Starting phenix.real_space_refine on Wed Jun 18 22:28:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9b_25755/06_2025/7t9b_25755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9b_25755/06_2025/7t9b_25755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9b_25755/06_2025/7t9b_25755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9b_25755/06_2025/7t9b_25755.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9b_25755/06_2025/7t9b_25755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9b_25755/06_2025/7t9b_25755.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.039 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 131 5.16 5 C 13523 2.51 5 N 3572 2.21 5 O 4366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21592 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3433 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3425 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3387 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 23, 'TRANS': 405} Chain breaks: 4 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" 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: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" 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: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 14.11, per 1000 atoms: 0.65 Number of scatterers: 21592 At special positions: 0 Unit cell: (124.2, 127.65, 188.6, 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 131 16.00 O 4366 8.00 N 3572 7.00 C 13523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 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 B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.00 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.15 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " 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 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 3 " " NAG i 1 " - " FUC i 2 " " NAG j 1 " - " FUC j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 625 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 133 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 197 " " NAG g 1 " - " ASN E 156 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN F 618 " " NAG j 1 " - " ASN F 611 " Time building additional restraints: 6.73 Conformation dependent library (CDL) restraints added in 2.8 seconds 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 38 sheets defined 18.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.515A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.525A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.355A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.600A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.610A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.519A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.278A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.671A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 removed outlier: 3.715A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.755A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.581A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.846A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 526 removed outlier: 4.403A pdb=" N GLY F 525 " --> pdb=" O GLY F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 534 through 540 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 639 through 662 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.381A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (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 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.489A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 3.988A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 12 through 13 current: chain 'K' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 48 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.376A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.490A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.663A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AC3, first strand: chain 'N' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 12 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.515A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AD1, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AD2, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.457A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.722A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD4, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'O' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 11 through 12 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AD6, first strand: chain 'P' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 12 through 13 current: chain 'P' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 96 through 98 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.966A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 96 through 98 555 hydrogen bonds defined for protein. 1455 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: 8.78 Time building geometry restraints manager: 7.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4674 1.32 - 1.46: 7079 1.46 - 1.59: 10059 1.59 - 1.73: 46 1.73 - 1.87: 175 Bond restraints: 22033 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.00e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.361 0.155 2.50e-02 1.60e+03 3.84e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.75e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.392 -0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.649 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 22028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.60: 29874 7.60 - 15.21: 43 15.21 - 22.81: 0 22.81 - 30.42: 0 30.42 - 38.02: 3 Bond angle restraints: 29920 Sorted by residual: angle pdb=" C2 NAG d 1 " pdb=" N2 NAG d 1 " pdb=" C7 NAG d 1 " ideal model delta sigma weight residual 124.56 162.58 -38.02 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 161.38 -36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C2 NAG X 1 " pdb=" N2 NAG X 1 " pdb=" C7 NAG X 1 " ideal model delta sigma weight residual 124.56 160.89 -36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N HIS C 85 " pdb=" CA HIS C 85 " pdb=" C HIS C 85 " ideal model delta sigma weight residual 111.82 120.98 -9.16 1.16e+00 7.43e-01 6.23e+01 angle pdb=" N GLU C 83 " pdb=" CA GLU C 83 " pdb=" C GLU C 83 " ideal model delta sigma weight residual 109.96 121.71 -11.75 1.50e+00 4.44e-01 6.14e+01 ... (remaining 29915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 13871 21.78 - 43.56: 327 43.56 - 65.34: 102 65.34 - 87.12: 59 87.12 - 108.90: 24 Dihedral angle restraints: 14383 sinusoidal: 6957 harmonic: 7426 Sorted by residual: dihedral pdb=" CA ASN C 197 " pdb=" C ASN C 197 " pdb=" N THR C 198 " pdb=" CA THR C 198 " ideal model delta harmonic sigma weight residual 180.00 147.63 32.37 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA VAL C 68 " pdb=" C VAL C 68 " pdb=" N TRP C 69 " pdb=" CA TRP C 69 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR A 198 " pdb=" C THR A 198 " pdb=" N SER A 199 " pdb=" CA SER A 199 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 14380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 3289 0.218 - 0.435: 316 0.435 - 0.653: 24 0.653 - 0.871: 0 0.871 - 1.088: 1 Chirality restraints: 3630 Sorted by residual: chirality pdb=" C1 FUC i 2 " pdb=" O6 NAG i 1 " pdb=" C2 FUC i 2 " pdb=" O5 FUC i 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-02 2.50e+03 2.96e+03 chirality pdb=" C1 NAG S 2 " pdb=" O6 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-02 2.50e+03 6.46e+02 chirality pdb=" C1 MAN S 6 " pdb=" O6 MAN S 4 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.93 0.47 2.00e-02 2.50e+03 5.41e+02 ... (remaining 3627 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " 0.348 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG S 2 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " 0.318 2.00e-02 2.50e+03 2.78e-01 9.64e+02 pdb=" C7 NAG j 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " -0.324 2.00e-02 2.50e+03 2.75e-01 9.47e+02 pdb=" C7 NAG F 701 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.055 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5451 2.81 - 3.33: 19130 3.33 - 3.86: 36326 3.86 - 4.38: 43973 4.38 - 4.90: 70120 Nonbonded interactions: 175000 Sorted by model distance: nonbonded pdb=" O5 NAG j 1 " pdb=" O6 NAG j 1 " model vdw 2.289 2.432 nonbonded pdb=" N ASP J 84 " pdb=" OD1 ASP J 84 " model vdw 2.370 3.120 nonbonded pdb=" N ASP O 84 " pdb=" OD1 ASP O 84 " model vdw 2.370 3.120 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.370 3.120 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.411 3.120 ... (remaining 174995 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 72 through 503 or resid 601 through \ 611)) selection = (chain 'C' and (resid 33 through 57 or resid 72 through 503 or resid 601 through \ 611)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'e' } ncs_group { reference = (chain 'R' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } 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: 1.900 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: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 53.760 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.021 0.155 22174 Z= 1.146 Angle : 1.797 38.021 30303 Z= 1.146 Chirality : 0.133 1.088 3630 Planarity : 0.015 0.294 3673 Dihedral : 12.572 108.899 9505 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.71 % Favored : 95.62 % Rotamer: Outliers : 0.98 % Allowed : 0.76 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 2535 helix: -0.34 (0.24), residues: 385 sheet: 0.93 (0.18), residues: 817 loop : 0.13 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.008 TRP A 96 HIS 0.009 0.002 HIS J 82A PHE 0.044 0.006 PHE L 98 TYR 0.070 0.007 TYR L 87 ARG 0.012 0.001 ARG J 71 Details of bonding type rmsd link_NAG-ASN : bond 0.06922 ( 63) link_NAG-ASN : angle 2.62635 ( 189) link_ALPHA1-6 : bond 0.00449 ( 2) link_ALPHA1-6 : angle 2.71457 ( 6) link_BETA1-4 : bond 0.05873 ( 24) link_BETA1-4 : angle 4.02949 ( 72) link_ALPHA1-3 : bond 0.06139 ( 5) link_ALPHA1-3 : angle 3.43561 ( 15) hydrogen bonds : bond 0.16830 ( 555) hydrogen bonds : angle 6.86540 ( 1455) link_BETA1-6 : bond 0.02558 ( 7) link_BETA1-6 : angle 4.60429 ( 21) SS BOND : bond 0.02375 ( 40) SS BOND : angle 2.43405 ( 80) covalent geometry : bond 0.02105 (22033) covalent geometry : angle 1.77494 (29920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 395 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8555 (m-80) cc_final: 0.8237 (m-10) REVERT: A 475 MET cc_start: 0.8713 (mmm) cc_final: 0.8353 (mmm) REVERT: A 482 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7969 (mm-30) REVERT: J 2 VAL cc_start: 0.9262 (t) cc_final: 0.8702 (t) REVERT: K 11 VAL cc_start: 0.8529 (t) cc_final: 0.8194 (p) REVERT: K 47 MET cc_start: 0.8336 (mmm) cc_final: 0.8056 (mmt) REVERT: K 94 ARG cc_start: 0.6115 (mpt180) cc_final: 0.5237 (mmt180) REVERT: K 104 LEU cc_start: 0.8447 (tp) cc_final: 0.7759 (tt) REVERT: C 72 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6650 (p90) REVERT: C 107 ASP cc_start: 0.8076 (m-30) cc_final: 0.7734 (t0) REVERT: C 153 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8298 (tt0) REVERT: C 449 ILE cc_start: 0.9419 (mt) cc_final: 0.9217 (mm) REVERT: D 616 ASN cc_start: 0.9247 (p0) cc_final: 0.8814 (p0) REVERT: D 624 ASP cc_start: 0.8310 (p0) cc_final: 0.7721 (p0) REVERT: D 626 MET cc_start: 0.8826 (ttm) cc_final: 0.8613 (ttm) REVERT: M 78 LEU cc_start: 0.9138 (tp) cc_final: 0.8922 (tp) REVERT: N 47 MET cc_start: 0.8484 (mmm) cc_final: 0.8238 (mmp) REVERT: N 58 VAL cc_start: 0.8613 (m) cc_final: 0.8390 (p) REVERT: N 94 ARG cc_start: 0.6713 (mpt180) cc_final: 0.6141 (tpt170) REVERT: N 102 THR cc_start: 0.8431 (m) cc_final: 0.8120 (p) REVERT: E 104 MET cc_start: 0.8272 (ttm) cc_final: 0.8010 (ttt) REVERT: F 571 TRP cc_start: 0.5920 (t-100) cc_final: 0.5585 (p-90) REVERT: F 581 LEU cc_start: 0.8928 (pp) cc_final: 0.8712 (tp) REVERT: O 52 ASN cc_start: 0.8951 (t0) cc_final: 0.8700 (t0) REVERT: P 42 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8034 (ttpt) REVERT: P 94 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7679 (tpt170) REVERT: H 27 PHE cc_start: 0.5955 (t80) cc_final: 0.5594 (t80) REVERT: H 80 LEU cc_start: 0.7504 (tp) cc_final: 0.7066 (tp) REVERT: H 98 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8063 (p) REVERT: L 42 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8155 (mp10) REVERT: L 71 PHE cc_start: 0.4742 (m-80) cc_final: 0.3278 (m-80) REVERT: L 75 ILE cc_start: 0.7447 (mt) cc_final: 0.6937 (mt) REVERT: L 77 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7515 (tmm-80) REVERT: L 89 GLN cc_start: 0.8572 (tt0) cc_final: 0.8090 (tm-30) outliers start: 22 outliers final: 2 residues processed: 412 average time/residue: 0.4055 time to fit residues: 243.2160 Evaluate side-chains 195 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 302 ASN A 425 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN C 195 ASN C 425 ASN D 653 GLN E 130 GLN E 195 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.083633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.064846 restraints weight = 62387.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067191 restraints weight = 33340.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068668 restraints weight = 22493.044| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22174 Z= 0.164 Angle : 0.757 16.431 30303 Z= 0.367 Chirality : 0.047 0.329 3630 Planarity : 0.004 0.066 3673 Dihedral : 8.940 73.125 4866 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.59 % Favored : 96.21 % Rotamer: Outliers : 1.43 % Allowed : 6.11 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2535 helix: 1.58 (0.27), residues: 375 sheet: 0.73 (0.18), residues: 785 loop : -0.30 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 PHE 0.024 0.002 PHE H 29 TYR 0.016 0.001 TYR C 173 ARG 0.005 0.001 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 63) link_NAG-ASN : angle 2.46559 ( 189) link_ALPHA1-6 : bond 0.01037 ( 2) link_ALPHA1-6 : angle 1.50571 ( 6) link_BETA1-4 : bond 0.00582 ( 24) link_BETA1-4 : angle 2.64682 ( 72) link_ALPHA1-3 : bond 0.01235 ( 5) link_ALPHA1-3 : angle 2.15070 ( 15) hydrogen bonds : bond 0.05501 ( 555) hydrogen bonds : angle 5.28993 ( 1455) link_BETA1-6 : bond 0.01236 ( 7) link_BETA1-6 : angle 2.52079 ( 21) SS BOND : bond 0.00250 ( 40) SS BOND : angle 0.78140 ( 80) covalent geometry : bond 0.00357 (22033) covalent geometry : angle 0.71879 (29920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8151 (m-80) cc_final: 0.7804 (m-80) REVERT: A 475 MET cc_start: 0.8454 (mmm) cc_final: 0.8240 (mmm) REVERT: A 482 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 648 GLU cc_start: 0.8093 (tp30) cc_final: 0.7818 (tm-30) REVERT: K 27 ASP cc_start: 0.8857 (t70) cc_final: 0.8593 (t70) REVERT: K 47 MET cc_start: 0.7932 (mmm) cc_final: 0.7717 (mmt) REVERT: K 94 ARG cc_start: 0.5311 (mpt180) cc_final: 0.4744 (mmt180) REVERT: D 616 ASN cc_start: 0.9010 (p0) cc_final: 0.8715 (p0) REVERT: M 86 ASP cc_start: 0.8306 (m-30) cc_final: 0.8011 (m-30) REVERT: N 95 THR cc_start: 0.8718 (p) cc_final: 0.8509 (p) REVERT: E 104 MET cc_start: 0.7792 (ttm) cc_final: 0.7581 (ttt) REVERT: F 586 TYR cc_start: 0.9350 (t80) cc_final: 0.9105 (t80) REVERT: O 52 ASN cc_start: 0.8878 (t0) cc_final: 0.8547 (t0) REVERT: P 27 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8456 (t70) REVERT: P 94 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7521 (tpt170) REVERT: H 27 PHE cc_start: 0.5634 (t80) cc_final: 0.5278 (t80) REVERT: H 38 ARG cc_start: 0.7589 (ptt180) cc_final: 0.7295 (ptp-170) REVERT: H 80 LEU cc_start: 0.7288 (tp) cc_final: 0.7029 (tp) REVERT: L 104 VAL cc_start: 0.7968 (t) cc_final: 0.7761 (p) outliers start: 32 outliers final: 15 residues processed: 260 average time/residue: 0.3543 time to fit residues: 141.1682 Evaluate side-chains 194 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 243 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 220 optimal weight: 0.0270 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN E 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.073172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.053755 restraints weight = 63238.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.055454 restraints weight = 37969.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.056581 restraints weight = 27404.707| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22174 Z= 0.214 Angle : 0.720 17.227 30303 Z= 0.346 Chirality : 0.047 0.377 3630 Planarity : 0.004 0.043 3673 Dihedral : 7.516 63.919 4861 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 1.43 % Allowed : 7.59 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2535 helix: 1.51 (0.27), residues: 384 sheet: 0.72 (0.18), residues: 754 loop : -0.43 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 479 HIS 0.007 0.001 HIS E 105 PHE 0.016 0.002 PHE L 33 TYR 0.016 0.001 TYR A 484 ARG 0.007 0.001 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 63) link_NAG-ASN : angle 2.34661 ( 189) link_ALPHA1-6 : bond 0.00768 ( 2) link_ALPHA1-6 : angle 1.42163 ( 6) link_BETA1-4 : bond 0.00454 ( 24) link_BETA1-4 : angle 2.13360 ( 72) link_ALPHA1-3 : bond 0.01088 ( 5) link_ALPHA1-3 : angle 1.50548 ( 15) hydrogen bonds : bond 0.04801 ( 555) hydrogen bonds : angle 5.01605 ( 1455) link_BETA1-6 : bond 0.00874 ( 7) link_BETA1-6 : angle 2.22231 ( 21) SS BOND : bond 0.00279 ( 40) SS BOND : angle 0.82602 ( 80) covalent geometry : bond 0.00491 (22033) covalent geometry : angle 0.68779 (29920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6718 (t-90) REVERT: A 475 MET cc_start: 0.8507 (mmm) cc_final: 0.7980 (mmm) REVERT: K 27 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8695 (t70) REVERT: K 94 ARG cc_start: 0.5638 (mpt180) cc_final: 0.4755 (mmt180) REVERT: C 434 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7905 (tpp) REVERT: D 616 ASN cc_start: 0.9096 (p0) cc_final: 0.8796 (p0) REVERT: E 104 MET cc_start: 0.8180 (ttm) cc_final: 0.7893 (ttt) REVERT: F 586 TYR cc_start: 0.9383 (t80) cc_final: 0.8959 (t80) REVERT: P 27 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8690 (t70) REVERT: P 94 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7633 (tpt170) REVERT: H 3 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7554 (tm-30) REVERT: H 27 PHE cc_start: 0.5004 (t80) cc_final: 0.4608 (t80) REVERT: H 38 ARG cc_start: 0.7695 (ptt180) cc_final: 0.7171 (ptp-170) REVERT: H 91 TYR cc_start: 0.7613 (m-80) cc_final: 0.7083 (m-80) REVERT: H 97 GLU cc_start: 0.6536 (tt0) cc_final: 0.6268 (tt0) REVERT: H 101 ASP cc_start: 0.8339 (t0) cc_final: 0.7829 (t0) outliers start: 32 outliers final: 19 residues processed: 209 average time/residue: 0.3525 time to fit residues: 112.9108 Evaluate side-chains 181 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 206 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 302 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN E 82 GLN F 570 HIS L 37 GLN ** L 89 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 = 0.3287 r_free = 0.3287 target = 0.072552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.053186 restraints weight = 64591.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054873 restraints weight = 38705.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055974 restraints weight = 27861.118| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22174 Z= 0.193 Angle : 0.665 16.649 30303 Z= 0.319 Chirality : 0.045 0.297 3630 Planarity : 0.004 0.047 3673 Dihedral : 6.565 56.471 4861 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 1.70 % Allowed : 7.90 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2535 helix: 1.61 (0.27), residues: 387 sheet: 0.58 (0.19), residues: 744 loop : -0.55 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 PHE 0.017 0.002 PHE H 29 TYR 0.017 0.001 TYR B 586 ARG 0.008 0.000 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 63) link_NAG-ASN : angle 2.29845 ( 189) link_ALPHA1-6 : bond 0.00835 ( 2) link_ALPHA1-6 : angle 1.35219 ( 6) link_BETA1-4 : bond 0.00377 ( 24) link_BETA1-4 : angle 1.98167 ( 72) link_ALPHA1-3 : bond 0.01038 ( 5) link_ALPHA1-3 : angle 1.68551 ( 15) hydrogen bonds : bond 0.04414 ( 555) hydrogen bonds : angle 4.82517 ( 1455) link_BETA1-6 : bond 0.00712 ( 7) link_BETA1-6 : angle 2.05887 ( 21) SS BOND : bond 0.00314 ( 40) SS BOND : angle 0.75362 ( 80) covalent geometry : bond 0.00442 (22033) covalent geometry : angle 0.63118 (29920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9440 (t) cc_final: 0.9149 (m) REVERT: A 72 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6826 (t-90) REVERT: A 475 MET cc_start: 0.8562 (mmm) cc_final: 0.7849 (tmm) REVERT: K 94 ARG cc_start: 0.5723 (mpt180) cc_final: 0.4791 (mmt180) REVERT: D 616 ASN cc_start: 0.9102 (p0) cc_final: 0.8798 (p0) REVERT: D 617 ARG cc_start: 0.8620 (ttm170) cc_final: 0.8270 (mtt90) REVERT: E 475 MET cc_start: 0.8397 (mmp) cc_final: 0.8055 (mmm) REVERT: F 586 TYR cc_start: 0.9335 (t80) cc_final: 0.8939 (t80) REVERT: O 75 LYS cc_start: 0.8938 (mttm) cc_final: 0.8578 (mttp) REVERT: P 27 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: P 94 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7642 (tpt170) REVERT: H 3 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7563 (tm-30) REVERT: H 20 LEU cc_start: 0.6324 (mt) cc_final: 0.5926 (mt) REVERT: H 27 PHE cc_start: 0.4978 (t80) cc_final: 0.4684 (t80) REVERT: H 38 ARG cc_start: 0.7702 (ptt180) cc_final: 0.7432 (ptp-170) REVERT: H 75 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7928 (mtmm) REVERT: H 91 TYR cc_start: 0.7482 (m-80) cc_final: 0.6966 (m-80) REVERT: H 101 ASP cc_start: 0.8411 (t0) cc_final: 0.8005 (t0) REVERT: L 70 ASP cc_start: 0.7352 (p0) cc_final: 0.7131 (m-30) outliers start: 38 outliers final: 23 residues processed: 200 average time/residue: 0.3780 time to fit residues: 115.7459 Evaluate side-chains 183 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 190 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 199 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN P 39 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053498 restraints weight = 64157.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.055182 restraints weight = 38133.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056296 restraints weight = 27505.725| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22174 Z= 0.151 Angle : 0.624 15.934 30303 Z= 0.299 Chirality : 0.044 0.277 3630 Planarity : 0.004 0.045 3673 Dihedral : 6.103 59.533 4861 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 1.78 % Allowed : 8.26 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2535 helix: 1.87 (0.28), residues: 377 sheet: 0.48 (0.19), residues: 747 loop : -0.57 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 PHE 0.017 0.001 PHE M 102 TYR 0.017 0.001 TYR E 484 ARG 0.008 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 63) link_NAG-ASN : angle 2.16738 ( 189) link_ALPHA1-6 : bond 0.00883 ( 2) link_ALPHA1-6 : angle 1.33428 ( 6) link_BETA1-4 : bond 0.00369 ( 24) link_BETA1-4 : angle 1.78608 ( 72) link_ALPHA1-3 : bond 0.01058 ( 5) link_ALPHA1-3 : angle 1.56968 ( 15) hydrogen bonds : bond 0.04076 ( 555) hydrogen bonds : angle 4.66249 ( 1455) link_BETA1-6 : bond 0.00601 ( 7) link_BETA1-6 : angle 2.00339 ( 21) SS BOND : bond 0.00240 ( 40) SS BOND : angle 0.69078 ( 80) covalent geometry : bond 0.00343 (22033) covalent geometry : angle 0.59321 (29920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9430 (t) cc_final: 0.9159 (m) REVERT: A 72 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6832 (t-90) REVERT: A 475 MET cc_start: 0.8531 (mmm) cc_final: 0.7898 (tmm) REVERT: J 83 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7392 (tpp80) REVERT: K 94 ARG cc_start: 0.5785 (mpt180) cc_final: 0.4791 (mmt180) REVERT: C 72 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7285 (p90) REVERT: C 434 MET cc_start: 0.8230 (tpp) cc_final: 0.7939 (tpp) REVERT: D 616 ASN cc_start: 0.9116 (p0) cc_final: 0.8905 (p0) REVERT: E 475 MET cc_start: 0.8486 (mmp) cc_final: 0.8122 (mmm) REVERT: F 586 TYR cc_start: 0.9316 (t80) cc_final: 0.8929 (t80) REVERT: O 75 LYS cc_start: 0.8956 (mttm) cc_final: 0.8613 (mttp) REVERT: P 27 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: P 94 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7667 (tpt170) REVERT: H 3 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7529 (tm-30) REVERT: H 27 PHE cc_start: 0.4857 (t80) cc_final: 0.4548 (t80) REVERT: H 38 ARG cc_start: 0.7694 (ptt180) cc_final: 0.7387 (ptp-170) REVERT: H 91 TYR cc_start: 0.7482 (m-80) cc_final: 0.6960 (m-80) REVERT: L 70 ASP cc_start: 0.7441 (p0) cc_final: 0.7071 (m-30) REVERT: L 77 ARG cc_start: 0.8072 (tmm-80) cc_final: 0.7702 (ttp80) outliers start: 40 outliers final: 22 residues processed: 193 average time/residue: 0.3683 time to fit residues: 108.8368 Evaluate side-chains 179 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 250 optimal weight: 40.0000 chunk 22 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3313 r_free = 0.3313 target = 0.073757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054612 restraints weight = 63829.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.056332 restraints weight = 37872.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.057470 restraints weight = 27215.819| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22174 Z= 0.113 Angle : 0.589 15.014 30303 Z= 0.284 Chirality : 0.043 0.288 3630 Planarity : 0.004 0.045 3673 Dihedral : 5.617 53.645 4861 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.56 % Allowed : 8.52 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2535 helix: 1.94 (0.28), residues: 383 sheet: 0.52 (0.18), residues: 770 loop : -0.54 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 PHE 0.020 0.001 PHE M 102 TYR 0.011 0.001 TYR C 173 ARG 0.011 0.000 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 63) link_NAG-ASN : angle 2.06380 ( 189) link_ALPHA1-6 : bond 0.00911 ( 2) link_ALPHA1-6 : angle 1.21637 ( 6) link_BETA1-4 : bond 0.00378 ( 24) link_BETA1-4 : angle 1.62624 ( 72) link_ALPHA1-3 : bond 0.01023 ( 5) link_ALPHA1-3 : angle 1.52977 ( 15) hydrogen bonds : bond 0.03556 ( 555) hydrogen bonds : angle 4.44767 ( 1455) link_BETA1-6 : bond 0.00607 ( 7) link_BETA1-6 : angle 1.87650 ( 21) SS BOND : bond 0.00215 ( 40) SS BOND : angle 0.71541 ( 80) covalent geometry : bond 0.00242 (22033) covalent geometry : angle 0.55910 (29920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 2.299 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 42 VAL cc_start: 0.9421 (t) cc_final: 0.9122 (m) REVERT: A 72 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6792 (t-90) REVERT: A 452 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7792 (mt) REVERT: A 475 MET cc_start: 0.8523 (mmm) cc_final: 0.7930 (tmm) REVERT: B 586 TYR cc_start: 0.8868 (t80) cc_final: 0.8537 (t80) REVERT: J 83 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7423 (tpp80) REVERT: K 94 ARG cc_start: 0.5898 (mpt180) cc_final: 0.5202 (tpp-160) REVERT: C 434 MET cc_start: 0.8299 (tpp) cc_final: 0.7927 (tpp) REVERT: D 616 ASN cc_start: 0.9087 (p0) cc_final: 0.8858 (p0) REVERT: F 586 TYR cc_start: 0.9272 (t80) cc_final: 0.8931 (t80) REVERT: O 43 LYS cc_start: 0.8415 (mmtm) cc_final: 0.8132 (mmmt) REVERT: O 75 LYS cc_start: 0.8942 (mttm) cc_final: 0.8613 (mttp) REVERT: P 27 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8722 (m-30) REVERT: P 94 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7682 (tpt170) REVERT: H 3 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7571 (tm-30) REVERT: H 20 LEU cc_start: 0.5860 (mp) cc_final: 0.5532 (mm) REVERT: H 27 PHE cc_start: 0.4912 (t80) cc_final: 0.4608 (t80) REVERT: H 38 ARG cc_start: 0.7701 (ptt180) cc_final: 0.7381 (ptp-170) REVERT: H 75 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8039 (ptpp) REVERT: L 70 ASP cc_start: 0.7258 (p0) cc_final: 0.6842 (m-30) REVERT: L 77 ARG cc_start: 0.8190 (tmm-80) cc_final: 0.7438 (ttp80) outliers start: 35 outliers final: 22 residues processed: 196 average time/residue: 0.3457 time to fit residues: 104.1112 Evaluate side-chains 183 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 49 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3315 r_free = 0.3315 target = 0.073819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.054705 restraints weight = 63845.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056398 restraints weight = 37765.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057560 restraints weight = 27163.576| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22174 Z= 0.108 Angle : 0.571 14.333 30303 Z= 0.275 Chirality : 0.043 0.303 3630 Planarity : 0.004 0.041 3673 Dihedral : 5.429 54.047 4861 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 1.38 % Allowed : 9.15 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2535 helix: 2.00 (0.28), residues: 383 sheet: 0.56 (0.18), residues: 800 loop : -0.55 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 69 HIS 0.004 0.001 HIS E 105 PHE 0.022 0.001 PHE M 102 TYR 0.020 0.001 TYR L 49 ARG 0.009 0.000 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 63) link_NAG-ASN : angle 1.98098 ( 189) link_ALPHA1-6 : bond 0.00915 ( 2) link_ALPHA1-6 : angle 1.24353 ( 6) link_BETA1-4 : bond 0.00366 ( 24) link_BETA1-4 : angle 1.59226 ( 72) link_ALPHA1-3 : bond 0.00984 ( 5) link_ALPHA1-3 : angle 1.49052 ( 15) hydrogen bonds : bond 0.03473 ( 555) hydrogen bonds : angle 4.36747 ( 1455) link_BETA1-6 : bond 0.00531 ( 7) link_BETA1-6 : angle 1.82932 ( 21) SS BOND : bond 0.00223 ( 40) SS BOND : angle 0.64552 ( 80) covalent geometry : bond 0.00240 (22033) covalent geometry : angle 0.54227 (29920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9409 (t) cc_final: 0.9116 (m) REVERT: A 72 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6799 (t-90) REVERT: A 452 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7784 (mt) REVERT: A 475 MET cc_start: 0.8494 (mmm) cc_final: 0.7934 (tmm) REVERT: J 83 ARG cc_start: 0.7773 (tpp80) cc_final: 0.7414 (tpp80) REVERT: K 94 ARG cc_start: 0.5914 (mpt180) cc_final: 0.5201 (tpp-160) REVERT: C 434 MET cc_start: 0.8278 (tpp) cc_final: 0.7987 (tpp) REVERT: D 616 ASN cc_start: 0.9085 (p0) cc_final: 0.8855 (p0) REVERT: E 475 MET cc_start: 0.8291 (mmp) cc_final: 0.7846 (mmm) REVERT: F 586 TYR cc_start: 0.9271 (t80) cc_final: 0.8929 (t80) REVERT: P 27 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8724 (m-30) REVERT: P 94 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7709 (tpt170) REVERT: H 3 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7568 (tm-30) REVERT: H 27 PHE cc_start: 0.5039 (t80) cc_final: 0.4667 (t80) REVERT: H 38 ARG cc_start: 0.7696 (ptt180) cc_final: 0.7356 (ptp-170) REVERT: L 70 ASP cc_start: 0.7311 (p0) cc_final: 0.6940 (m-30) REVERT: L 77 ARG cc_start: 0.8172 (tmm-80) cc_final: 0.7389 (ttp80) outliers start: 31 outliers final: 25 residues processed: 185 average time/residue: 0.3378 time to fit residues: 97.2896 Evaluate side-chains 186 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 44 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 7 optimal weight: 0.0170 chunk 185 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN N 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052627 restraints weight = 64789.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.054291 restraints weight = 38745.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.055426 restraints weight = 28065.819| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 22174 Z= 0.319 Angle : 0.749 12.125 30303 Z= 0.362 Chirality : 0.048 0.340 3630 Planarity : 0.005 0.045 3673 Dihedral : 6.118 56.552 4861 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.25 % Favored : 94.60 % Rotamer: Outliers : 1.92 % Allowed : 8.84 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2535 helix: 1.52 (0.28), residues: 380 sheet: 0.26 (0.19), residues: 749 loop : -0.73 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 479 HIS 0.008 0.002 HIS E 105 PHE 0.028 0.002 PHE H 29 TYR 0.029 0.002 TYR A 484 ARG 0.007 0.001 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 63) link_NAG-ASN : angle 2.37781 ( 189) link_ALPHA1-6 : bond 0.00849 ( 2) link_ALPHA1-6 : angle 1.36863 ( 6) link_BETA1-4 : bond 0.00403 ( 24) link_BETA1-4 : angle 1.83802 ( 72) link_ALPHA1-3 : bond 0.00921 ( 5) link_ALPHA1-3 : angle 1.79302 ( 15) hydrogen bonds : bond 0.04917 ( 555) hydrogen bonds : angle 4.98818 ( 1455) link_BETA1-6 : bond 0.00476 ( 7) link_BETA1-6 : angle 1.91607 ( 21) SS BOND : bond 0.00514 ( 40) SS BOND : angle 0.89181 ( 80) covalent geometry : bond 0.00745 (22033) covalent geometry : angle 0.71934 (29920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6864 (t-90) REVERT: A 184 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8111 (ptt) REVERT: A 452 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 475 MET cc_start: 0.8629 (mmm) cc_final: 0.8077 (tmm) REVERT: B 586 TYR cc_start: 0.8991 (t80) cc_final: 0.8681 (t80) REVERT: J 83 ARG cc_start: 0.7733 (tpp80) cc_final: 0.7440 (tpp80) REVERT: K 47 MET cc_start: 0.7464 (mmm) cc_final: 0.7152 (mmm) REVERT: K 94 ARG cc_start: 0.6028 (mpt180) cc_final: 0.4669 (mmt180) REVERT: C 72 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7433 (p90) REVERT: D 616 ASN cc_start: 0.9185 (p0) cc_final: 0.8965 (p0) REVERT: E 138 ILE cc_start: 0.8586 (mp) cc_final: 0.8226 (tt) REVERT: F 586 TYR cc_start: 0.9400 (t80) cc_final: 0.9048 (t80) REVERT: O 75 LYS cc_start: 0.8972 (mttm) cc_final: 0.8723 (mttp) REVERT: H 3 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7662 (tm-30) REVERT: H 38 ARG cc_start: 0.7810 (ptt180) cc_final: 0.7303 (ptp-170) REVERT: L 70 ASP cc_start: 0.7417 (p0) cc_final: 0.7029 (m-30) REVERT: L 77 ARG cc_start: 0.8269 (tmm-80) cc_final: 0.7927 (tmm-80) outliers start: 43 outliers final: 29 residues processed: 181 average time/residue: 0.3418 time to fit residues: 97.9025 Evaluate side-chains 178 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 231 optimal weight: 0.0980 chunk 2 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** L 89 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 = 0.3322 r_free = 0.3322 target = 0.074006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054953 restraints weight = 63939.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.056762 restraints weight = 37271.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.057974 restraints weight = 26391.786| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22174 Z= 0.124 Angle : 0.590 11.254 30303 Z= 0.286 Chirality : 0.044 0.319 3630 Planarity : 0.004 0.044 3673 Dihedral : 5.605 55.835 4857 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 1.43 % Allowed : 9.50 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2535 helix: 1.91 (0.28), residues: 380 sheet: 0.48 (0.19), residues: 755 loop : -0.72 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 69 HIS 0.004 0.001 HIS E 105 PHE 0.023 0.001 PHE H 29 TYR 0.013 0.001 TYR A 484 ARG 0.006 0.000 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 63) link_NAG-ASN : angle 2.09745 ( 189) link_ALPHA1-6 : bond 0.00995 ( 2) link_ALPHA1-6 : angle 1.25552 ( 6) link_BETA1-4 : bond 0.00343 ( 24) link_BETA1-4 : angle 1.57496 ( 72) link_ALPHA1-3 : bond 0.00923 ( 5) link_ALPHA1-3 : angle 1.58722 ( 15) hydrogen bonds : bond 0.03827 ( 555) hydrogen bonds : angle 4.54162 ( 1455) link_BETA1-6 : bond 0.00491 ( 7) link_BETA1-6 : angle 1.86515 ( 21) SS BOND : bond 0.00254 ( 40) SS BOND : angle 0.78327 ( 80) covalent geometry : bond 0.00279 (22033) covalent geometry : angle 0.55993 (29920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6858 (t-90) REVERT: A 184 MET cc_start: 0.8272 (ptt) cc_final: 0.7953 (ptt) REVERT: A 452 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7883 (mt) REVERT: A 475 MET cc_start: 0.8496 (mmm) cc_final: 0.8050 (tmm) REVERT: B 586 TYR cc_start: 0.8886 (t80) cc_final: 0.8551 (t80) REVERT: J 83 ARG cc_start: 0.7617 (tpp80) cc_final: 0.7382 (tpp80) REVERT: K 94 ARG cc_start: 0.5952 (mpt180) cc_final: 0.5144 (tpp-160) REVERT: C 72 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7389 (p90) REVERT: D 616 ASN cc_start: 0.9161 (p0) cc_final: 0.8939 (p0) REVERT: E 138 ILE cc_start: 0.8510 (mp) cc_final: 0.8189 (tt) REVERT: E 475 MET cc_start: 0.8398 (mmp) cc_final: 0.7962 (mmm) REVERT: F 528 MET cc_start: 0.7888 (mtt) cc_final: 0.7473 (mtt) REVERT: F 586 TYR cc_start: 0.9301 (t80) cc_final: 0.8947 (t80) REVERT: O 75 LYS cc_start: 0.8937 (mttm) cc_final: 0.8612 (mttp) REVERT: H 3 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7776 (tm-30) REVERT: H 38 ARG cc_start: 0.7772 (ptt180) cc_final: 0.7344 (ptp-170) REVERT: L 70 ASP cc_start: 0.7538 (p0) cc_final: 0.7118 (m-30) REVERT: L 77 ARG cc_start: 0.8186 (tmm-80) cc_final: 0.7826 (tmm-80) outliers start: 32 outliers final: 27 residues processed: 185 average time/residue: 0.3318 time to fit residues: 96.7223 Evaluate side-chains 185 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 245 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 225 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** L 89 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 = 0.3309 r_free = 0.3309 target = 0.073382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.054389 restraints weight = 64469.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.056137 restraints weight = 37367.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.057362 restraints weight = 26585.820| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22174 Z= 0.167 Angle : 0.600 10.888 30303 Z= 0.291 Chirality : 0.044 0.302 3630 Planarity : 0.004 0.043 3673 Dihedral : 5.569 56.205 4857 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.73 % Favored : 95.07 % Rotamer: Outliers : 1.29 % Allowed : 9.64 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2535 helix: 1.89 (0.28), residues: 380 sheet: 0.42 (0.19), residues: 775 loop : -0.78 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 69 HIS 0.005 0.001 HIS E 105 PHE 0.026 0.001 PHE H 29 TYR 0.017 0.001 TYR A 484 ARG 0.006 0.000 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 63) link_NAG-ASN : angle 2.13079 ( 189) link_ALPHA1-6 : bond 0.00958 ( 2) link_ALPHA1-6 : angle 1.27446 ( 6) link_BETA1-4 : bond 0.00315 ( 24) link_BETA1-4 : angle 1.55624 ( 72) link_ALPHA1-3 : bond 0.00875 ( 5) link_ALPHA1-3 : angle 1.59203 ( 15) hydrogen bonds : bond 0.03949 ( 555) hydrogen bonds : angle 4.55754 ( 1455) link_BETA1-6 : bond 0.00405 ( 7) link_BETA1-6 : angle 1.79627 ( 21) SS BOND : bond 0.00248 ( 40) SS BOND : angle 0.75078 ( 80) covalent geometry : bond 0.00384 (22033) covalent geometry : angle 0.57031 (29920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7037 (OUTLIER) cc_final: 0.6748 (t-90) REVERT: A 184 MET cc_start: 0.8261 (ptt) cc_final: 0.7977 (ptt) REVERT: A 452 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7917 (mt) REVERT: B 586 TYR cc_start: 0.8920 (t80) cc_final: 0.8570 (t80) REVERT: K 94 ARG cc_start: 0.5888 (mpt180) cc_final: 0.4864 (tpp-160) REVERT: D 616 ASN cc_start: 0.9157 (p0) cc_final: 0.8928 (p0) REVERT: E 138 ILE cc_start: 0.8546 (mp) cc_final: 0.8229 (tt) REVERT: F 528 MET cc_start: 0.8005 (mtt) cc_final: 0.7522 (mtt) REVERT: F 586 TYR cc_start: 0.9328 (t80) cc_final: 0.8984 (t80) REVERT: H 3 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7960 (tm-30) REVERT: H 38 ARG cc_start: 0.7916 (ptt180) cc_final: 0.7560 (ptp90) REVERT: H 75 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7848 (ptpp) REVERT: L 70 ASP cc_start: 0.7545 (p0) cc_final: 0.7141 (m-30) REVERT: L 77 ARG cc_start: 0.8219 (tmm-80) cc_final: 0.7858 (tmm-80) outliers start: 29 outliers final: 23 residues processed: 182 average time/residue: 0.3338 time to fit residues: 96.5164 Evaluate side-chains 177 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 163 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 133 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 230 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN P 38 GLN ** L 89 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 = 0.3302 r_free = 0.3302 target = 0.073094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054032 restraints weight = 64505.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055805 restraints weight = 38232.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.056976 restraints weight = 27262.907| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22174 Z= 0.184 Angle : 0.620 10.698 30303 Z= 0.299 Chirality : 0.044 0.301 3630 Planarity : 0.004 0.042 3673 Dihedral : 5.657 56.320 4857 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.46 % Favored : 95.35 % Rotamer: Outliers : 1.29 % Allowed : 9.77 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2535 helix: 1.84 (0.28), residues: 380 sheet: 0.37 (0.19), residues: 760 loop : -0.82 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.005 0.001 HIS E 105 PHE 0.022 0.002 PHE H 29 TYR 0.018 0.001 TYR A 484 ARG 0.007 0.000 ARG D 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 63) link_NAG-ASN : angle 2.13010 ( 189) link_ALPHA1-6 : bond 0.00966 ( 2) link_ALPHA1-6 : angle 1.27398 ( 6) link_BETA1-4 : bond 0.00306 ( 24) link_BETA1-4 : angle 1.53833 ( 72) link_ALPHA1-3 : bond 0.00834 ( 5) link_ALPHA1-3 : angle 1.62304 ( 15) hydrogen bonds : bond 0.04036 ( 555) hydrogen bonds : angle 4.60499 ( 1455) link_BETA1-6 : bond 0.00375 ( 7) link_BETA1-6 : angle 1.78370 ( 21) SS BOND : bond 0.00267 ( 40) SS BOND : angle 0.77345 ( 80) covalent geometry : bond 0.00426 (22033) covalent geometry : angle 0.59158 (29920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6319.03 seconds wall clock time: 111 minutes 8.11 seconds (6668.11 seconds total)