Starting phenix.real_space_refine on Sun Aug 24 16:23:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4j_41884/08_2025/8u4j_41884_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4j_41884/08_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_41884/08_2025/8u4j_41884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4j_41884/08_2025/8u4j_41884.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4j_41884/08_2025/8u4j_41884_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4j_41884/08_2025/8u4j_41884_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.98, per 1000 atoms: 0.19 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: 1.84 Conformation dependent library (CDL) restraints added in 481.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.49 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: 4.99 Time building geometry restraints manager: 2.40 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 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: 5.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.540 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (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 ARG 0.006 0.000 ARG A 106 TYR 0.102 0.006 TYR A 157 PHE 0.056 0.004 PHE B 154 TRP 0.065 0.005 TRP B 198 HIS 0.008 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.01363 (11067) covalent geometry : angle 1.53954 (14980) SS BOND : bond 0.04774 ( 56) SS BOND : angle 3.68422 ( 112) hydrogen bonds : bond 0.21780 ( 227) hydrogen bonds : angle 8.76697 ( 414) link_ALPHA1-3 : bond 0.02594 ( 8) link_ALPHA1-3 : angle 3.96482 ( 24) 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_NAG-ASN : bond 0.05312 ( 16) link_NAG-ASN : angle 5.93551 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 0.645 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: 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: 0.6953 (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: 0.4020 time to fit residues: 92.2830 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 : 0.571 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.137401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.097261 restraints weight = 59386.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.101791 restraints weight = 29371.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.104801 restraints weight = 18981.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106742 restraints weight = 14495.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.107961 restraints weight = 12325.329| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11181 Z= 0.161 Angle : 0.781 13.350 15266 Z= 0.380 Chirality : 0.049 0.314 1799 Planarity : 0.005 0.059 1878 Dihedral : 15.199 88.024 2575 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.23), residues: 1281 helix: -2.15 (0.49), residues: 94 sheet: -1.34 (0.35), residues: 172 loop : -0.06 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 114 TYR 0.013 0.001 TYR B 53 PHE 0.015 0.001 PHE B 154 TRP 0.007 0.001 TRP A 513 HIS 0.008 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00354 (11067) covalent geometry : angle 0.70311 (14980) SS BOND : bond 0.00352 ( 56) SS BOND : angle 1.23887 ( 112) hydrogen bonds : bond 0.05711 ( 227) hydrogen bonds : angle 7.73053 ( 414) link_ALPHA1-3 : bond 0.01083 ( 8) link_ALPHA1-3 : angle 2.13831 ( 24) link_ALPHA1-6 : bond 0.01080 ( 8) link_ALPHA1-6 : angle 2.00675 ( 24) link_BETA1-4 : bond 0.01077 ( 26) link_BETA1-4 : angle 3.50827 ( 78) link_NAG-ASN : bond 0.01055 ( 16) link_NAG-ASN : angle 3.46492 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.588 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: 0.7575 (p0) cc_final: 0.7331 (p0) REVERT: C 110 PHE cc_start: 0.7633 (m-80) cc_final: 0.7264 (m-10) outliers start: 5 outliers final: 4 residues processed: 102 average time/residue: 0.4084 time to fit residues: 52.2723 Evaluate side-chains 81 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 33 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.141023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.101145 restraints weight = 69797.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.103647 restraints weight = 34284.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.104462 restraints weight = 21737.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.105436 restraints weight = 20430.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.105705 restraints weight = 17976.938| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11181 Z= 0.193 Angle : 0.705 9.882 15266 Z= 0.344 Chirality : 0.049 0.236 1799 Planarity : 0.005 0.071 1878 Dihedral : 11.730 72.848 2574 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.22 % Allowed : 5.40 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.22), residues: 1281 helix: -2.38 (0.46), residues: 101 sheet: -1.51 (0.36), residues: 162 loop : -0.46 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 95 TYR 0.013 0.002 TYR A 148 PHE 0.015 0.001 PHE B 252 TRP 0.017 0.002 TRP B 474 HIS 0.006 0.001 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00431 (11067) covalent geometry : angle 0.65794 (14980) SS BOND : bond 0.00369 ( 56) SS BOND : angle 0.96928 ( 112) hydrogen bonds : bond 0.04868 ( 227) hydrogen bonds : angle 7.17556 ( 414) link_ALPHA1-3 : bond 0.01123 ( 8) link_ALPHA1-3 : angle 1.63024 ( 24) link_ALPHA1-6 : bond 0.01184 ( 8) link_ALPHA1-6 : angle 1.84878 ( 24) link_BETA1-4 : bond 0.00758 ( 26) link_BETA1-4 : angle 2.49199 ( 78) link_NAG-ASN : bond 0.00364 ( 16) link_NAG-ASN : angle 2.80377 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.561 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: B 261 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8281 (tp-100) REVERT: C 110 PHE cc_start: 0.7764 (m-80) cc_final: 0.7385 (m-10) outliers start: 14 outliers final: 13 residues processed: 90 average time/residue: 0.3113 time to fit residues: 37.3949 Evaluate side-chains 80 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 67 SER 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 67 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.142385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.105457 restraints weight = 69725.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.106563 restraints weight = 32334.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.106734 restraints weight = 22448.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107603 restraints weight = 21127.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.107848 restraints weight = 19498.716| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11181 Z= 0.111 Angle : 0.624 9.209 15266 Z= 0.301 Chirality : 0.047 0.226 1799 Planarity : 0.004 0.054 1878 Dihedral : 9.803 63.777 2574 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.13 % Allowed : 6.18 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.23), residues: 1281 helix: -1.75 (0.53), residues: 84 sheet: -1.34 (0.39), residues: 148 loop : -0.39 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.010 0.001 TYR B 459 PHE 0.009 0.001 PHE A 252 TRP 0.022 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00245 (11067) covalent geometry : angle 0.57422 (14980) SS BOND : bond 0.00244 ( 56) SS BOND : angle 1.15563 ( 112) hydrogen bonds : bond 0.03870 ( 227) hydrogen bonds : angle 6.79226 ( 414) link_ALPHA1-3 : bond 0.01020 ( 8) link_ALPHA1-3 : angle 1.85126 ( 24) link_ALPHA1-6 : bond 0.01219 ( 8) link_ALPHA1-6 : angle 1.84792 ( 24) link_BETA1-4 : bond 0.00582 ( 26) link_BETA1-4 : angle 2.25672 ( 78) link_NAG-ASN : bond 0.00447 ( 16) link_NAG-ASN : angle 2.48212 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.520 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: 0.8027 (p0) cc_final: 0.7677 (p0) REVERT: B 53 TYR cc_start: 0.8245 (m-80) cc_final: 0.7982 (m-10) REVERT: C 110 PHE cc_start: 0.7743 (m-80) cc_final: 0.7263 (m-80) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.3212 time to fit residues: 34.2689 Evaluate side-chains 74 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 60 MET 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 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 117 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.140320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.096312 restraints weight = 69666.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.101144 restraints weight = 32419.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.104284 restraints weight = 20864.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.106210 restraints weight = 16039.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107425 restraints weight = 13720.225| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11181 Z= 0.144 Angle : 0.614 9.337 15266 Z= 0.297 Chirality : 0.047 0.240 1799 Planarity : 0.004 0.060 1878 Dihedral : 8.379 56.821 2574 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.31 % Allowed : 6.53 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.23), residues: 1281 helix: -1.94 (0.51), residues: 90 sheet: -1.52 (0.38), residues: 150 loop : -0.49 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 232 TYR 0.009 0.001 TYR A 148 PHE 0.011 0.001 PHE B 447 TRP 0.008 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00329 (11067) covalent geometry : angle 0.57092 (14980) SS BOND : bond 0.00363 ( 56) SS BOND : angle 1.10082 ( 112) hydrogen bonds : bond 0.03809 ( 227) hydrogen bonds : angle 6.58600 ( 414) link_ALPHA1-3 : bond 0.00996 ( 8) link_ALPHA1-3 : angle 1.60659 ( 24) link_ALPHA1-6 : bond 0.01264 ( 8) link_ALPHA1-6 : angle 1.87446 ( 24) link_BETA1-4 : bond 0.00584 ( 26) link_BETA1-4 : angle 2.00616 ( 78) link_NAG-ASN : bond 0.00322 ( 16) link_NAG-ASN : angle 2.42582 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.625 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: 0.7924 (p0) cc_final: 0.7543 (p0) REVERT: B 134 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8478 (tt) outliers start: 15 outliers final: 13 residues processed: 73 average time/residue: 0.3071 time to fit residues: 30.0977 Evaluate side-chains 74 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 60 MET 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 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 104 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.138623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.093694 restraints weight = 69931.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.098555 restraints weight = 32339.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.101756 restraints weight = 20803.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.103641 restraints weight = 16012.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.104832 restraints weight = 13723.143| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11181 Z= 0.175 Angle : 0.622 9.086 15266 Z= 0.306 Chirality : 0.046 0.210 1799 Planarity : 0.004 0.061 1878 Dihedral : 7.610 57.150 2574 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.22 % Allowed : 6.36 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.23), residues: 1281 helix: -1.86 (0.52), residues: 90 sheet: -1.50 (0.38), residues: 155 loop : -0.68 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 83 TYR 0.014 0.001 TYR B 53 PHE 0.014 0.001 PHE B 447 TRP 0.008 0.001 TRP B 198 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00399 (11067) covalent geometry : angle 0.58353 (14980) SS BOND : bond 0.00367 ( 56) SS BOND : angle 1.05220 ( 112) hydrogen bonds : bond 0.03965 ( 227) hydrogen bonds : angle 6.56157 ( 414) link_ALPHA1-3 : bond 0.00861 ( 8) link_ALPHA1-3 : angle 1.68910 ( 24) link_ALPHA1-6 : bond 0.01234 ( 8) link_ALPHA1-6 : angle 1.61448 ( 24) link_BETA1-4 : bond 0.00513 ( 26) link_BETA1-4 : angle 1.89608 ( 78) link_NAG-ASN : bond 0.00247 ( 16) link_NAG-ASN : angle 2.40831 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.589 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: 0.7985 (p0) cc_final: 0.7571 (p0) REVERT: B 134 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8565 (tt) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.2798 time to fit residues: 27.7291 Evaluate side-chains 76 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 60 MET 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 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 18 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.0060 chunk 64 optimal weight: 0.0060 chunk 56 optimal weight: 0.5980 overall best weight: 0.4612 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.140219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.101217 restraints weight = 69621.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.103035 restraints weight = 34589.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.104929 restraints weight = 21872.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.105849 restraints weight = 19338.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.105681 restraints weight = 17447.302| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11181 Z= 0.096 Angle : 0.565 8.681 15266 Z= 0.275 Chirality : 0.045 0.204 1799 Planarity : 0.004 0.061 1878 Dihedral : 7.087 58.650 2574 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.22 % Allowed : 6.79 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.23), residues: 1281 helix: -1.86 (0.51), residues: 90 sheet: -1.38 (0.38), residues: 156 loop : -0.54 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.007 0.001 TYR B 53 PHE 0.010 0.001 PHE B 447 TRP 0.008 0.001 TRP B 474 HIS 0.003 0.000 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00213 (11067) covalent geometry : angle 0.52801 (14980) SS BOND : bond 0.00270 ( 56) SS BOND : angle 0.82012 ( 112) hydrogen bonds : bond 0.03243 ( 227) hydrogen bonds : angle 6.32398 ( 414) link_ALPHA1-3 : bond 0.00885 ( 8) link_ALPHA1-3 : angle 1.48128 ( 24) link_ALPHA1-6 : bond 0.01260 ( 8) link_ALPHA1-6 : angle 1.65990 ( 24) link_BETA1-4 : bond 0.00506 ( 26) link_BETA1-4 : angle 1.80512 ( 78) link_NAG-ASN : bond 0.00324 ( 16) link_NAG-ASN : angle 2.27580 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.600 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: 0.8132 (p0) cc_final: 0.7746 (p0) REVERT: B 134 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8550 (tt) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.2604 time to fit residues: 27.3926 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 : 0.559 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.139271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.099528 restraints weight = 70556.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.101180 restraints weight = 35781.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102081 restraints weight = 23228.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.103402 restraints weight = 21441.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.103395 restraints weight = 18510.402| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11181 Z= 0.133 Angle : 0.570 8.676 15266 Z= 0.280 Chirality : 0.044 0.200 1799 Planarity : 0.004 0.065 1878 Dihedral : 6.947 59.402 2574 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.23), residues: 1281 helix: -1.58 (0.55), residues: 84 sheet: -1.45 (0.38), residues: 165 loop : -0.56 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 232 TYR 0.009 0.001 TYR B 53 PHE 0.010 0.001 PHE B 447 TRP 0.007 0.001 TRP A 198 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00304 (11067) covalent geometry : angle 0.53396 (14980) SS BOND : bond 0.00292 ( 56) SS BOND : angle 0.82858 ( 112) hydrogen bonds : bond 0.03465 ( 227) hydrogen bonds : angle 6.27344 ( 414) link_ALPHA1-3 : bond 0.00820 ( 8) link_ALPHA1-3 : angle 1.48989 ( 24) link_ALPHA1-6 : bond 0.01216 ( 8) link_ALPHA1-6 : angle 1.62828 ( 24) link_BETA1-4 : bond 0.00504 ( 26) link_BETA1-4 : angle 1.76421 ( 78) link_NAG-ASN : bond 0.00252 ( 16) link_NAG-ASN : angle 2.26342 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.615 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: 0.8170 (p0) cc_final: 0.7794 (p0) REVERT: B 134 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8606 (tt) outliers start: 13 outliers final: 12 residues processed: 71 average time/residue: 0.2830 time to fit residues: 27.8019 Evaluate side-chains 75 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 120 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.140128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.100626 restraints weight = 69950.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.102430 restraints weight = 35829.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.103356 restraints weight = 22965.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.104931 restraints weight = 21096.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.104867 restraints weight = 18217.103| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11181 Z= 0.096 Angle : 0.542 8.602 15266 Z= 0.264 Chirality : 0.044 0.188 1799 Planarity : 0.004 0.065 1878 Dihedral : 6.567 58.460 2574 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.05 % Allowed : 6.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.23), residues: 1281 helix: -1.55 (0.54), residues: 84 sheet: -1.38 (0.38), residues: 165 loop : -0.48 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.008 0.001 TYR A 148 PHE 0.009 0.001 PHE B 447 TRP 0.007 0.001 TRP B 474 HIS 0.005 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00217 (11067) covalent geometry : angle 0.50587 (14980) SS BOND : bond 0.00217 ( 56) SS BOND : angle 0.75357 ( 112) hydrogen bonds : bond 0.03094 ( 227) hydrogen bonds : angle 6.15360 ( 414) link_ALPHA1-3 : bond 0.00778 ( 8) link_ALPHA1-3 : angle 1.41507 ( 24) link_ALPHA1-6 : bond 0.01123 ( 8) link_ALPHA1-6 : angle 1.61690 ( 24) link_BETA1-4 : bond 0.00493 ( 26) link_BETA1-4 : angle 1.73061 ( 78) link_NAG-ASN : bond 0.00307 ( 16) link_NAG-ASN : angle 2.23351 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.607 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: 0.8172 (p0) cc_final: 0.7784 (p0) REVERT: B 134 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8632 (tt) outliers start: 12 outliers final: 11 residues processed: 73 average time/residue: 0.2261 time to fit residues: 23.5763 Evaluate side-chains 73 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.138660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.094152 restraints weight = 70047.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.098920 restraints weight = 33088.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.102022 restraints weight = 21399.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103824 restraints weight = 16549.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.104734 restraints weight = 14281.750| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11181 Z= 0.148 Angle : 0.568 8.688 15266 Z= 0.279 Chirality : 0.044 0.204 1799 Planarity : 0.004 0.066 1878 Dihedral : 6.630 59.007 2574 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.23), residues: 1281 helix: -1.55 (0.55), residues: 84 sheet: -1.45 (0.38), residues: 165 loop : -0.57 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.010 0.001 TYR B 53 PHE 0.012 0.001 PHE B 447 TRP 0.007 0.001 TRP B 198 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00340 (11067) covalent geometry : angle 0.53344 (14980) SS BOND : bond 0.00323 ( 56) SS BOND : angle 0.87946 ( 112) hydrogen bonds : bond 0.03506 ( 227) hydrogen bonds : angle 6.19594 ( 414) link_ALPHA1-3 : bond 0.00715 ( 8) link_ALPHA1-3 : angle 1.42287 ( 24) link_ALPHA1-6 : bond 0.01135 ( 8) link_ALPHA1-6 : angle 1.57811 ( 24) link_BETA1-4 : bond 0.00441 ( 26) link_BETA1-4 : angle 1.68705 ( 78) link_NAG-ASN : bond 0.00223 ( 16) link_NAG-ASN : angle 2.28795 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.602 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: 0.8081 (p0) cc_final: 0.7701 (p0) REVERT: B 134 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8690 (tt) outliers start: 13 outliers final: 12 residues processed: 75 average time/residue: 0.2403 time to fit residues: 25.7694 Evaluate side-chains 75 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.139790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.095873 restraints weight = 70320.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.100638 restraints weight = 32517.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.103732 restraints weight = 20934.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.105714 restraints weight = 16162.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.106821 restraints weight = 13837.067| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4926 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= 0.092 Angle : 0.539 8.400 15266 Z= 0.263 Chirality : 0.043 0.190 1799 Planarity : 0.004 0.065 1878 Dihedral : 6.415 58.498 2574 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.13 % Allowed : 7.06 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.24), residues: 1281 helix: -1.55 (0.54), residues: 84 sheet: -1.43 (0.37), residues: 170 loop : -0.46 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.006 0.001 TYR A 148 PHE 0.008 0.001 PHE B 447 TRP 0.008 0.001 TRP B 474 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00206 (11067) covalent geometry : angle 0.50328 (14980) SS BOND : bond 0.00240 ( 56) SS BOND : angle 0.78281 ( 112) hydrogen bonds : bond 0.03080 ( 227) hydrogen bonds : angle 6.09733 ( 414) link_ALPHA1-3 : bond 0.00718 ( 8) link_ALPHA1-3 : angle 1.38881 ( 24) link_ALPHA1-6 : bond 0.01178 ( 8) link_ALPHA1-6 : angle 1.62894 ( 24) link_BETA1-4 : bond 0.00463 ( 26) link_BETA1-4 : angle 1.69320 ( 78) link_NAG-ASN : bond 0.00288 ( 16) link_NAG-ASN : angle 2.21698 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.86 seconds wall clock time: 72 minutes 24.34 seconds (4344.34 seconds total)