) ********************** 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 76 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.788 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: A 318 ASN cc_start: 0.8279 (p0) cc_final: 0.7908 (p0) REVERT: B 41 ASP cc_start: 0.7432 (t0) cc_final: 0.6677 (m-30) outliers start: 12 outliers final: 11 residues processed: 73 average time/residue: 0.5112 time to fit residues: 53.7613 Evaluate side-chains 69 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** 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 = 0.4225 r_free = 0.4225 target = 0.129442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085636 restraints weight = 66980.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089621 restraints weight = 33428.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.092350 restraints weight = 22165.809| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11181 Z= 0.216 Angle : 0.626 8.912 15266 Z= 0.312 Chirality : 0.046 0.215 1799 Planarity : 0.004 0.070 1878 Dihedral : 7.029 57.474 2574 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.13 % Allowed : 7.23 % Favored : 91.64 % 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: -1.43 (0.23), residues: 1281 helix: -1.61 (0.56), residues: 84 sheet: -1.73 (0.36), residues: 166 loop : -0.79 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 198 HIS 0.005 0.001 HIS B 374 PHE 0.016 0.002 PHE B 447 TYR 0.012 0.002 TYR A 459 ARG 0.008 0.001 ARG C 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 16) link_NAG-ASN : angle 2.39525 ( 48) link_ALPHA1-6 : bond 0.01093 ( 8) link_ALPHA1-6 : angle 1.56479 ( 24) link_BETA1-4 : bond 0.00470 ( 26) link_BETA1-4 : angle 1.72579 ( 78) link_ALPHA1-3 : bond 0.00679 ( 8) link_ALPHA1-3 : angle 1.45141 ( 24) hydrogen bonds : bond 0.04089 ( 227) hydrogen bonds : angle 6.37177 ( 414) SS BOND : bond 0.00491 ( 56) SS BOND : angle 1.11205 ( 112) covalent geometry : bond 0.00498 (11067) covalent geometry : angle 0.59108 (14980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6716.42 seconds wall clock time: 116 minutes 33.82 seconds (6993.82 seconds total)