Starting phenix.real_space_refine on Sun Aug 24 13:36:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sas_40278/08_2025/8sas_40278_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sas_40278/08_2025/8sas_40278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sas_40278/08_2025/8sas_40278_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sas_40278/08_2025/8sas_40278_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sas_40278/08_2025/8sas_40278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sas_40278/08_2025/8sas_40278.map" } resolution = 4.0 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= 0.354 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12531 2.51 5 N 3318 2.21 5 O 4047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s 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: 20028 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "N" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "E" 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "S" 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: "T" 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: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.64, per 1000 atoms: 0.23 Number of scatterers: 20028 At special positions: 0 Unit cell: (160.966, 162.032, 143.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4047 8.00 N 3318 7.00 C 12531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 320 " distance=2.04 Simple disulfide: pdb=" SG CYS D 321 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.02 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.01 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.02 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.05 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS I 321 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.04 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.02 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.02 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.04 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " distance=2.04 Simple disulfide: pdb=" SG CYS N 321 " - pdb=" SG CYS N 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN U 4 " - " MAN U 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA Q 3 " - " MAN Q 6 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA U 3 " - " MAN U 6 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " " BMA W 3 " - " MAN W 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 548.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 46 sheets defined 17.8% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.852A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.658A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.670A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.568A pdb=" N ARG A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 removed outlier: 3.583A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 571 through 577 removed outlier: 3.667A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.867A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 654 Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.524A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.694A pdb=" N GLN F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 350 removed outlier: 4.310A pdb=" N ILE F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 349 " --> pdb=" O VAL F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.654A pdb=" N ARG F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 537 through 542 removed outlier: 3.797A pdb=" N ALA G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 580 removed outlier: 5.232A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG G 579 " --> pdb=" O GLN G 575 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL G 580 " --> pdb=" O LEU G 576 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 585 removed outlier: 3.550A pdb=" N GLU G 584 " --> pdb=" O VAL G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 596 Processing helix chain 'G' and resid 618 through 625 removed outlier: 3.701A pdb=" N ILE G 622 " --> pdb=" O ASN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.543A pdb=" N TRP G 631 " --> pdb=" O THR G 627 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 649 Processing helix chain 'G' and resid 649 through 654 Processing helix chain 'G' and resid 656 through 663 removed outlier: 4.538A pdb=" N LEU G 663 " --> pdb=" O ASP G 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.689A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 262 removed outlier: 3.777A pdb=" N LYS I 261 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE I 262 " --> pdb=" O VAL I 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 258 through 262' Processing helix chain 'I' and resid 311 through 315 removed outlier: 3.540A pdb=" N GLU I 315 " --> pdb=" O VAL I 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.776A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.508A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 334 through 350 Processing helix chain 'K' and resid 474 through 484 removed outlier: 4.455A pdb=" N GLU K 482 " --> pdb=" O ASN K 478 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR K 484 " --> pdb=" O ARG K 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 520 through 524 removed outlier: 4.145A pdb=" N LEU L 523 " --> pdb=" O LEU L 520 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY L 524 " --> pdb=" O GLY L 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 520 through 524' Processing helix chain 'L' and resid 571 through 580 removed outlier: 4.446A pdb=" N GLN L 577 " --> pdb=" O ILE L 573 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG L 579 " --> pdb=" O GLN L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 585 Processing helix chain 'L' and resid 585 through 596 removed outlier: 3.896A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 Processing helix chain 'L' and resid 638 through 650 Processing helix chain 'L' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) Processing helix chain 'L' and resid 659 through 663 removed outlier: 3.810A pdb=" N ALA L 662 " --> pdb=" O ASP L 659 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'N' and resid 258 through 262 Processing helix chain 'N' and resid 311 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 496 removed outlier: 3.791A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.502A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.572A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 273 removed outlier: 4.250A pdb=" N ARG A 273 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 removed outlier: 4.250A pdb=" N ARG A 273 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308 removed outlier: 3.549A pdb=" N ALA A 319 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 307 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 317 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 4.102A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 395 " --> pdb=" O ILE A 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.610A pdb=" N THR C 124 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 12 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 37 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.734A pdb=" N ALA C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 247 through 253 removed outlier: 3.675A pdb=" N ALA D 303 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.215A pdb=" N TYR D 278 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLN D 269 " --> pdb=" O TYR D 278 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE D 280 " --> pdb=" O TRP D 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.215A pdb=" N TYR D 278 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLN D 269 " --> pdb=" O TYR D 278 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE D 280 " --> pdb=" O TRP D 267 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 40 removed outlier: 3.710A pdb=" N THR F 499 " --> pdb=" O TRP F 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.568A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 245 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.055A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 169 through 176 removed outlier: 3.585A pdb=" N ALA F 174 " --> pdb=" O CYS F 157 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS F 157 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR F 191 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 260 removed outlier: 6.614A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.407A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N ASP F 457 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N ILE F 284 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 378 " --> pdb=" O GLU F 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 271 through 273 removed outlier: 12.582A pdb=" N ILE F 284 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N ASP F 457 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.407A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR F 467 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC4, first strand: chain 'F' and resid 423 through 425 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.040A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 60 removed outlier: 4.060A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 248 through 253 removed outlier: 3.597A pdb=" N ILE I 248 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER I 299 " --> pdb=" O THR I 302 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER I 304 " --> pdb=" O SER I 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 277 through 280 removed outlier: 3.708A pdb=" N LEU I 279 " --> pdb=" O TRP I 267 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP I 267 " --> pdb=" O LEU I 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 277 through 280 removed outlier: 3.708A pdb=" N LEU I 279 " --> pdb=" O TRP I 267 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP I 267 " --> pdb=" O LEU I 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 495 through 499 removed outlier: 3.976A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'K' and resid 55 through 56 removed outlier: 4.101A pdb=" N SER K 56 " --> pdb=" O VAL K 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 94 removed outlier: 4.195A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 129 through 130 removed outlier: 3.546A pdb=" N TYR K 191 " --> pdb=" O LEU K 129 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 155 through 161 removed outlier: 4.080A pdb=" N CYS K 157 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA K 174 " --> pdb=" O CYS K 157 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS K 170 " --> pdb=" O THR K 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 259 through 260 removed outlier: 3.770A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG K 273 " --> pdb=" O ILE K 285 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 259 through 260 removed outlier: 3.770A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 330 through 333 removed outlier: 3.692A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 304 through 309 removed outlier: 4.014A pdb=" N GLN K 315 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 359 through 360 removed outlier: 3.747A pdb=" N ILE K 359 " --> pdb=" O TYR K 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR K 395 " --> pdb=" O ILE K 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'K' and resid 374 through 375 removed outlier: 3.516A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.684A pdb=" N THR M 124 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL M 37 " --> pdb=" O TYR M 95 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS M 35 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 20 through 22 removed outlier: 3.967A pdb=" N VAL M 20 " --> pdb=" O MET M 81 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR M 71 " --> pdb=" O TYR M 80 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 239 through 240 Processing sheet with id=AE9, first strand: chain 'N' and resid 249 through 253 removed outlier: 3.637A pdb=" N THR N 302 " --> pdb=" O SER N 299 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER N 304 " --> pdb=" O SER N 297 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 274 through 281 removed outlier: 5.314A pdb=" N ALA N 275 " --> pdb=" O HIS N 271 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N HIS N 271 " --> pdb=" O ALA N 275 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP N 267 " --> pdb=" O LEU N 279 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1305 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: 3.21 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6264 1.35 - 1.48: 5496 1.48 - 1.61: 8526 1.61 - 1.74: 3 1.74 - 1.88: 174 Bond restraints: 20463 Sorted by residual: bond pdb=" CA GLN K 258 " pdb=" C GLN K 258 " ideal model delta sigma weight residual 1.527 1.455 0.072 1.21e-02 6.83e+03 3.54e+01 bond pdb=" C1 MAN R 11 " pdb=" C2 MAN R 11 " ideal model delta sigma weight residual 1.526 1.631 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 MAN R 7 " pdb=" C2 MAN R 7 " ideal model delta sigma weight residual 1.526 1.615 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.614 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CA GLU K 370 " pdb=" C GLU K 370 " ideal model delta sigma weight residual 1.525 1.581 -0.056 1.35e-02 5.49e+03 1.74e+01 ... (remaining 20458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 27043 3.13 - 6.27: 739 6.27 - 9.40: 58 9.40 - 12.53: 7 12.53 - 15.67: 2 Bond angle restraints: 27849 Sorted by residual: angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 136.00 -14.30 1.80e+00 3.09e-01 6.31e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.76 -12.06 1.80e+00 3.09e-01 4.49e+01 angle pdb=" C SER D 326 " pdb=" N ALA D 327 " pdb=" CA ALA D 327 " ideal model delta sigma weight residual 121.70 132.16 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 131.90 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C SER N 326 " pdb=" N ALA N 327 " pdb=" CA ALA N 327 " ideal model delta sigma weight residual 121.70 131.82 -10.12 1.80e+00 3.09e-01 3.16e+01 ... (remaining 27844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 12136 22.58 - 45.15: 683 45.15 - 67.73: 88 67.73 - 90.31: 95 90.31 - 112.88: 48 Dihedral angle restraints: 13050 sinusoidal: 5940 harmonic: 7110 Sorted by residual: dihedral pdb=" CA CYS K 247 " pdb=" C CYS K 247 " pdb=" N THR K 248 " pdb=" CA THR K 248 " ideal model delta harmonic sigma weight residual -180.00 -128.62 -51.38 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CB CYS K 228 " pdb=" SG CYS K 228 " pdb=" SG CYS K 239 " pdb=" CB CYS K 239 " ideal model delta sinusoidal sigma weight residual -86.00 0.39 -86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS K 501 " pdb=" SG CYS K 501 " pdb=" SG CYS L 605 " pdb=" CB CYS L 605 " ideal model delta sinusoidal sigma weight residual -86.00 0.30 -86.30 1 1.00e+01 1.00e-02 8.98e+01 ... (remaining 13047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2517 0.061 - 0.122: 628 0.122 - 0.183: 139 0.183 - 0.244: 28 0.244 - 0.305: 15 Chirality restraints: 3327 Sorted by residual: chirality pdb=" C1 MAN R 11 " pdb=" O2 MAN R 10 " pdb=" C2 MAN R 11 " pdb=" O5 MAN R 11 " both_signs ideal model delta sigma weight residual False 2.40 2.36 0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" CA PRO D 272 " pdb=" N PRO D 272 " pdb=" C PRO D 272 " pdb=" CB PRO D 272 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3324 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 271 " -0.098 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO D 272 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 272 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO D 272 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 36 " -0.003 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP M 36 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP M 36 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP M 36 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP M 36 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP M 36 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP M 36 " 0.031 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 36 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 36 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP M 36 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 338 " 0.024 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP K 338 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP K 338 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP K 338 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 338 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 338 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 338 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 338 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 338 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP K 338 " 0.003 2.00e-02 2.50e+03 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 216 2.58 - 3.16: 16854 3.16 - 3.74: 28691 3.74 - 4.32: 39941 4.32 - 4.90: 65398 Nonbonded interactions: 151100 Sorted by model distance: nonbonded pdb=" OG1 THR A 163 " pdb=" OE1 GLU A 164 " model vdw 2.002 3.040 nonbonded pdb=" OG SER I 299 " pdb=" O THR I 302 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR F 163 " pdb=" OE1 GLU F 164 " model vdw 2.047 3.040 nonbonded pdb=" O VAL F 36 " pdb=" OG1 THR G 606 " model vdw 2.060 3.040 nonbonded pdb=" OG1 THR F 161 " pdb=" O LYS F 170 " model vdw 2.077 3.040 ... (remaining 151095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'W' selection = chain 'X' } 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.000 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.008 0.105 20574 Z= 0.396 Angle : 1.236 15.665 28137 Z= 0.642 Chirality : 0.061 0.305 3327 Planarity : 0.008 0.151 3456 Dihedral : 17.265 112.884 8367 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.66 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.95 % Twisted General : 0.21 % 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: -3.16 (0.15), residues: 2448 helix: -2.10 (0.26), residues: 298 sheet: -1.75 (0.20), residues: 590 loop : -2.34 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.002 ARG L 542 TYR 0.034 0.003 TYR A 486 PHE 0.029 0.004 PHE F 468 TRP 0.058 0.003 TRP K 338 HIS 0.028 0.004 HIS N 270 Details of bonding type rmsd covalent geometry : bond 0.00819 (20463) covalent geometry : angle 1.18206 (27849) SS BOND : bond 0.00663 ( 45) SS BOND : angle 2.15913 ( 90) hydrogen bonds : bond 0.27455 ( 486) hydrogen bonds : angle 10.44079 ( 1305) link_ALPHA1-2 : bond 0.01555 ( 11) link_ALPHA1-2 : angle 4.79578 ( 33) link_ALPHA1-3 : bond 0.01021 ( 9) link_ALPHA1-3 : angle 4.02625 ( 27) link_ALPHA1-6 : bond 0.01302 ( 10) link_ALPHA1-6 : angle 3.66093 ( 30) link_BETA1-4 : bond 0.01202 ( 24) link_BETA1-4 : angle 4.89971 ( 72) link_NAG-ASN : bond 0.01137 ( 12) link_NAG-ASN : angle 2.95607 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 0.682 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 114 GLN cc_start: 0.7733 (tt0) cc_final: 0.7444 (tt0) REVERT: A 154 MET cc_start: 0.8638 (pmm) cc_final: 0.8139 (pmm) REVERT: B 530 MET cc_start: 0.8283 (mmm) cc_final: 0.7960 (mpp) REVERT: C 13 ASN cc_start: 0.7542 (m110) cc_final: 0.7305 (t0) REVERT: C 101 TRP cc_start: 0.7573 (t60) cc_final: 0.7112 (t60) REVERT: D 282 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7285 (mt-10) REVERT: D 301 ASN cc_start: 0.8315 (m-40) cc_final: 0.7992 (t0) REVERT: D 326 SER cc_start: 0.7837 (m) cc_final: 0.6918 (p) REVERT: F 104 MET cc_start: 0.8814 (ttt) cc_final: 0.8518 (ttt) REVERT: F 161 THR cc_start: 0.6053 (p) cc_final: 0.5738 (p) REVERT: F 268 LYS cc_start: 0.8109 (ptmt) cc_final: 0.7849 (mttm) REVERT: F 318 TYR cc_start: 0.8362 (m-80) cc_final: 0.7830 (m-10) REVERT: F 427 TRP cc_start: 0.7686 (m-90) cc_final: 0.7465 (m-90) REVERT: G 610 TRP cc_start: 0.6804 (t-100) cc_final: 0.6074 (t-100) REVERT: H 84 ARG cc_start: 0.7175 (mpp80) cc_final: 0.6713 (mtm110) REVERT: I 326 SER cc_start: 0.7351 (m) cc_final: 0.6954 (p) REVERT: K 42 VAL cc_start: 0.9196 (t) cc_final: 0.8927 (p) REVERT: K 84 LEU cc_start: 0.7241 (tp) cc_final: 0.7005 (tt) REVERT: K 96 TRP cc_start: 0.7900 (m-90) cc_final: 0.7102 (m-90) REVERT: L 603 ILE cc_start: 0.9049 (mm) cc_final: 0.8827 (tt) REVERT: L 645 LEU cc_start: 0.8330 (mt) cc_final: 0.8016 (tp) REVERT: L 647 GLU cc_start: 0.6995 (pp20) cc_final: 0.6776 (pp20) REVERT: M 3 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7004 (tm-30) REVERT: M 103 SER cc_start: 0.8523 (t) cc_final: 0.8225 (p) REVERT: N 259 VAL cc_start: 0.8093 (t) cc_final: 0.7116 (p) REVERT: N 267 TRP cc_start: 0.7822 (m100) cc_final: 0.7597 (m100) REVERT: N 279 LEU cc_start: 0.8761 (pp) cc_final: 0.8500 (pp) REVERT: N 301 ASN cc_start: 0.7542 (m-40) cc_final: 0.6852 (t0) REVERT: N 336 LYS cc_start: 0.8700 (tptt) cc_final: 0.8425 (tppt) outliers start: 0 outliers final: 0 residues processed: 748 average time/residue: 0.1419 time to fit residues: 159.0840 Evaluate side-chains 371 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0270 chunk 194 optimal weight: 0.0060 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 653 GLN D 271 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 HIS F 300 ASN F 330 HIS G 577 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS ** L 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.153552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123589 restraints weight = 44048.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.126148 restraints weight = 29707.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.126813 restraints weight = 22458.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127274 restraints weight = 20051.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127513 restraints weight = 18730.689| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20574 Z= 0.166 Angle : 0.849 13.175 28137 Z= 0.423 Chirality : 0.050 0.274 3327 Planarity : 0.006 0.099 3456 Dihedral : 13.247 85.785 3954 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.17 % Favored : 93.50 % Rotamer: Outliers : 3.03 % Allowed : 13.26 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.69 (0.16), residues: 2448 helix: -1.30 (0.28), residues: 306 sheet: -1.44 (0.19), residues: 634 loop : -2.12 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 38 TYR 0.020 0.002 TYR K 217 PHE 0.031 0.002 PHE C 114 TRP 0.027 0.002 TRP K 479 HIS 0.009 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00355 (20463) covalent geometry : angle 0.81775 (27849) SS BOND : bond 0.00453 ( 45) SS BOND : angle 1.76543 ( 90) hydrogen bonds : bond 0.05084 ( 486) hydrogen bonds : angle 7.11023 ( 1305) link_ALPHA1-2 : bond 0.01424 ( 11) link_ALPHA1-2 : angle 2.80900 ( 33) link_ALPHA1-3 : bond 0.01078 ( 9) link_ALPHA1-3 : angle 2.01213 ( 27) link_ALPHA1-6 : bond 0.01643 ( 10) link_ALPHA1-6 : angle 2.29147 ( 30) link_BETA1-4 : bond 0.00963 ( 24) link_BETA1-4 : angle 3.17154 ( 72) link_NAG-ASN : bond 0.00676 ( 12) link_NAG-ASN : angle 1.77420 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 432 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8468 (mtmt) REVERT: A 57 ASP cc_start: 0.6503 (t0) cc_final: 0.6112 (p0) REVERT: A 83 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 530 MET cc_start: 0.8851 (mmm) cc_final: 0.8187 (mpp) REVERT: B 643 TYR cc_start: 0.8651 (m-10) cc_final: 0.8449 (m-80) REVERT: B 656 ASN cc_start: 0.8009 (t0) cc_final: 0.7752 (t0) REVERT: C 101 TRP cc_start: 0.7903 (t60) cc_final: 0.7271 (t60) REVERT: D 282 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7246 (mt-10) REVERT: D 301 ASN cc_start: 0.8540 (m-40) cc_final: 0.8122 (m-40) REVERT: F 104 MET cc_start: 0.9020 (ttt) cc_final: 0.8616 (ttm) REVERT: F 268 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7878 (mttm) REVERT: F 318 TYR cc_start: 0.7733 (m-80) cc_final: 0.7471 (m-10) REVERT: F 387 THR cc_start: 0.8037 (p) cc_final: 0.7480 (t) REVERT: F 426 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7429 (ptp) REVERT: H 31 ASP cc_start: 0.7782 (m-30) cc_final: 0.7563 (m-30) REVERT: H 39 LEU cc_start: 0.8302 (mt) cc_final: 0.8073 (mt) REVERT: H 84 ARG cc_start: 0.7281 (mpp80) cc_final: 0.7011 (mtm180) REVERT: H 105 TYR cc_start: 0.7706 (m-80) cc_final: 0.7397 (m-10) REVERT: I 284 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7961 (mmtp) REVERT: I 326 SER cc_start: 0.7756 (m) cc_final: 0.7382 (p) REVERT: K 96 TRP cc_start: 0.7897 (m-90) cc_final: 0.7132 (m-90) REVERT: L 646 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8993 (mm) REVERT: M 10 GLU cc_start: 0.6910 (pm20) cc_final: 0.6672 (pm20) REVERT: M 103 SER cc_start: 0.8701 (t) cc_final: 0.8476 (p) REVERT: N 301 ASN cc_start: 0.7394 (m-40) cc_final: 0.6931 (t0) outliers start: 65 outliers final: 33 residues processed: 468 average time/residue: 0.1486 time to fit residues: 107.7763 Evaluate side-chains 374 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 338 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 623 TRP Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 646 LEU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 187 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 234 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS B 653 GLN C 63 ASN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS F 187 ASN F 195 ASN G 591 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 311 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104792 restraints weight = 43693.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106200 restraints weight = 28234.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106950 restraints weight = 22084.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107501 restraints weight = 20684.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107622 restraints weight = 19437.791| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 20574 Z= 0.287 Angle : 0.938 11.970 28137 Z= 0.462 Chirality : 0.053 0.246 3327 Planarity : 0.006 0.081 3456 Dihedral : 9.826 58.311 3954 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.15 % Favored : 92.52 % Rotamer: Outliers : 5.32 % Allowed : 16.29 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.65 (0.15), residues: 2448 helix: -1.24 (0.27), residues: 328 sheet: -1.40 (0.18), residues: 688 loop : -2.11 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 38 TYR 0.034 0.003 TYR H 33 PHE 0.045 0.003 PHE C 114 TRP 0.037 0.003 TRP D 267 HIS 0.011 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00655 (20463) covalent geometry : angle 0.90574 (27849) SS BOND : bond 0.00682 ( 45) SS BOND : angle 2.00864 ( 90) hydrogen bonds : bond 0.05392 ( 486) hydrogen bonds : angle 6.50575 ( 1305) link_ALPHA1-2 : bond 0.01179 ( 11) link_ALPHA1-2 : angle 2.93372 ( 33) link_ALPHA1-3 : bond 0.01027 ( 9) link_ALPHA1-3 : angle 1.63120 ( 27) link_ALPHA1-6 : bond 0.02150 ( 10) link_ALPHA1-6 : angle 3.25679 ( 30) link_BETA1-4 : bond 0.00810 ( 24) link_BETA1-4 : angle 2.97456 ( 72) link_NAG-ASN : bond 0.00512 ( 12) link_NAG-ASN : angle 2.61634 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 366 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8944 (mtmt) cc_final: 0.8733 (mtmt) REVERT: A 83 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 280 ASN cc_start: 0.8359 (m110) cc_final: 0.7969 (m-40) REVERT: A 490 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (ttmm) REVERT: B 530 MET cc_start: 0.9205 (mmm) cc_final: 0.8828 (mpp) REVERT: B 632 ASP cc_start: 0.8529 (t0) cc_final: 0.8318 (t70) REVERT: B 643 TYR cc_start: 0.8847 (m-10) cc_final: 0.8620 (m-80) REVERT: B 656 ASN cc_start: 0.8212 (t0) cc_final: 0.7998 (t0) REVERT: C 60 GLN cc_start: 0.8247 (pm20) cc_final: 0.7484 (mm-40) REVERT: D 272 PRO cc_start: 0.7728 (OUTLIER) cc_final: 0.7259 (Cg_endo) REVERT: D 280 ILE cc_start: 0.7477 (mm) cc_final: 0.7222 (mm) REVERT: D 282 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7492 (mt-10) REVERT: D 314 ASP cc_start: 0.7612 (m-30) cc_final: 0.7235 (m-30) REVERT: F 103 GLN cc_start: 0.8539 (tp40) cc_final: 0.8093 (tp40) REVERT: F 104 MET cc_start: 0.9147 (ttt) cc_final: 0.8835 (ttt) REVERT: F 168 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8094 (tmmt) REVERT: F 217 TYR cc_start: 0.7716 (m-80) cc_final: 0.7492 (m-10) REVERT: F 268 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8049 (mttm) REVERT: G 542 ARG cc_start: 0.8119 (tmt170) cc_final: 0.7848 (tmt170) REVERT: H 13 ASN cc_start: 0.6886 (p0) cc_final: 0.6618 (p0) REVERT: H 39 LEU cc_start: 0.8251 (mt) cc_final: 0.8020 (mt) REVERT: K 369 MET cc_start: 0.7019 (tpp) cc_final: 0.6614 (ttt) REVERT: K 381 GLU cc_start: 0.7670 (tp30) cc_final: 0.7443 (tp30) REVERT: K 423 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8703 (mt) REVERT: M 47 TRP cc_start: 0.7199 (t60) cc_final: 0.6506 (t60) REVERT: M 102 ILE cc_start: 0.8592 (mt) cc_final: 0.8083 (pt) REVERT: M 103 SER cc_start: 0.9032 (t) cc_final: 0.8817 (p) REVERT: N 285 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8008 (ttmm) REVERT: N 301 ASN cc_start: 0.7983 (m-40) cc_final: 0.7556 (t0) outliers start: 114 outliers final: 72 residues processed: 434 average time/residue: 0.1459 time to fit residues: 99.1012 Evaluate side-chains 373 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 297 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 623 TRP Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 539 VAL Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 603 ILE Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 314 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 171 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN C 63 ASN D 246 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN F 362 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN I 311 GLN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 GLN L 575 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.138482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105837 restraints weight = 43497.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107809 restraints weight = 27458.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108542 restraints weight = 20956.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109014 restraints weight = 19806.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109164 restraints weight = 18595.616| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 20574 Z= 0.177 Angle : 0.796 15.445 28137 Z= 0.393 Chirality : 0.048 0.223 3327 Planarity : 0.005 0.076 3456 Dihedral : 8.687 58.961 3954 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.84 % Favored : 93.83 % Rotamer: Outliers : 4.76 % Allowed : 19.93 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -2.55 (0.15), residues: 2448 helix: -1.05 (0.28), residues: 335 sheet: -1.11 (0.19), residues: 655 loop : -2.21 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 542 TYR 0.021 0.002 TYR N 278 PHE 0.024 0.002 PHE C 114 TRP 0.020 0.002 TRP H 50 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00408 (20463) covalent geometry : angle 0.76415 (27849) SS BOND : bond 0.00608 ( 45) SS BOND : angle 2.20520 ( 90) hydrogen bonds : bond 0.04208 ( 486) hydrogen bonds : angle 6.04147 ( 1305) link_ALPHA1-2 : bond 0.01197 ( 11) link_ALPHA1-2 : angle 2.67800 ( 33) link_ALPHA1-3 : bond 0.00989 ( 9) link_ALPHA1-3 : angle 1.53852 ( 27) link_ALPHA1-6 : bond 0.01598 ( 10) link_ALPHA1-6 : angle 2.79235 ( 30) link_BETA1-4 : bond 0.00647 ( 24) link_BETA1-4 : angle 2.51151 ( 72) link_NAG-ASN : bond 0.00449 ( 12) link_NAG-ASN : angle 2.07007 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 343 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8710 (mtmt) REVERT: A 117 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8408 (mmtp) REVERT: A 217 TYR cc_start: 0.8429 (m-10) cc_final: 0.8110 (m-10) REVERT: A 280 ASN cc_start: 0.8537 (m110) cc_final: 0.8231 (m-40) REVERT: B 530 MET cc_start: 0.9169 (mmm) cc_final: 0.8788 (mpp) REVERT: B 656 ASN cc_start: 0.8176 (t0) cc_final: 0.7936 (t0) REVERT: C 3 GLN cc_start: 0.7716 (pm20) cc_final: 0.7380 (pp30) REVERT: C 60 GLN cc_start: 0.8295 (pm20) cc_final: 0.7614 (mm-40) REVERT: D 272 PRO cc_start: 0.7744 (OUTLIER) cc_final: 0.7325 (Cg_endo) REVERT: D 280 ILE cc_start: 0.7454 (mm) cc_final: 0.7238 (mm) REVERT: D 282 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7381 (mt-10) REVERT: D 314 ASP cc_start: 0.7624 (m-30) cc_final: 0.7256 (m-30) REVERT: F 103 GLN cc_start: 0.8439 (tp40) cc_final: 0.8021 (tp40) REVERT: F 104 MET cc_start: 0.9080 (ttt) cc_final: 0.8707 (ttt) REVERT: F 268 LYS cc_start: 0.8508 (ptmt) cc_final: 0.7964 (mttm) REVERT: F 307 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8179 (m) REVERT: G 530 MET cc_start: 0.8431 (mpp) cc_final: 0.8205 (mpp) REVERT: H 39 LEU cc_start: 0.8225 (mt) cc_final: 0.8008 (mt) REVERT: H 104 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8078 (t0) REVERT: I 281 TYR cc_start: 0.6962 (t80) cc_final: 0.6759 (t80) REVERT: K 369 MET cc_start: 0.7121 (tpp) cc_final: 0.6615 (ttt) REVERT: K 423 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8643 (mt) REVERT: K 426 MET cc_start: 0.6368 (ptt) cc_final: 0.5873 (ptt) REVERT: K 427 TRP cc_start: 0.8267 (m-10) cc_final: 0.8014 (m-10) REVERT: L 529 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8419 (t) REVERT: L 630 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: L 633 LYS cc_start: 0.9234 (pptt) cc_final: 0.8999 (pptt) REVERT: M 10 GLU cc_start: 0.7105 (pm20) cc_final: 0.6301 (pp20) REVERT: M 47 TRP cc_start: 0.6914 (t60) cc_final: 0.6423 (t60) REVERT: M 102 ILE cc_start: 0.8365 (mt) cc_final: 0.7900 (pt) REVERT: M 103 SER cc_start: 0.8963 (t) cc_final: 0.8730 (p) REVERT: M 104 ASP cc_start: 0.8395 (t0) cc_final: 0.8173 (t70) REVERT: N 301 ASN cc_start: 0.8024 (m-40) cc_final: 0.7650 (t0) outliers start: 102 outliers final: 67 residues processed: 407 average time/residue: 0.1441 time to fit residues: 93.8588 Evaluate side-chains 373 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 311 GLN Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 196 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 591 GLN D 246 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 GLN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105853 restraints weight = 43052.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108016 restraints weight = 28216.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108767 restraints weight = 21982.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109743 restraints weight = 20122.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109798 restraints weight = 18805.910| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20574 Z= 0.150 Angle : 0.767 12.774 28137 Z= 0.377 Chirality : 0.047 0.233 3327 Planarity : 0.005 0.075 3456 Dihedral : 8.069 58.963 3954 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.21 % Favored : 93.46 % Rotamer: Outliers : 4.34 % Allowed : 20.92 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.38 (0.16), residues: 2448 helix: -0.50 (0.30), residues: 320 sheet: -1.10 (0.18), residues: 693 loop : -2.16 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.021 0.001 TYR N 278 PHE 0.019 0.001 PHE C 114 TRP 0.020 0.002 TRP I 267 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00340 (20463) covalent geometry : angle 0.73776 (27849) SS BOND : bond 0.00498 ( 45) SS BOND : angle 2.04691 ( 90) hydrogen bonds : bond 0.03937 ( 486) hydrogen bonds : angle 5.73920 ( 1305) link_ALPHA1-2 : bond 0.01223 ( 11) link_ALPHA1-2 : angle 2.58360 ( 33) link_ALPHA1-3 : bond 0.00973 ( 9) link_ALPHA1-3 : angle 1.40079 ( 27) link_ALPHA1-6 : bond 0.01442 ( 10) link_ALPHA1-6 : angle 2.79977 ( 30) link_BETA1-4 : bond 0.00643 ( 24) link_BETA1-4 : angle 2.30621 ( 72) link_NAG-ASN : bond 0.00464 ( 12) link_NAG-ASN : angle 1.83082 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 334 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8699 (mtmt) REVERT: A 217 TYR cc_start: 0.8407 (m-10) cc_final: 0.8037 (m-10) REVERT: A 280 ASN cc_start: 0.8529 (m-40) cc_final: 0.8172 (m-40) REVERT: B 529 THR cc_start: 0.9016 (p) cc_final: 0.8728 (t) REVERT: B 530 MET cc_start: 0.9136 (mmm) cc_final: 0.8280 (mpp) REVERT: B 639 THR cc_start: 0.8490 (p) cc_final: 0.8145 (t) REVERT: B 656 ASN cc_start: 0.8223 (t0) cc_final: 0.7944 (t0) REVERT: C 60 GLN cc_start: 0.8200 (pm20) cc_final: 0.7534 (mm-40) REVERT: D 272 PRO cc_start: 0.7715 (OUTLIER) cc_final: 0.7281 (Cg_endo) REVERT: D 282 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7462 (mt-10) REVERT: D 314 ASP cc_start: 0.7546 (m-30) cc_final: 0.7185 (m-30) REVERT: F 104 MET cc_start: 0.9041 (ttt) cc_final: 0.8721 (ttt) REVERT: F 268 LYS cc_start: 0.8449 (ptmt) cc_final: 0.8055 (mmtm) REVERT: H 39 LEU cc_start: 0.8524 (mt) cc_final: 0.8137 (mt) REVERT: H 47 TRP cc_start: 0.8559 (t60) cc_final: 0.8349 (t60) REVERT: H 104 ASP cc_start: 0.8402 (m-30) cc_final: 0.8079 (t0) REVERT: K 46 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8271 (ptpt) REVERT: K 49 LYS cc_start: 0.8542 (tttt) cc_final: 0.8320 (ttpt) REVERT: K 369 MET cc_start: 0.7072 (tpp) cc_final: 0.6511 (ttt) REVERT: K 423 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8606 (mt) REVERT: K 426 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5718 (ptt) REVERT: K 479 TRP cc_start: 0.8517 (m-10) cc_final: 0.8095 (m-90) REVERT: L 529 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8430 (t) REVERT: L 630 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: L 633 LYS cc_start: 0.9263 (pptt) cc_final: 0.8919 (pptt) REVERT: M 10 GLU cc_start: 0.7190 (pm20) cc_final: 0.6455 (pp20) REVERT: M 51 MET cc_start: 0.7469 (ttt) cc_final: 0.7263 (tmm) REVERT: M 59 ASN cc_start: 0.8627 (t0) cc_final: 0.8075 (t0) REVERT: M 80 TYR cc_start: 0.7588 (m-80) cc_final: 0.7305 (m-80) REVERT: M 102 ILE cc_start: 0.8330 (mt) cc_final: 0.7893 (pt) REVERT: M 103 SER cc_start: 0.8997 (t) cc_final: 0.8718 (p) REVERT: M 104 ASP cc_start: 0.8400 (t0) cc_final: 0.8175 (t70) REVERT: N 301 ASN cc_start: 0.8085 (m-40) cc_final: 0.7682 (t0) outliers start: 93 outliers final: 64 residues processed: 394 average time/residue: 0.1255 time to fit residues: 80.0229 Evaluate side-chains 377 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 307 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.135746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102747 restraints weight = 43041.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105889 restraints weight = 28704.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106134 restraints weight = 21304.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106924 restraints weight = 20885.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106827 restraints weight = 18886.189| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20574 Z= 0.211 Angle : 0.793 12.435 28137 Z= 0.391 Chirality : 0.048 0.260 3327 Planarity : 0.005 0.074 3456 Dihedral : 7.886 58.357 3954 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.07 % Favored : 92.61 % Rotamer: Outliers : 4.90 % Allowed : 21.01 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.38 (0.16), residues: 2448 helix: -0.65 (0.29), residues: 341 sheet: -1.03 (0.18), residues: 696 loop : -2.17 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.024 0.002 TYR I 268 PHE 0.025 0.002 PHE M 64 TRP 0.025 0.002 TRP M 47 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00489 (20463) covalent geometry : angle 0.76550 (27849) SS BOND : bond 0.00544 ( 45) SS BOND : angle 2.06777 ( 90) hydrogen bonds : bond 0.04116 ( 486) hydrogen bonds : angle 5.64715 ( 1305) link_ALPHA1-2 : bond 0.01373 ( 11) link_ALPHA1-2 : angle 2.56200 ( 33) link_ALPHA1-3 : bond 0.00896 ( 9) link_ALPHA1-3 : angle 1.51511 ( 27) link_ALPHA1-6 : bond 0.01075 ( 10) link_ALPHA1-6 : angle 2.32942 ( 30) link_BETA1-4 : bond 0.00656 ( 24) link_BETA1-4 : angle 2.31047 ( 72) link_NAG-ASN : bond 0.00494 ( 12) link_NAG-ASN : angle 2.04760 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 330 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8691 (mtmt) REVERT: A 217 TYR cc_start: 0.8493 (m-10) cc_final: 0.8086 (m-10) REVERT: A 280 ASN cc_start: 0.8568 (m-40) cc_final: 0.7998 (t0) REVERT: A 439 ILE cc_start: 0.9670 (tp) cc_final: 0.9417 (mm) REVERT: A 490 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8335 (ttmm) REVERT: B 529 THR cc_start: 0.8890 (p) cc_final: 0.8682 (t) REVERT: B 530 MET cc_start: 0.9142 (mmm) cc_final: 0.8588 (mpp) REVERT: B 632 ASP cc_start: 0.8569 (t0) cc_final: 0.7941 (t0) REVERT: B 656 ASN cc_start: 0.8286 (t0) cc_final: 0.8012 (t0) REVERT: C 10 GLU cc_start: 0.8389 (tp30) cc_final: 0.7826 (tm-30) REVERT: C 60 GLN cc_start: 0.8266 (pm20) cc_final: 0.7622 (mm-40) REVERT: D 272 PRO cc_start: 0.7832 (OUTLIER) cc_final: 0.7407 (Cg_endo) REVERT: D 280 ILE cc_start: 0.7468 (mm) cc_final: 0.7244 (mm) REVERT: D 282 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7516 (mt-10) REVERT: D 301 ASN cc_start: 0.8856 (m-40) cc_final: 0.8619 (t0) REVERT: D 314 ASP cc_start: 0.7611 (m-30) cc_final: 0.7379 (m-30) REVERT: F 104 MET cc_start: 0.9055 (ttt) cc_final: 0.8735 (ttt) REVERT: F 268 LYS cc_start: 0.8389 (ptmt) cc_final: 0.7972 (mttm) REVERT: F 434 MET cc_start: 0.8450 (ttm) cc_final: 0.8151 (ttp) REVERT: F 446 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7832 (ttm110) REVERT: H 39 LEU cc_start: 0.8569 (mt) cc_final: 0.8170 (mt) REVERT: H 104 ASP cc_start: 0.8547 (m-30) cc_final: 0.8242 (t0) REVERT: I 234 LEU cc_start: 0.7595 (mt) cc_final: 0.7157 (mp) REVERT: I 268 TYR cc_start: 0.8716 (m-80) cc_final: 0.8490 (m-80) REVERT: I 307 ILE cc_start: 0.8261 (mm) cc_final: 0.7643 (tt) REVERT: K 49 LYS cc_start: 0.8480 (tttt) cc_final: 0.8055 (mtmt) REVERT: K 268 LYS cc_start: 0.8576 (pttt) cc_final: 0.8331 (mmtt) REVERT: K 369 MET cc_start: 0.7213 (tpp) cc_final: 0.6692 (ttt) REVERT: K 423 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8714 (mt) REVERT: K 426 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.6018 (ptt) REVERT: K 427 TRP cc_start: 0.8293 (m-10) cc_final: 0.8030 (m-10) REVERT: L 529 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8645 (t) REVERT: L 630 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: L 633 LYS cc_start: 0.9241 (pptt) cc_final: 0.8939 (pptt) REVERT: M 10 GLU cc_start: 0.7462 (pm20) cc_final: 0.6648 (pp20) REVERT: M 51 MET cc_start: 0.7793 (ttt) cc_final: 0.7493 (tmm) REVERT: M 59 ASN cc_start: 0.8692 (t0) cc_final: 0.8058 (t0) REVERT: M 80 TYR cc_start: 0.7626 (m-80) cc_final: 0.7368 (m-80) REVERT: M 103 SER cc_start: 0.9034 (t) cc_final: 0.8769 (p) REVERT: M 104 ASP cc_start: 0.8500 (t0) cc_final: 0.8275 (t70) REVERT: N 301 ASN cc_start: 0.8223 (m-40) cc_final: 0.7824 (t0) outliers start: 105 outliers final: 82 residues processed: 399 average time/residue: 0.1361 time to fit residues: 87.4415 Evaluate side-chains 401 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 312 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 246 GLN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 288 LEU Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 595 ILE Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 616 ASN C 62 GLN D 246 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 575 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106181 restraints weight = 43060.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107301 restraints weight = 32956.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108256 restraints weight = 25774.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108622 restraints weight = 21978.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109420 restraints weight = 20688.708| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 20574 Z= 0.143 Angle : 0.745 12.802 28137 Z= 0.368 Chirality : 0.046 0.230 3327 Planarity : 0.004 0.072 3456 Dihedral : 7.557 59.717 3954 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.29 % Favored : 93.38 % Rotamer: Outliers : 4.39 % Allowed : 22.46 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.23 (0.16), residues: 2448 helix: -0.33 (0.30), residues: 333 sheet: -0.85 (0.18), residues: 669 loop : -2.16 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 84 TYR 0.021 0.001 TYR I 268 PHE 0.025 0.001 PHE M 64 TRP 0.029 0.002 TRP I 267 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00333 (20463) covalent geometry : angle 0.71807 (27849) SS BOND : bond 0.00551 ( 45) SS BOND : angle 2.32998 ( 90) hydrogen bonds : bond 0.03748 ( 486) hydrogen bonds : angle 5.38995 ( 1305) link_ALPHA1-2 : bond 0.01258 ( 11) link_ALPHA1-2 : angle 2.46204 ( 33) link_ALPHA1-3 : bond 0.00931 ( 9) link_ALPHA1-3 : angle 1.37270 ( 27) link_ALPHA1-6 : bond 0.00810 ( 10) link_ALPHA1-6 : angle 1.76038 ( 30) link_BETA1-4 : bond 0.00626 ( 24) link_BETA1-4 : angle 2.12479 ( 72) link_NAG-ASN : bond 0.00457 ( 12) link_NAG-ASN : angle 1.72785 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 334 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8653 (mtmt) REVERT: A 217 TYR cc_start: 0.8324 (m-10) cc_final: 0.7901 (m-10) REVERT: A 280 ASN cc_start: 0.8595 (m-40) cc_final: 0.8123 (t0) REVERT: A 317 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7735 (p90) REVERT: A 439 ILE cc_start: 0.9646 (tp) cc_final: 0.9378 (mm) REVERT: B 530 MET cc_start: 0.9037 (mmm) cc_final: 0.8407 (mmm) REVERT: B 632 ASP cc_start: 0.8601 (t0) cc_final: 0.7976 (t0) REVERT: B 656 ASN cc_start: 0.8159 (t0) cc_final: 0.7903 (t0) REVERT: C 10 GLU cc_start: 0.8261 (tp30) cc_final: 0.7824 (tm-30) REVERT: C 60 GLN cc_start: 0.8143 (pm20) cc_final: 0.7521 (mm-40) REVERT: D 234 LEU cc_start: 0.7209 (mt) cc_final: 0.6734 (mp) REVERT: D 272 PRO cc_start: 0.7848 (OUTLIER) cc_final: 0.7433 (Cg_endo) REVERT: D 282 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 311 GLN cc_start: 0.8827 (pm20) cc_final: 0.8503 (pm20) REVERT: D 314 ASP cc_start: 0.7783 (m-30) cc_final: 0.7403 (m-30) REVERT: F 104 MET cc_start: 0.8976 (ttt) cc_final: 0.8506 (ttt) REVERT: F 268 LYS cc_start: 0.8466 (ptmt) cc_final: 0.8102 (mttm) REVERT: F 282 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7999 (mppt) REVERT: F 434 MET cc_start: 0.8183 (ttm) cc_final: 0.7979 (ttp) REVERT: F 446 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7814 (ttm110) REVERT: H 3 GLN cc_start: 0.8257 (pm20) cc_final: 0.8056 (pm20) REVERT: H 39 LEU cc_start: 0.8524 (mt) cc_final: 0.8159 (mt) REVERT: H 97 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8098 (m) REVERT: H 104 ASP cc_start: 0.8523 (m-30) cc_final: 0.8219 (t0) REVERT: I 234 LEU cc_start: 0.7628 (mt) cc_final: 0.7259 (mp) REVERT: I 268 TYR cc_start: 0.8614 (m-80) cc_final: 0.8321 (m-10) REVERT: I 307 ILE cc_start: 0.8217 (mm) cc_final: 0.7694 (tt) REVERT: K 49 LYS cc_start: 0.8473 (tttt) cc_final: 0.8218 (ttpt) REVERT: K 268 LYS cc_start: 0.8617 (pttt) cc_final: 0.8344 (mmtt) REVERT: K 369 MET cc_start: 0.7224 (tpp) cc_final: 0.6654 (ttt) REVERT: K 423 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8633 (mt) REVERT: K 479 TRP cc_start: 0.8449 (m-10) cc_final: 0.8179 (m-90) REVERT: L 529 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8596 (t) REVERT: L 623 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.7967 (m-90) REVERT: L 630 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: L 646 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9072 (mm) REVERT: M 6 GLN cc_start: 0.7663 (pt0) cc_final: 0.7035 (pt0) REVERT: M 10 GLU cc_start: 0.7404 (pm20) cc_final: 0.6686 (pp20) REVERT: M 59 ASN cc_start: 0.8708 (t0) cc_final: 0.8065 (t0) REVERT: M 103 SER cc_start: 0.8830 (t) cc_final: 0.8613 (p) REVERT: M 104 ASP cc_start: 0.8424 (t0) cc_final: 0.8173 (t70) REVERT: N 301 ASN cc_start: 0.8142 (m-40) cc_final: 0.7828 (t0) outliers start: 94 outliers final: 65 residues processed: 400 average time/residue: 0.1335 time to fit residues: 86.0420 Evaluate side-chains 385 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 311 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 623 TRP Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 646 LEU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 17 optimal weight: 0.0020 chunk 89 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 HIS L 575 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.142673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111708 restraints weight = 43659.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112649 restraints weight = 33533.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.113720 restraints weight = 27333.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114055 restraints weight = 23490.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114397 restraints weight = 22308.609| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20574 Z= 0.133 Angle : 0.738 12.808 28137 Z= 0.365 Chirality : 0.046 0.231 3327 Planarity : 0.004 0.070 3456 Dihedral : 7.236 57.226 3954 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.21 % Favored : 93.46 % Rotamer: Outliers : 4.30 % Allowed : 22.83 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.10 (0.16), residues: 2448 helix: -0.16 (0.30), residues: 325 sheet: -0.68 (0.19), residues: 657 loop : -2.13 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 38 TYR 0.024 0.001 TYR M 94 PHE 0.022 0.001 PHE M 64 TRP 0.036 0.002 TRP H 47 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00304 (20463) covalent geometry : angle 0.71377 (27849) SS BOND : bond 0.00424 ( 45) SS BOND : angle 2.12318 ( 90) hydrogen bonds : bond 0.03538 ( 486) hydrogen bonds : angle 5.20173 ( 1305) link_ALPHA1-2 : bond 0.01301 ( 11) link_ALPHA1-2 : angle 2.40964 ( 33) link_ALPHA1-3 : bond 0.00947 ( 9) link_ALPHA1-3 : angle 1.33754 ( 27) link_ALPHA1-6 : bond 0.00642 ( 10) link_ALPHA1-6 : angle 1.65123 ( 30) link_BETA1-4 : bond 0.00632 ( 24) link_BETA1-4 : angle 2.04609 ( 72) link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 1.63944 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 331 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8563 (mtmt) REVERT: A 104 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7662 (tpt) REVERT: A 280 ASN cc_start: 0.8538 (m-40) cc_final: 0.8132 (t0) REVERT: A 317 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7581 (p90) REVERT: A 439 ILE cc_start: 0.9627 (tp) cc_final: 0.9421 (mm) REVERT: B 530 MET cc_start: 0.8846 (mmm) cc_final: 0.8395 (mmm) REVERT: B 632 ASP cc_start: 0.8436 (t0) cc_final: 0.7919 (t0) REVERT: B 656 ASN cc_start: 0.8047 (t0) cc_final: 0.7813 (t0) REVERT: C 10 GLU cc_start: 0.8213 (tp30) cc_final: 0.7940 (tm-30) REVERT: C 102 ILE cc_start: 0.9058 (mp) cc_final: 0.8796 (pt) REVERT: D 272 PRO cc_start: 0.7787 (OUTLIER) cc_final: 0.7369 (Cg_endo) REVERT: D 282 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7437 (mt-10) REVERT: D 301 ASN cc_start: 0.8420 (t0) cc_final: 0.7935 (t0) REVERT: D 311 GLN cc_start: 0.8818 (pm20) cc_final: 0.8575 (pm20) REVERT: D 314 ASP cc_start: 0.7894 (m-30) cc_final: 0.7502 (m-30) REVERT: F 104 MET cc_start: 0.8942 (ttt) cc_final: 0.8707 (ttt) REVERT: F 268 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7954 (mttm) REVERT: F 282 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8097 (mppt) REVERT: F 446 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7788 (ttm110) REVERT: F 492 GLU cc_start: 0.8827 (pm20) cc_final: 0.8616 (pm20) REVERT: H 39 LEU cc_start: 0.8449 (mt) cc_final: 0.8083 (mt) REVERT: H 47 TRP cc_start: 0.7981 (t60) cc_final: 0.7563 (t60) REVERT: H 51 MET cc_start: 0.7740 (tpp) cc_final: 0.7485 (ttt) REVERT: H 97 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8087 (m) REVERT: H 104 ASP cc_start: 0.8390 (m-30) cc_final: 0.8096 (t0) REVERT: I 234 LEU cc_start: 0.7729 (mt) cc_final: 0.7306 (mp) REVERT: I 268 TYR cc_start: 0.8492 (m-80) cc_final: 0.8250 (m-10) REVERT: I 307 ILE cc_start: 0.8194 (mm) cc_final: 0.7686 (tt) REVERT: K 49 LYS cc_start: 0.8425 (tttt) cc_final: 0.8154 (ttpt) REVERT: K 104 MET cc_start: 0.8516 (ttt) cc_final: 0.8296 (ttt) REVERT: K 268 LYS cc_start: 0.8551 (pttt) cc_final: 0.8306 (mmtt) REVERT: K 280 ASN cc_start: 0.7859 (m-40) cc_final: 0.7619 (t0) REVERT: K 369 MET cc_start: 0.7257 (tpp) cc_final: 0.6623 (ttt) REVERT: K 423 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8688 (mt) REVERT: L 529 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8588 (t) REVERT: L 646 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9160 (mm) REVERT: M 10 GLU cc_start: 0.7291 (pm20) cc_final: 0.6687 (pp20) REVERT: M 59 ASN cc_start: 0.8682 (t0) cc_final: 0.8050 (t0) REVERT: M 103 SER cc_start: 0.8692 (t) cc_final: 0.8449 (p) REVERT: N 299 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8622 (p) REVERT: N 301 ASN cc_start: 0.8220 (m-40) cc_final: 0.7862 (t0) outliers start: 92 outliers final: 69 residues processed: 397 average time/residue: 0.1344 time to fit residues: 85.7535 Evaluate side-chains 389 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 311 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 575 GLN Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 646 LEU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 299 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 129 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 chunk 95 optimal weight: 0.6980 chunk 179 optimal weight: 0.0870 chunk 77 optimal weight: 20.0000 chunk 183 optimal weight: 0.0000 chunk 165 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 575 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112574 restraints weight = 43300.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113926 restraints weight = 33332.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114642 restraints weight = 27358.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115129 restraints weight = 23969.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.115353 restraints weight = 21677.256| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20574 Z= 0.130 Angle : 0.737 12.839 28137 Z= 0.362 Chirality : 0.046 0.311 3327 Planarity : 0.004 0.067 3456 Dihedral : 6.999 56.482 3954 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.25 % Favored : 93.46 % Rotamer: Outliers : 3.78 % Allowed : 23.25 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.01 (0.16), residues: 2448 helix: 0.04 (0.31), residues: 313 sheet: -0.65 (0.19), residues: 660 loop : -2.06 (0.14), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 38 TYR 0.021 0.001 TYR L 643 PHE 0.022 0.001 PHE M 64 TRP 0.049 0.002 TRP K 479 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00295 (20463) covalent geometry : angle 0.71566 (27849) SS BOND : bond 0.00418 ( 45) SS BOND : angle 1.93629 ( 90) hydrogen bonds : bond 0.03509 ( 486) hydrogen bonds : angle 5.16138 ( 1305) link_ALPHA1-2 : bond 0.01331 ( 11) link_ALPHA1-2 : angle 2.36532 ( 33) link_ALPHA1-3 : bond 0.00938 ( 9) link_ALPHA1-3 : angle 1.31546 ( 27) link_ALPHA1-6 : bond 0.00626 ( 10) link_ALPHA1-6 : angle 1.58659 ( 30) link_BETA1-4 : bond 0.00631 ( 24) link_BETA1-4 : angle 1.96537 ( 72) link_NAG-ASN : bond 0.00453 ( 12) link_NAG-ASN : angle 1.53554 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7677 (tpt) REVERT: A 280 ASN cc_start: 0.8574 (m-40) cc_final: 0.8172 (t0) REVERT: A 439 ILE cc_start: 0.9625 (tp) cc_final: 0.9404 (mm) REVERT: B 530 MET cc_start: 0.8765 (mmm) cc_final: 0.8370 (mmm) REVERT: B 581 LEU cc_start: 0.7879 (tp) cc_final: 0.7525 (tp) REVERT: B 632 ASP cc_start: 0.8393 (t0) cc_final: 0.7898 (t0) REVERT: B 656 ASN cc_start: 0.7918 (t0) cc_final: 0.7701 (t0) REVERT: C 102 ILE cc_start: 0.9056 (mp) cc_final: 0.8807 (pt) REVERT: D 272 PRO cc_start: 0.7752 (OUTLIER) cc_final: 0.7323 (Cg_endo) REVERT: D 282 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7435 (mt-10) REVERT: D 301 ASN cc_start: 0.8336 (t0) cc_final: 0.7875 (t0) REVERT: D 314 ASP cc_start: 0.7853 (m-30) cc_final: 0.7448 (m-30) REVERT: F 84 LEU cc_start: 0.8192 (tp) cc_final: 0.7848 (mt) REVERT: F 104 MET cc_start: 0.8935 (ttt) cc_final: 0.8648 (ttt) REVERT: F 268 LYS cc_start: 0.8359 (ptmt) cc_final: 0.8046 (mttm) REVERT: F 282 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8078 (mppt) REVERT: F 446 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7761 (ttm110) REVERT: F 492 GLU cc_start: 0.8854 (pm20) cc_final: 0.8620 (pm20) REVERT: H 3 GLN cc_start: 0.8191 (pm20) cc_final: 0.7985 (pm20) REVERT: H 39 LEU cc_start: 0.8492 (mt) cc_final: 0.8129 (mt) REVERT: H 47 TRP cc_start: 0.7979 (t60) cc_final: 0.7437 (t60) REVERT: H 51 MET cc_start: 0.7761 (tpp) cc_final: 0.7546 (ttt) REVERT: H 97 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8084 (m) REVERT: H 104 ASP cc_start: 0.8367 (m-30) cc_final: 0.8080 (t0) REVERT: H 106 TYR cc_start: 0.9146 (p90) cc_final: 0.8564 (p90) REVERT: I 234 LEU cc_start: 0.7724 (mt) cc_final: 0.7303 (mp) REVERT: I 267 TRP cc_start: 0.5344 (m-10) cc_final: 0.5110 (m-10) REVERT: I 307 ILE cc_start: 0.8201 (mm) cc_final: 0.7734 (tt) REVERT: K 49 LYS cc_start: 0.8338 (tttt) cc_final: 0.7979 (mtmt) REVERT: K 268 LYS cc_start: 0.8575 (pttt) cc_final: 0.8332 (mmtt) REVERT: K 280 ASN cc_start: 0.7980 (m-40) cc_final: 0.7767 (t0) REVERT: K 369 MET cc_start: 0.7279 (tpp) cc_final: 0.6621 (ttt) REVERT: K 423 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8687 (mt) REVERT: L 529 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8535 (t) REVERT: L 575 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7596 (pp30) REVERT: L 646 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9036 (mm) REVERT: M 6 GLN cc_start: 0.7493 (pt0) cc_final: 0.6624 (pt0) REVERT: M 10 GLU cc_start: 0.7278 (pm20) cc_final: 0.6650 (pp20) REVERT: M 59 ASN cc_start: 0.8626 (t0) cc_final: 0.8064 (t0) REVERT: M 103 SER cc_start: 0.8642 (t) cc_final: 0.8403 (p) REVERT: N 299 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8509 (p) REVERT: N 301 ASN cc_start: 0.8195 (m-40) cc_final: 0.7896 (t0) outliers start: 81 outliers final: 62 residues processed: 397 average time/residue: 0.1231 time to fit residues: 79.0116 Evaluate side-chains 386 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 315 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 599 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 575 GLN Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 632 ASP Chi-restraints excluded: chain L residue 646 LEU Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 257 TYR Chi-restraints excluded: chain N residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 63 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 216 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 575 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.140922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110648 restraints weight = 43399.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111534 restraints weight = 33963.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112622 restraints weight = 27666.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113013 restraints weight = 23271.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113369 restraints weight = 21896.696| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20574 Z= 0.167 Angle : 0.766 12.493 28137 Z= 0.378 Chirality : 0.047 0.262 3327 Planarity : 0.005 0.065 3456 Dihedral : 6.977 59.706 3954 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.86 % Favored : 92.85 % Rotamer: Outliers : 3.41 % Allowed : 23.72 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.07 (0.16), residues: 2448 helix: -0.18 (0.30), residues: 331 sheet: -0.74 (0.18), residues: 710 loop : -2.09 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 432 TYR 0.024 0.001 TYR I 268 PHE 0.022 0.001 PHE M 64 TRP 0.053 0.002 TRP D 267 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00392 (20463) covalent geometry : angle 0.74409 (27849) SS BOND : bond 0.00457 ( 45) SS BOND : angle 2.08569 ( 90) hydrogen bonds : bond 0.03723 ( 486) hydrogen bonds : angle 5.19930 ( 1305) link_ALPHA1-2 : bond 0.01164 ( 11) link_ALPHA1-2 : angle 2.34550 ( 33) link_ALPHA1-3 : bond 0.00837 ( 9) link_ALPHA1-3 : angle 1.40801 ( 27) link_ALPHA1-6 : bond 0.00675 ( 10) link_ALPHA1-6 : angle 1.56579 ( 30) link_BETA1-4 : bond 0.00607 ( 24) link_BETA1-4 : angle 2.01385 ( 72) link_NAG-ASN : bond 0.00456 ( 12) link_NAG-ASN : angle 1.81943 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 323 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.8594 (m-40) cc_final: 0.8253 (t0) REVERT: B 530 MET cc_start: 0.8767 (mmm) cc_final: 0.8299 (mmm) REVERT: B 581 LEU cc_start: 0.7983 (tp) cc_final: 0.7622 (tp) REVERT: B 632 ASP cc_start: 0.8459 (t0) cc_final: 0.7953 (t0) REVERT: B 656 ASN cc_start: 0.7938 (t0) cc_final: 0.7734 (t0) REVERT: C 102 ILE cc_start: 0.9047 (mp) cc_final: 0.8759 (pt) REVERT: D 272 PRO cc_start: 0.7697 (OUTLIER) cc_final: 0.7291 (Cg_endo) REVERT: D 282 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7458 (mt-10) REVERT: D 301 ASN cc_start: 0.8471 (t0) cc_final: 0.8020 (t0) REVERT: D 314 ASP cc_start: 0.7807 (m-30) cc_final: 0.7581 (m-30) REVERT: F 84 LEU cc_start: 0.8202 (tp) cc_final: 0.7870 (mt) REVERT: F 104 MET cc_start: 0.8943 (ttt) cc_final: 0.8666 (ttt) REVERT: F 268 LYS cc_start: 0.8382 (ptmt) cc_final: 0.8028 (mttm) REVERT: F 282 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8114 (mppt) REVERT: F 446 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7866 (ttm110) REVERT: F 492 GLU cc_start: 0.8852 (pm20) cc_final: 0.8637 (pm20) REVERT: H 39 LEU cc_start: 0.8455 (mt) cc_final: 0.8084 (mt) REVERT: H 51 MET cc_start: 0.7855 (tpp) cc_final: 0.7610 (ttt) REVERT: H 104 ASP cc_start: 0.8438 (m-30) cc_final: 0.8163 (t0) REVERT: I 234 LEU cc_start: 0.7791 (mt) cc_final: 0.7376 (mp) REVERT: I 307 ILE cc_start: 0.8230 (mm) cc_final: 0.7748 (tt) REVERT: K 49 LYS cc_start: 0.8418 (tttt) cc_final: 0.8023 (mtmt) REVERT: K 268 LYS cc_start: 0.8526 (pttt) cc_final: 0.8284 (mmtt) REVERT: K 280 ASN cc_start: 0.8018 (m-40) cc_final: 0.7808 (t0) REVERT: K 369 MET cc_start: 0.7379 (tpp) cc_final: 0.6759 (ttt) REVERT: K 423 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8756 (mt) REVERT: L 529 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8614 (t) REVERT: L 646 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9196 (mm) REVERT: M 6 GLN cc_start: 0.7482 (pt0) cc_final: 0.6611 (pt0) REVERT: M 10 GLU cc_start: 0.7441 (pm20) cc_final: 0.6774 (pp20) REVERT: M 59 ASN cc_start: 0.8666 (t0) cc_final: 0.8137 (t0) REVERT: M 103 SER cc_start: 0.8721 (t) cc_final: 0.8412 (p) REVERT: N 299 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8463 (p) REVERT: N 301 ASN cc_start: 0.8310 (m-40) cc_final: 0.8018 (t0) outliers start: 73 outliers final: 60 residues processed: 380 average time/residue: 0.1103 time to fit residues: 68.2987 Evaluate side-chains 369 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 246 GLN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 293 GLU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 423 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 575 GLN Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 646 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 257 TYR Chi-restraints excluded: chain N residue 299 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 41 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 HIS F 362 ASN H 62 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.137454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107852 restraints weight = 44044.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108912 restraints weight = 35413.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.109686 restraints weight = 28526.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110189 restraints weight = 23332.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110443 restraints weight = 21688.923| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 20574 Z= 0.235 Angle : 0.843 13.148 28137 Z= 0.419 Chirality : 0.049 0.250 3327 Planarity : 0.005 0.061 3456 Dihedral : 7.257 59.906 3954 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.80 % Favored : 91.95 % Rotamer: Outliers : 3.83 % Allowed : 23.48 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.17 (0.16), residues: 2448 helix: -0.41 (0.29), residues: 351 sheet: -0.71 (0.18), residues: 690 loop : -2.17 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 588 TYR 0.026 0.002 TYR B 643 PHE 0.023 0.002 PHE M 64 TRP 0.040 0.003 TRP I 267 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00555 (20463) covalent geometry : angle 0.81608 (27849) SS BOND : bond 0.00663 ( 45) SS BOND : angle 2.55684 ( 90) hydrogen bonds : bond 0.04220 ( 486) hydrogen bonds : angle 5.51147 ( 1305) link_ALPHA1-2 : bond 0.01271 ( 11) link_ALPHA1-2 : angle 2.42153 ( 33) link_ALPHA1-3 : bond 0.00725 ( 9) link_ALPHA1-3 : angle 1.65467 ( 27) link_ALPHA1-6 : bond 0.00750 ( 10) link_ALPHA1-6 : angle 1.59337 ( 30) link_BETA1-4 : bond 0.00614 ( 24) link_BETA1-4 : angle 2.15999 ( 72) link_NAG-ASN : bond 0.00558 ( 12) link_NAG-ASN : angle 2.15934 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3338.81 seconds wall clock time: 58 minutes 50.26 seconds (3530.26 seconds total)