Starting phenix.real_space_refine on Wed Jun 18 03:44:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7txd_26157/06_2025/7txd_26157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7txd_26157/06_2025/7txd_26157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7txd_26157/06_2025/7txd_26157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7txd_26157/06_2025/7txd_26157.map" model { file = "/net/cci-nas-00/data/ceres_data/7txd_26157/06_2025/7txd_26157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7txd_26157/06_2025/7txd_26157.cif" } resolution = 3.87 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= 0.004 sd= 0.032 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 105 5.16 5 C 12854 2.51 5 N 3463 2.21 5 O 4133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 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: 20555 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1004 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "D" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 900 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "I" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "J" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "K" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "M" 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: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: "R" 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: "S" 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "Z" 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: "a" 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: "b" 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: "c" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "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: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 15.44, per 1000 atoms: 0.75 Number of scatterers: 20555 At special positions: 0 Unit cell: (126.26, 188.32, 185.11, 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 105 16.00 O 4133 8.00 N 3463 7.00 C 12854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.07 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 130 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 130 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.03 Simple disulfide: pdb=" SG CYS I 130 " - pdb=" SG CYS I 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA V 3 " - " MAN V 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 7 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 332 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 462 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG C 601 " - " ASN C 355 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 88 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 301 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG D 703 " - " ASN D 618 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 332 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 339 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 625 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 448 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 355 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 448 " " NAG e 1 " - " ASN E 276 " " NAG f 1 " - " ASN E 363 " " NAG g 1 " - " ASN E 392 " " NAG h 1 " - " ASN F 611 " Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 3.2 seconds 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 35 sheets defined 31.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 100 through 116 removed outlier: 4.557A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.687A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 520 removed outlier: 4.047A pdb=" N LEU B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 removed outlier: 3.853A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.502A pdb=" N THR B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 4.088A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.295A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.952A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.868A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.597A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.639A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.717A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 594 removed outlier: 3.714A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.164A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.529A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 655 Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.732A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 removed outlier: 3.513A pdb=" N ILE E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.650A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 483 removed outlier: 3.654A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 523 removed outlier: 3.835A pdb=" N LEU F 523 " --> pdb=" O PHE F 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 519 through 523' Processing helix chain 'F' and resid 529 through 542 removed outlier: 3.852A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 596 Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.612A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.670A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 657 removed outlier: 3.663A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.569A pdb=" N LEU G 61 " --> pdb=" O ARG G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 removed outlier: 3.550A pdb=" N SER G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'H' and resid 58 through 62 removed outlier: 3.602A pdb=" N TRP H 62 " --> pdb=" O ARG H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 removed outlier: 3.556A pdb=" N ASP H 78 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER H 79 " --> pdb=" O ILE H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 75 through 79' Processing helix chain 'H' and resid 150 through 154 removed outlier: 3.510A pdb=" N SER H 154 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.698A pdb=" N LEU I 61 " --> pdb=" O ARG I 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP I 62 " --> pdb=" O ARG I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 62' Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.511A pdb=" N SER I 154 " --> pdb=" O LEU I 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 Processing helix chain 'J' and resid 49 through 60 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.849A pdb=" N LEU J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 105 through 113 removed outlier: 3.575A pdb=" N LYS J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 125 Processing helix chain 'J' and resid 138 through 146 Processing helix chain 'J' and resid 148 through 161 removed outlier: 3.761A pdb=" N ALA J 152 " --> pdb=" O ASN J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 47 removed outlier: 3.748A pdb=" N LEU K 43 " --> pdb=" O THR K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 3.797A pdb=" N VAL K 53 " --> pdb=" O HIS K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.634A pdb=" N LEU K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 92 removed outlier: 3.524A pdb=" N VAL K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 113 removed outlier: 4.094A pdb=" N LYS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 126 Processing helix chain 'K' and resid 138 through 146 Processing helix chain 'K' and resid 148 through 161 removed outlier: 3.589A pdb=" N ALA K 152 " --> pdb=" O ASN K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 Processing helix chain 'L' and resid 49 through 60 removed outlier: 3.567A pdb=" N VAL L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 80 removed outlier: 3.596A pdb=" N LEU L 76 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET L 80 " --> pdb=" O LEU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 removed outlier: 3.716A pdb=" N VAL L 86 " --> pdb=" O HIS L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 113 removed outlier: 3.533A pdb=" N LEU L 109 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS L 113 " --> pdb=" O LEU L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 125 Processing helix chain 'L' and resid 138 through 146 Processing helix chain 'L' and resid 148 through 161 removed outlier: 3.506A pdb=" N ALA L 152 " --> pdb=" O ASN L 148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL L 154 " --> pdb=" O ASP L 150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU L 161 " --> pdb=" O LYS L 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.091A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.733A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.567A pdb=" N THR C 37 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.862A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.004A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 196 through 202 removed outlier: 3.590A pdb=" N LEU C 125 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 424 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.508A pdb=" N GLN C 287 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 260 removed outlier: 4.407A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.638A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.194A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.885A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 196 through 202 Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 260 removed outlier: 3.727A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 413 through 417 removed outlier: 4.293A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 366 through 367 removed outlier: 3.670A pdb=" N GLY E 366 " --> pdb=" O LYS I 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AC6, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.236A pdb=" N LYS G 2 " --> pdb=" O GLU G 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP G 28 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN G 40 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 43 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 12 through 14 removed outlier: 3.637A pdb=" N VAL G 12 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 71 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.346A pdb=" N GLN G 112 " --> pdb=" O GLN G 148 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN G 148 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 131 Processing sheet with id=AD1, first strand: chain 'H' and resid 2 through 5 removed outlier: 4.213A pdb=" N LYS H 2 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS H 29 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP H 28 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN H 40 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE H 43 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD3, first strand: chain 'H' and resid 99 through 102 removed outlier: 3.511A pdb=" N GLY H 99 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN H 112 " --> pdb=" O GLN H 148 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN H 148 " --> pdb=" O GLN H 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 138 through 139 Processing sheet with id=AD5, first strand: chain 'I' and resid 2 through 6 removed outlier: 4.057A pdb=" N LYS I 2 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS I 29 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP I 28 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD7, first strand: chain 'I' and resid 99 through 102 Processing sheet with id=AD8, first strand: chain 'I' and resid 138 through 139 724 hydrogen bonds defined for protein. 1977 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: 12.80 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 6568 1.35 - 1.50: 5501 1.50 - 1.65: 8710 1.65 - 1.80: 44 1.80 - 1.94: 94 Bond restraints: 20917 Sorted by residual: bond pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " ideal model delta sigma weight residual 1.808 1.945 -0.137 3.30e-02 9.18e+02 1.72e+01 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C3 BMA V 3 " pdb=" O3 BMA V 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" N LYS A 502 " pdb=" CA LYS A 502 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.705 0.103 3.30e-02 9.18e+02 9.76e+00 ... (remaining 20912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.57: 28156 4.57 - 9.14: 205 9.14 - 13.71: 17 13.71 - 18.28: 1 18.28 - 22.85: 1 Bond angle restraints: 28380 Sorted by residual: angle pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 114.40 137.25 -22.85 2.30e+00 1.89e-01 9.87e+01 angle pdb=" CA ASN C 99 " pdb=" CB ASN C 99 " pdb=" CG ASN C 99 " ideal model delta sigma weight residual 112.60 106.74 5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" N CYS A 296 " pdb=" CA CYS A 296 " pdb=" C CYS A 296 " ideal model delta sigma weight residual 108.99 118.12 -9.13 1.57e+00 4.06e-01 3.38e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 127.48 -13.08 2.30e+00 1.89e-01 3.24e+01 angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 113.18 106.84 6.34 1.21e+00 6.83e-01 2.75e+01 ... (remaining 28375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.91: 12874 21.91 - 43.83: 733 43.83 - 65.74: 98 65.74 - 87.65: 99 87.65 - 109.57: 47 Dihedral angle restraints: 13851 sinusoidal: 6737 harmonic: 7114 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -168.98 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.11 -73.11 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 165.00 -72.00 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 13848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3058 0.090 - 0.180: 426 0.180 - 0.269: 39 0.269 - 0.359: 13 0.359 - 0.449: 5 Chirality restraints: 3541 Sorted by residual: chirality pdb=" CB ILE F 603 " pdb=" CA ILE F 603 " pdb=" CG1 ILE F 603 " pdb=" CG2 ILE F 603 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.44e+00 chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 392 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 3538 not shown) Planarity restraints: 3551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 1 " -0.261 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" C7 NAG h 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG h 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG h 1 " 0.381 2.00e-02 2.50e+03 pdb=" O7 NAG h 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.167 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG F 703 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.224 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.096 2.00e-02 2.50e+03 7.97e-02 7.94e+01 pdb=" C7 NAG h 2 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.127 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 3548 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5118 2.81 - 3.33: 17730 3.33 - 3.85: 32834 3.85 - 4.38: 35559 4.38 - 4.90: 62132 Nonbonded interactions: 153373 Sorted by model distance: nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.287 3.040 nonbonded pdb=" OG SER A 365 " pdb=" O LYS G 46 " model vdw 2.301 3.040 nonbonded pdb=" OD2 ASP C 107 " pdb=" OH TYR C 217 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O CYS B 604 " model vdw 2.309 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.311 3.040 ... (remaining 153368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 33 through 504 or resid 601 through 606)) selection = (chain 'E' and (resid 33 through 504 or resid 601 through 606)) } ncs_group { reference = (chain 'B' and ((resid 522 through 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 542 or resid 564 through 655 or resid 701 t \ hrough 703)) selection = chain 'D' selection = (chain 'F' and ((resid 522 through 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 542 or resid 564 through 655 or resid 701 t \ hrough 703)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'b' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'h' } 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: 187.490 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: 0.040 Extract box with map and model: 7.830 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 57.260 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.260 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:4.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.006 0.137 21048 Z= 0.313 Angle : 1.098 22.845 28737 Z= 0.548 Chirality : 0.062 0.449 3541 Planarity : 0.008 0.222 3499 Dihedral : 16.168 109.566 9133 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.15), residues: 2441 helix: -1.69 (0.17), residues: 682 sheet: -0.32 (0.24), residues: 475 loop : -1.74 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 112 HIS 0.014 0.001 HIS C 66 PHE 0.028 0.002 PHE H 26 TYR 0.020 0.002 TYR E 435 ARG 0.026 0.001 ARG H 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 52) link_NAG-ASN : angle 3.44349 ( 156) link_ALPHA1-6 : bond 0.00450 ( 3) link_ALPHA1-6 : angle 1.41923 ( 9) link_BETA1-4 : bond 0.00847 ( 33) link_BETA1-4 : angle 2.57942 ( 99) link_ALPHA1-2 : bond 0.00215 ( 4) link_ALPHA1-2 : angle 2.51570 ( 12) link_ALPHA1-3 : bond 0.00791 ( 3) link_ALPHA1-3 : angle 2.97069 ( 9) hydrogen bonds : bond 0.17028 ( 720) hydrogen bonds : angle 7.24077 ( 1977) SS BOND : bond 0.00730 ( 36) SS BOND : angle 2.03772 ( 72) covalent geometry : bond 0.00595 (20917) covalent geometry : angle 1.05594 (28380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8409 (p90) cc_final: 0.6375 (m-10) REVERT: A 236 THR cc_start: 0.7999 (p) cc_final: 0.7716 (p) REVERT: A 321 ASP cc_start: 0.8286 (m-30) cc_final: 0.8021 (m-30) REVERT: A 426 MET cc_start: 0.7525 (mtm) cc_final: 0.7185 (mtm) REVERT: B 529 THR cc_start: 0.8008 (m) cc_final: 0.7578 (p) REVERT: B 589 ASP cc_start: 0.8668 (t0) cc_final: 0.8030 (t0) REVERT: D 621 GLU cc_start: 0.8313 (pm20) cc_final: 0.8069 (pm20) REVERT: F 591 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8153 (tm-30) REVERT: F 599 SER cc_start: 0.7961 (p) cc_final: 0.7751 (p) REVERT: F 647 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7666 (tm-30) REVERT: G 91 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6533 (tm-30) REVERT: G 95 LEU cc_start: 0.8793 (tp) cc_final: 0.8484 (tp) REVERT: H 91 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6441 (tm-30) REVERT: I 70 ILE cc_start: 0.8662 (mm) cc_final: 0.8434 (mt) REVERT: I 169 GLU cc_start: 0.9126 (pt0) cc_final: 0.8736 (mp0) REVERT: J 54 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8119 (pt0) REVERT: J 66 ARG cc_start: 0.7293 (mpt180) cc_final: 0.6644 (tpp80) REVERT: K 105 THR cc_start: 0.7696 (p) cc_final: 0.7071 (p) REVERT: K 108 HIS cc_start: 0.7117 (m90) cc_final: 0.6605 (t70) REVERT: K 150 ASP cc_start: 0.8340 (t0) cc_final: 0.7994 (m-30) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3244 time to fit residues: 188.2663 Evaluate side-chains 255 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN B 590 GLN C 114 GLN C 197 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.110834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078959 restraints weight = 52617.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079289 restraints weight = 34790.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080571 restraints weight = 24902.189| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 21048 Z= 0.314 Angle : 0.859 11.730 28737 Z= 0.415 Chirality : 0.051 0.321 3541 Planarity : 0.005 0.051 3499 Dihedral : 11.595 84.663 4544 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.87 % Allowed : 11.01 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2441 helix: -0.40 (0.19), residues: 705 sheet: -0.58 (0.22), residues: 512 loop : -1.52 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 112 HIS 0.009 0.002 HIS C 374 PHE 0.024 0.002 PHE C 376 TYR 0.032 0.003 TYR E 384 ARG 0.012 0.001 ARG H 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 52) link_NAG-ASN : angle 2.97027 ( 156) link_ALPHA1-6 : bond 0.00420 ( 3) link_ALPHA1-6 : angle 2.38107 ( 9) link_BETA1-4 : bond 0.00462 ( 33) link_BETA1-4 : angle 2.63755 ( 99) link_ALPHA1-2 : bond 0.00313 ( 4) link_ALPHA1-2 : angle 2.38704 ( 12) link_ALPHA1-3 : bond 0.00754 ( 3) link_ALPHA1-3 : angle 2.90330 ( 9) hydrogen bonds : bond 0.05102 ( 720) hydrogen bonds : angle 5.90720 ( 1977) SS BOND : bond 0.00531 ( 36) SS BOND : angle 1.68750 ( 72) covalent geometry : bond 0.00692 (20917) covalent geometry : angle 0.81284 (28380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8861 (p90) cc_final: 0.6675 (m-10) REVERT: A 368 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8510 (t70) REVERT: A 446 VAL cc_start: 0.8734 (t) cc_final: 0.8453 (p) REVERT: A 492 GLU cc_start: 0.8235 (tt0) cc_final: 0.7881 (tt0) REVERT: B 589 ASP cc_start: 0.9202 (t0) cc_final: 0.8615 (t0) REVERT: B 651 ASN cc_start: 0.8979 (t0) cc_final: 0.8776 (t0) REVERT: C 66 HIS cc_start: 0.7502 (t70) cc_final: 0.7121 (t70) REVERT: C 479 TRP cc_start: 0.8455 (m-10) cc_final: 0.7961 (m-90) REVERT: D 530 MET cc_start: 0.6388 (mmt) cc_final: 0.5873 (mmt) REVERT: D 652 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: F 591 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8490 (tm-30) REVERT: F 647 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8391 (tm-30) REVERT: G 78 ASP cc_start: 0.8546 (m-30) cc_final: 0.8329 (m-30) REVERT: G 95 LEU cc_start: 0.8978 (tp) cc_final: 0.8543 (tp) REVERT: H 26 PHE cc_start: 0.8897 (p90) cc_final: 0.8607 (p90) REVERT: H 96 LEU cc_start: 0.8787 (tt) cc_final: 0.8305 (mm) REVERT: J 54 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8254 (pt0) REVERT: J 66 ARG cc_start: 0.7274 (mpt180) cc_final: 0.6656 (tpp80) REVERT: J 84 GLU cc_start: 0.8912 (mp0) cc_final: 0.8703 (mp0) REVERT: L 84 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7588 (mm-30) REVERT: L 156 GLN cc_start: 0.8527 (pp30) cc_final: 0.8229 (pp30) outliers start: 40 outliers final: 25 residues processed: 286 average time/residue: 0.2946 time to fit residues: 134.1273 Evaluate side-chains 244 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 74 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 148 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN J 49 HIS J 125 HIS K 97 ASN ** K 108 HIS ** 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 = 0.3931 r_free = 0.3931 target = 0.114369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.082959 restraints weight = 52538.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.083637 restraints weight = 32938.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.084609 restraints weight = 23797.048| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21048 Z= 0.139 Angle : 0.664 12.111 28737 Z= 0.313 Chirality : 0.046 0.309 3541 Planarity : 0.004 0.059 3499 Dihedral : 9.912 78.322 4544 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.40 % Allowed : 13.99 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2441 helix: 0.29 (0.20), residues: 700 sheet: -0.46 (0.22), residues: 503 loop : -1.35 (0.16), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 112 HIS 0.009 0.001 HIS K 108 PHE 0.025 0.001 PHE L 135 TYR 0.012 0.001 TYR E 40 ARG 0.009 0.000 ARG H 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 52) link_NAG-ASN : angle 2.70163 ( 156) link_ALPHA1-6 : bond 0.00569 ( 3) link_ALPHA1-6 : angle 1.92883 ( 9) link_BETA1-4 : bond 0.00503 ( 33) link_BETA1-4 : angle 2.30881 ( 99) link_ALPHA1-2 : bond 0.00177 ( 4) link_ALPHA1-2 : angle 2.15418 ( 12) link_ALPHA1-3 : bond 0.01138 ( 3) link_ALPHA1-3 : angle 2.68372 ( 9) hydrogen bonds : bond 0.03905 ( 720) hydrogen bonds : angle 5.39856 ( 1977) SS BOND : bond 0.00522 ( 36) SS BOND : angle 1.34489 ( 72) covalent geometry : bond 0.00307 (20917) covalent geometry : angle 0.61460 (28380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 2.161 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 61 TYR cc_start: 0.8829 (p90) cc_final: 0.6665 (m-10) REVERT: A 104 MET cc_start: 0.8761 (tpt) cc_final: 0.8552 (tpt) REVERT: A 446 VAL cc_start: 0.8678 (t) cc_final: 0.8422 (p) REVERT: B 589 ASP cc_start: 0.9235 (t0) cc_final: 0.8674 (t0) REVERT: C 479 TRP cc_start: 0.8379 (m-10) cc_final: 0.7768 (m-90) REVERT: D 530 MET cc_start: 0.6190 (mmt) cc_final: 0.5599 (mmt) REVERT: D 621 GLU cc_start: 0.8351 (pm20) cc_final: 0.7939 (pm20) REVERT: D 648 GLU cc_start: 0.8097 (pp20) cc_final: 0.7734 (pp20) REVERT: E 295 ASN cc_start: 0.6933 (m-40) cc_final: 0.6511 (m-40) REVERT: F 647 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8148 (tm-30) REVERT: G 78 ASP cc_start: 0.8470 (m-30) cc_final: 0.8201 (m-30) REVERT: H 96 LEU cc_start: 0.8843 (tt) cc_final: 0.8403 (mm) REVERT: I 88 ASP cc_start: 0.8507 (p0) cc_final: 0.8099 (p0) REVERT: J 54 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8176 (pt0) REVERT: J 66 ARG cc_start: 0.7236 (mpt180) cc_final: 0.6608 (tpp80) REVERT: J 155 LEU cc_start: 0.8971 (mm) cc_final: 0.8586 (tt) REVERT: L 87 GLU cc_start: 0.8743 (pp20) cc_final: 0.8500 (pp20) REVERT: L 91 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8427 (mmtm) REVERT: L 134 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7388 (pttm) outliers start: 30 outliers final: 20 residues processed: 281 average time/residue: 0.2868 time to fit residues: 130.5922 Evaluate side-chains 250 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 134 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 109 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 164 optimal weight: 0.0060 chunk 233 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 591 GLN ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.114011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082533 restraints weight = 52857.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.084026 restraints weight = 30692.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.084718 restraints weight = 22391.996| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 21048 Z= 0.119 Angle : 0.641 12.802 28737 Z= 0.299 Chirality : 0.045 0.301 3541 Planarity : 0.003 0.042 3499 Dihedral : 8.711 70.434 4544 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.63 % Allowed : 15.67 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2441 helix: 0.63 (0.20), residues: 703 sheet: -0.37 (0.23), residues: 503 loop : -1.27 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 112 HIS 0.005 0.001 HIS C 374 PHE 0.026 0.001 PHE L 135 TYR 0.014 0.001 TYR E 40 ARG 0.006 0.000 ARG H 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 52) link_NAG-ASN : angle 2.64926 ( 156) link_ALPHA1-6 : bond 0.00741 ( 3) link_ALPHA1-6 : angle 1.92080 ( 9) link_BETA1-4 : bond 0.00475 ( 33) link_BETA1-4 : angle 2.15970 ( 99) link_ALPHA1-2 : bond 0.00199 ( 4) link_ALPHA1-2 : angle 2.02201 ( 12) link_ALPHA1-3 : bond 0.00930 ( 3) link_ALPHA1-3 : angle 2.55794 ( 9) hydrogen bonds : bond 0.03479 ( 720) hydrogen bonds : angle 5.13525 ( 1977) SS BOND : bond 0.00382 ( 36) SS BOND : angle 1.41938 ( 72) covalent geometry : bond 0.00266 (20917) covalent geometry : angle 0.59275 (28380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8788 (p90) cc_final: 0.6602 (m-10) REVERT: A 102 GLU cc_start: 0.8535 (tp30) cc_final: 0.8133 (tp30) REVERT: A 321 ASP cc_start: 0.8301 (m-30) cc_final: 0.7981 (m-30) REVERT: A 446 VAL cc_start: 0.8665 (t) cc_final: 0.8399 (p) REVERT: B 589 ASP cc_start: 0.9236 (t0) cc_final: 0.8617 (t0) REVERT: C 479 TRP cc_start: 0.8312 (m-10) cc_final: 0.7791 (m-90) REVERT: D 530 MET cc_start: 0.5775 (mmt) cc_final: 0.5196 (mmt) REVERT: D 648 GLU cc_start: 0.8130 (pp20) cc_final: 0.7764 (pp20) REVERT: H 62 TRP cc_start: 0.8096 (m-10) cc_final: 0.7661 (m-10) REVERT: H 96 LEU cc_start: 0.8822 (tt) cc_final: 0.8444 (mm) REVERT: I 172 ILE cc_start: 0.7888 (mm) cc_final: 0.7579 (mt) REVERT: J 54 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8216 (pt0) REVERT: J 66 ARG cc_start: 0.7183 (mpt180) cc_final: 0.6609 (mmm-85) REVERT: J 155 LEU cc_start: 0.8875 (mm) cc_final: 0.8655 (tt) REVERT: L 91 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8473 (mmtm) outliers start: 35 outliers final: 21 residues processed: 284 average time/residue: 0.2936 time to fit residues: 134.2158 Evaluate side-chains 251 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 230 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN G 164 ASN ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 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 = 0.3902 r_free = 0.3902 target = 0.111997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081054 restraints weight = 53198.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.081715 restraints weight = 32948.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083093 restraints weight = 23826.125| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21048 Z= 0.177 Angle : 0.668 11.031 28737 Z= 0.316 Chirality : 0.045 0.304 3541 Planarity : 0.004 0.044 3499 Dihedral : 8.179 62.839 4544 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.10 % Allowed : 16.32 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2441 helix: 0.79 (0.20), residues: 710 sheet: -0.41 (0.24), residues: 461 loop : -1.27 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 571 HIS 0.016 0.001 HIS K 42 PHE 0.035 0.002 PHE H 26 TYR 0.016 0.002 TYR E 40 ARG 0.006 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 52) link_NAG-ASN : angle 2.72210 ( 156) link_ALPHA1-6 : bond 0.00777 ( 3) link_ALPHA1-6 : angle 1.95765 ( 9) link_BETA1-4 : bond 0.00439 ( 33) link_BETA1-4 : angle 2.09464 ( 99) link_ALPHA1-2 : bond 0.00193 ( 4) link_ALPHA1-2 : angle 1.94239 ( 12) link_ALPHA1-3 : bond 0.00860 ( 3) link_ALPHA1-3 : angle 2.76739 ( 9) hydrogen bonds : bond 0.03650 ( 720) hydrogen bonds : angle 5.12158 ( 1977) SS BOND : bond 0.00400 ( 36) SS BOND : angle 1.47821 ( 72) covalent geometry : bond 0.00395 (20917) covalent geometry : angle 0.62065 (28380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 2.455 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 61 TYR cc_start: 0.8742 (p90) cc_final: 0.6575 (m-10) REVERT: A 446 VAL cc_start: 0.8697 (t) cc_final: 0.8390 (p) REVERT: B 589 ASP cc_start: 0.9254 (t0) cc_final: 0.8623 (t0) REVERT: C 479 TRP cc_start: 0.8313 (m-10) cc_final: 0.7790 (m-90) REVERT: D 626 MET cc_start: 0.6038 (ttt) cc_final: 0.5591 (ttt) REVERT: D 648 GLU cc_start: 0.8092 (pp20) cc_final: 0.7761 (pp20) REVERT: I 169 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: I 172 ILE cc_start: 0.7860 (mm) cc_final: 0.7555 (mt) REVERT: J 66 ARG cc_start: 0.7232 (mpt180) cc_final: 0.6561 (tpp80) REVERT: J 155 LEU cc_start: 0.8897 (mm) cc_final: 0.8534 (tt) REVERT: K 50 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8551 (mt) REVERT: L 156 GLN cc_start: 0.8310 (pp30) cc_final: 0.8043 (pp30) outliers start: 45 outliers final: 36 residues processed: 268 average time/residue: 0.2990 time to fit residues: 128.5824 Evaluate side-chains 255 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 136 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 238 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** 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 = 0.3915 r_free = 0.3915 target = 0.113262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081293 restraints weight = 52854.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083498 restraints weight = 30983.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084307 restraints weight = 20497.585| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21048 Z= 0.143 Angle : 0.649 12.471 28737 Z= 0.305 Chirality : 0.045 0.299 3541 Planarity : 0.003 0.045 3499 Dihedral : 7.840 59.588 4544 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.33 % Allowed : 16.79 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2441 helix: 0.97 (0.20), residues: 704 sheet: -0.37 (0.24), residues: 469 loop : -1.20 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 571 HIS 0.005 0.001 HIS A 374 PHE 0.034 0.001 PHE H 26 TYR 0.013 0.001 TYR E 40 ARG 0.007 0.000 ARG I 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 52) link_NAG-ASN : angle 2.70730 ( 156) link_ALPHA1-6 : bond 0.00906 ( 3) link_ALPHA1-6 : angle 1.76805 ( 9) link_BETA1-4 : bond 0.00452 ( 33) link_BETA1-4 : angle 1.97412 ( 99) link_ALPHA1-2 : bond 0.00173 ( 4) link_ALPHA1-2 : angle 1.91889 ( 12) link_ALPHA1-3 : bond 0.00878 ( 3) link_ALPHA1-3 : angle 2.60391 ( 9) hydrogen bonds : bond 0.03478 ( 720) hydrogen bonds : angle 5.02145 ( 1977) SS BOND : bond 0.00357 ( 36) SS BOND : angle 1.31808 ( 72) covalent geometry : bond 0.00321 (20917) covalent geometry : angle 0.60341 (28380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 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: symmetry clash REVERT: A 61 TYR cc_start: 0.8744 (p90) cc_final: 0.6557 (m-10) REVERT: A 446 VAL cc_start: 0.8679 (t) cc_final: 0.8399 (p) REVERT: B 589 ASP cc_start: 0.9280 (t0) cc_final: 0.8630 (t0) REVERT: C 479 TRP cc_start: 0.8318 (m-10) cc_final: 0.7788 (m-90) REVERT: D 530 MET cc_start: 0.5870 (mmt) cc_final: 0.5616 (mmt) REVERT: D 626 MET cc_start: 0.6119 (ttt) cc_final: 0.5620 (ttt) REVERT: D 648 GLU cc_start: 0.8073 (pp20) cc_final: 0.7778 (pp20) REVERT: E 92 GLU cc_start: 0.7939 (tp30) cc_final: 0.7669 (tp30) REVERT: G 85 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: G 91 GLU cc_start: 0.6682 (tm-30) cc_final: 0.6108 (tm-30) REVERT: H 96 LEU cc_start: 0.8660 (tt) cc_final: 0.8276 (mm) REVERT: I 169 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8348 (tm-30) REVERT: I 172 ILE cc_start: 0.8002 (mm) cc_final: 0.7598 (mt) REVERT: J 66 ARG cc_start: 0.7236 (mpt180) cc_final: 0.6619 (tpp80) REVERT: J 155 LEU cc_start: 0.8916 (mm) cc_final: 0.8565 (tp) outliers start: 50 outliers final: 37 residues processed: 275 average time/residue: 0.2954 time to fit residues: 130.0336 Evaluate side-chains 263 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 153 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 215 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 chunk 169 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN G 164 ASN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** 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 = 0.3898 r_free = 0.3898 target = 0.111685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079596 restraints weight = 52702.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081613 restraints weight = 31276.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082317 restraints weight = 20894.817| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21048 Z= 0.157 Angle : 0.657 12.379 28737 Z= 0.310 Chirality : 0.045 0.297 3541 Planarity : 0.004 0.043 3499 Dihedral : 7.585 59.903 4544 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.94 % Allowed : 16.93 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2441 helix: 1.03 (0.20), residues: 704 sheet: -0.38 (0.24), residues: 469 loop : -1.15 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 571 HIS 0.006 0.001 HIS A 374 PHE 0.035 0.002 PHE H 26 TYR 0.015 0.001 TYR E 40 ARG 0.008 0.000 ARG I 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 52) link_NAG-ASN : angle 2.66469 ( 156) link_ALPHA1-6 : bond 0.01033 ( 3) link_ALPHA1-6 : angle 1.50024 ( 9) link_BETA1-4 : bond 0.00444 ( 33) link_BETA1-4 : angle 1.91870 ( 99) link_ALPHA1-2 : bond 0.00157 ( 4) link_ALPHA1-2 : angle 1.89713 ( 12) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 2.56268 ( 9) hydrogen bonds : bond 0.03475 ( 720) hydrogen bonds : angle 4.97872 ( 1977) SS BOND : bond 0.00369 ( 36) SS BOND : angle 1.26984 ( 72) covalent geometry : bond 0.00351 (20917) covalent geometry : angle 0.61344 (28380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8762 (p90) cc_final: 0.6596 (m-10) REVERT: A 446 VAL cc_start: 0.8697 (t) cc_final: 0.8402 (p) REVERT: B 589 ASP cc_start: 0.9294 (t0) cc_final: 0.8592 (t0) REVERT: C 479 TRP cc_start: 0.8300 (m-10) cc_final: 0.7728 (m-90) REVERT: D 530 MET cc_start: 0.6221 (mmt) cc_final: 0.5850 (mmt) REVERT: D 626 MET cc_start: 0.6144 (ttt) cc_final: 0.5645 (ttt) REVERT: D 648 GLU cc_start: 0.8052 (pp20) cc_final: 0.7767 (pp20) REVERT: E 92 GLU cc_start: 0.7975 (tp30) cc_final: 0.7690 (tp30) REVERT: G 85 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: H 96 LEU cc_start: 0.8751 (tt) cc_final: 0.8382 (mm) REVERT: I 169 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: J 66 ARG cc_start: 0.7246 (mpt180) cc_final: 0.6658 (tpp80) REVERT: J 155 LEU cc_start: 0.8983 (mm) cc_final: 0.8644 (tp) REVERT: L 156 GLN cc_start: 0.8574 (pp30) cc_final: 0.8373 (pp30) outliers start: 63 outliers final: 49 residues processed: 280 average time/residue: 0.2816 time to fit residues: 127.7310 Evaluate side-chains 280 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 153 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 18 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN I 52 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** 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 = 0.3880 r_free = 0.3880 target = 0.110626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.079632 restraints weight = 53281.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080585 restraints weight = 32468.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081200 restraints weight = 24427.910| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21048 Z= 0.197 Angle : 0.700 11.947 28737 Z= 0.332 Chirality : 0.046 0.299 3541 Planarity : 0.004 0.044 3499 Dihedral : 7.566 59.725 4544 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.31 % Allowed : 16.98 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2441 helix: 1.07 (0.20), residues: 699 sheet: -0.48 (0.23), residues: 494 loop : -1.15 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 157 HIS 0.007 0.001 HIS L 82 PHE 0.034 0.002 PHE H 26 TYR 0.019 0.002 TYR E 40 ARG 0.009 0.000 ARG I 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 52) link_NAG-ASN : angle 2.75972 ( 156) link_ALPHA1-6 : bond 0.01126 ( 3) link_ALPHA1-6 : angle 1.14942 ( 9) link_BETA1-4 : bond 0.00450 ( 33) link_BETA1-4 : angle 1.92646 ( 99) link_ALPHA1-2 : bond 0.00182 ( 4) link_ALPHA1-2 : angle 1.89080 ( 12) link_ALPHA1-3 : bond 0.00974 ( 3) link_ALPHA1-3 : angle 2.56193 ( 9) hydrogen bonds : bond 0.03692 ( 720) hydrogen bonds : angle 5.08655 ( 1977) SS BOND : bond 0.00485 ( 36) SS BOND : angle 1.49924 ( 72) covalent geometry : bond 0.00441 (20917) covalent geometry : angle 0.65692 (28380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 240 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8793 (p90) cc_final: 0.6633 (m-10) REVERT: A 446 VAL cc_start: 0.8724 (t) cc_final: 0.8440 (p) REVERT: B 530 MET cc_start: 0.8419 (tpp) cc_final: 0.7990 (mtp) REVERT: B 589 ASP cc_start: 0.9288 (t0) cc_final: 0.8595 (t0) REVERT: C 95 MET cc_start: 0.8572 (ppp) cc_final: 0.8346 (ppp) REVERT: C 426 MET cc_start: 0.8371 (ptm) cc_final: 0.8112 (ptp) REVERT: C 479 TRP cc_start: 0.8334 (m-10) cc_final: 0.7688 (m-90) REVERT: D 530 MET cc_start: 0.6206 (mmt) cc_final: 0.5817 (mmt) REVERT: D 626 MET cc_start: 0.6081 (ttt) cc_final: 0.5637 (ttt) REVERT: D 648 GLU cc_start: 0.8103 (pp20) cc_final: 0.7858 (pp20) REVERT: G 85 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: H 96 LEU cc_start: 0.8860 (tt) cc_final: 0.8502 (mm) REVERT: I 169 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: J 66 ARG cc_start: 0.7413 (mpt180) cc_final: 0.6658 (tpp80) REVERT: J 125 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7021 (m-70) REVERT: J 135 PHE cc_start: 0.8309 (m-80) cc_final: 0.8003 (t80) REVERT: J 155 LEU cc_start: 0.9054 (mm) cc_final: 0.8672 (tp) REVERT: L 80 MET cc_start: 0.8381 (mtm) cc_final: 0.8090 (mtt) REVERT: L 85 ILE cc_start: 0.7706 (mm) cc_final: 0.7458 (mm) REVERT: L 91 LYS cc_start: 0.8667 (mmtm) cc_final: 0.8341 (mmtm) REVERT: L 156 GLN cc_start: 0.8645 (pp30) cc_final: 0.8276 (pp30) outliers start: 71 outliers final: 56 residues processed: 291 average time/residue: 0.2960 time to fit residues: 138.8052 Evaluate side-chains 285 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 169 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 153 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 75 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 40 GLN H 129 GLN I 52 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** 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 = 0.3911 r_free = 0.3911 target = 0.112588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080623 restraints weight = 52767.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082300 restraints weight = 31026.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.083222 restraints weight = 21345.954| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21048 Z= 0.122 Angle : 0.672 12.384 28737 Z= 0.317 Chirality : 0.045 0.351 3541 Planarity : 0.003 0.043 3499 Dihedral : 7.327 59.969 4544 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.15 % Allowed : 18.28 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2441 helix: 1.17 (0.20), residues: 704 sheet: -0.43 (0.23), residues: 518 loop : -1.07 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 157 HIS 0.007 0.001 HIS C 374 PHE 0.028 0.002 PHE H 26 TYR 0.017 0.001 TYR C 61 ARG 0.009 0.000 ARG I 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 52) link_NAG-ASN : angle 2.62351 ( 156) link_ALPHA1-6 : bond 0.01235 ( 3) link_ALPHA1-6 : angle 1.07424 ( 9) link_BETA1-4 : bond 0.00483 ( 33) link_BETA1-4 : angle 1.80941 ( 99) link_ALPHA1-2 : bond 0.00154 ( 4) link_ALPHA1-2 : angle 1.90317 ( 12) link_ALPHA1-3 : bond 0.00971 ( 3) link_ALPHA1-3 : angle 2.28549 ( 9) hydrogen bonds : bond 0.03365 ( 720) hydrogen bonds : angle 4.88964 ( 1977) SS BOND : bond 0.00400 ( 36) SS BOND : angle 1.35805 ( 72) covalent geometry : bond 0.00276 (20917) covalent geometry : angle 0.63247 (28380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8754 (p90) cc_final: 0.6590 (m-10) REVERT: A 446 VAL cc_start: 0.8658 (t) cc_final: 0.8378 (p) REVERT: B 530 MET cc_start: 0.8267 (tpp) cc_final: 0.7788 (mtp) REVERT: B 589 ASP cc_start: 0.9291 (t0) cc_final: 0.8584 (t0) REVERT: C 95 MET cc_start: 0.8561 (ppp) cc_final: 0.8308 (ppp) REVERT: C 479 TRP cc_start: 0.8300 (m-10) cc_final: 0.7671 (m-90) REVERT: D 530 MET cc_start: 0.5806 (mmt) cc_final: 0.5469 (mmt) REVERT: D 626 MET cc_start: 0.5556 (ttt) cc_final: 0.5052 (ttt) REVERT: D 648 GLU cc_start: 0.8025 (pp20) cc_final: 0.7751 (pp20) REVERT: E 377 ASN cc_start: 0.8228 (p0) cc_final: 0.7969 (p0) REVERT: F 602 LEU cc_start: 0.8628 (pt) cc_final: 0.8422 (mp) REVERT: G 85 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: I 24 ILE cc_start: 0.8486 (pt) cc_final: 0.8247 (mm) REVERT: I 169 GLU cc_start: 0.8783 (tt0) cc_final: 0.8317 (tm-30) REVERT: J 66 ARG cc_start: 0.7352 (mpt180) cc_final: 0.6627 (tpp80) REVERT: J 135 PHE cc_start: 0.8267 (m-80) cc_final: 0.8011 (t80) REVERT: J 155 LEU cc_start: 0.9057 (mm) cc_final: 0.8708 (tp) REVERT: L 80 MET cc_start: 0.8284 (mtm) cc_final: 0.7988 (mtt) REVERT: L 87 GLU cc_start: 0.8510 (pp20) cc_final: 0.8209 (pp20) REVERT: L 91 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8057 (mmtm) outliers start: 46 outliers final: 38 residues processed: 282 average time/residue: 0.2912 time to fit residues: 133.0145 Evaluate side-chains 278 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 318 TYR Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 GLN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 153 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 130 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 116 optimal weight: 0.0870 chunk 88 optimal weight: 0.5980 chunk 184 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 283 ASN D 591 GLN I 139 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.112737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081098 restraints weight = 52647.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.082413 restraints weight = 31033.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.083605 restraints weight = 21783.479| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21048 Z= 0.124 Angle : 0.679 12.297 28737 Z= 0.321 Chirality : 0.045 0.335 3541 Planarity : 0.003 0.043 3499 Dihedral : 7.166 59.822 4544 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.87 % Allowed : 18.61 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2441 helix: 1.18 (0.20), residues: 705 sheet: -0.39 (0.23), residues: 480 loop : -1.03 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 157 HIS 0.006 0.001 HIS C 374 PHE 0.033 0.001 PHE C 317 TYR 0.016 0.001 TYR C 61 ARG 0.010 0.000 ARG I 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 52) link_NAG-ASN : angle 2.56308 ( 156) link_ALPHA1-6 : bond 0.01241 ( 3) link_ALPHA1-6 : angle 1.06472 ( 9) link_BETA1-4 : bond 0.00474 ( 33) link_BETA1-4 : angle 1.77720 ( 99) link_ALPHA1-2 : bond 0.00147 ( 4) link_ALPHA1-2 : angle 1.89411 ( 12) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 2.23629 ( 9) hydrogen bonds : bond 0.03371 ( 720) hydrogen bonds : angle 4.87056 ( 1977) SS BOND : bond 0.00388 ( 36) SS BOND : angle 1.30929 ( 72) covalent geometry : bond 0.00282 (20917) covalent geometry : angle 0.64146 (28380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8730 (p90) cc_final: 0.6563 (m-10) REVERT: A 446 VAL cc_start: 0.8631 (t) cc_final: 0.8355 (p) REVERT: B 530 MET cc_start: 0.8236 (tpp) cc_final: 0.7736 (mtp) REVERT: B 589 ASP cc_start: 0.9285 (t0) cc_final: 0.8550 (t0) REVERT: C 95 MET cc_start: 0.8545 (ppp) cc_final: 0.8297 (ppp) REVERT: C 426 MET cc_start: 0.8223 (ptm) cc_final: 0.7781 (ptp) REVERT: C 479 TRP cc_start: 0.8299 (m-10) cc_final: 0.7619 (m-90) REVERT: D 626 MET cc_start: 0.5762 (ttt) cc_final: 0.5302 (ttt) REVERT: D 648 GLU cc_start: 0.8069 (pp20) cc_final: 0.7816 (pp20) REVERT: E 377 ASN cc_start: 0.8179 (p0) cc_final: 0.7813 (p0) REVERT: G 85 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: H 96 LEU cc_start: 0.8691 (tt) cc_final: 0.8341 (mp) REVERT: I 24 ILE cc_start: 0.8449 (pt) cc_final: 0.8213 (mm) REVERT: I 169 GLU cc_start: 0.8762 (tt0) cc_final: 0.8370 (tm-30) REVERT: J 66 ARG cc_start: 0.7332 (mpt180) cc_final: 0.6607 (tpp80) REVERT: J 135 PHE cc_start: 0.8261 (m-80) cc_final: 0.8020 (t80) REVERT: J 155 LEU cc_start: 0.9038 (mm) cc_final: 0.8692 (tp) REVERT: L 80 MET cc_start: 0.8256 (mtm) cc_final: 0.7960 (mtt) REVERT: L 87 GLU cc_start: 0.8534 (pp20) cc_final: 0.8271 (pp20) REVERT: L 91 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8209 (mmtm) REVERT: L 156 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8253 (pp30) outliers start: 40 outliers final: 34 residues processed: 270 average time/residue: 0.2831 time to fit residues: 124.0831 Evaluate side-chains 273 residues out of total 2150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 428 GLN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain J residue 30 VAL Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain L residue 75 HIS Chi-restraints excluded: chain L residue 153 GLU Chi-restraints excluded: chain L residue 156 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 3 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 chunk 217 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN K 97 ASN ** K 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.111081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078750 restraints weight = 52451.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080297 restraints weight = 32201.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081255 restraints weight = 22424.107| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21048 Z= 0.153 Angle : 0.682 12.010 28737 Z= 0.324 Chirality : 0.045 0.347 3541 Planarity : 0.004 0.043 3499 Dihedral : 7.108 59.877 4544 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.10 % Allowed : 18.47 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2441 helix: 1.18 (0.20), residues: 705 sheet: -0.44 (0.23), residues: 484 loop : -1.05 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 157 HIS 0.005 0.001 HIS A 374 PHE 0.036 0.002 PHE C 317 TYR 0.016 0.001 TYR C 61 ARG 0.010 0.000 ARG I 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 52) link_NAG-ASN : angle 2.55439 ( 156) link_ALPHA1-6 : bond 0.01209 ( 3) link_ALPHA1-6 : angle 1.08485 ( 9) link_BETA1-4 : bond 0.00445 ( 33) link_BETA1-4 : angle 1.79715 ( 99) link_ALPHA1-2 : bond 0.00148 ( 4) link_ALPHA1-2 : angle 1.86550 ( 12) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 2.24525 ( 9) hydrogen bonds : bond 0.03509 ( 720) hydrogen bonds : angle 4.91543 ( 1977) SS BOND : bond 0.00392 ( 36) SS BOND : angle 1.31422 ( 72) covalent geometry : bond 0.00348 (20917) covalent geometry : angle 0.64532 (28380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7233.23 seconds wall clock time: 128 minutes 12.96 seconds (7692.96 seconds total)