Starting phenix.real_space_refine on Fri Jun 27 18:10:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtk_32789/06_2025/7wtk_32789.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtk_32789/06_2025/7wtk_32789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtk_32789/06_2025/7wtk_32789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtk_32789/06_2025/7wtk_32789.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtk_32789/06_2025/7wtk_32789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtk_32789/06_2025/7wtk_32789.cif" } resolution = 3.6 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= -0.001 sd= 0.078 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 135 5.16 5 C 20282 2.51 5 N 5239 2.21 5 O 6239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31895 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "G" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 878 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "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: 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.42, per 1000 atoms: 0.55 Number of scatterers: 31895 At special positions: 0 Unit cell: (156.22, 173.34, 241.82, 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 135 16.00 O 6239 8.00 N 5239 7.00 C 20282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 434 " distance=2.04 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 527 " distance=2.04 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 651 " distance=2.03 Simple disulfide: pdb=" SG CYS C 664 " - pdb=" SG CYS C 673 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 762 " distance=2.01 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 751 " distance=2.03 Simple disulfide: pdb=" SG CYS C1034 " - pdb=" SG CYS C1045 " distance=2.03 Simple disulfide: pdb=" SG CYS C1084 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 434 " distance=2.04 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 527 " distance=2.07 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 651 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 762 " distance=2.05 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 751 " distance=2.03 Simple disulfide: pdb=" SG CYS B1034 " - pdb=" SG CYS B1045 " distance=2.03 Simple disulfide: pdb=" SG CYS B1084 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 381 " - pdb=" SG CYS A 434 " distance=2.04 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 651 " distance=2.03 Simple disulfide: pdb=" SG CYS A 664 " - pdb=" SG CYS A 673 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 762 " distance=2.01 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 751 " distance=2.03 Simple disulfide: pdb=" SG CYS A1034 " - pdb=" SG CYS A1045 " distance=2.03 Simple disulfide: pdb=" SG CYS A1084 " - pdb=" SG CYS A1128 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " 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=8, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " 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 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A1201 " - " ASN A1160 " " NAG A1202 " - " ASN A 125 " " NAG A1203 " - " ASN A 145 " " NAG A1204 " - " ASN A 17 " " NAG A1205 " - " ASN A 61 " " NAG A1206 " - " ASN A 605 " " NAG A1207 " - " ASN A 659 " " NAG A1208 " - " ASN A 618 " " NAG A1209 " - " ASN A 711 " " NAG B1202 " - " ASN B1160 " " NAG B1203 " - " ASN B 125 " " NAG B1204 " - " ASN B 145 " " NAG B1205 " - " ASN B 17 " " NAG B1206 " - " ASN B 61 " " NAG B1207 " - " ASN B 605 " " NAG B1208 " - " ASN B 659 " " NAG B1209 " - " ASN B 618 " " NAG B1210 " - " ASN B 711 " " NAG C1201 " - " ASN C1160 " " NAG C1204 " - " ASN C 61 " " NAG C1206 " - " ASN C 605 " " NAG C1207 " - " ASN C 659 " " NAG C1208 " - " ASN C 618 " " NAG C1209 " - " ASN C 711 " " NAG D 1 " - " ASN C 719 " " NAG F 1 " - " ASN C 803 " " NAG M 1 " - " ASN C1100 " " NAG N 1 " - " ASN C1136 " " NAG Q 1 " - " ASN B 719 " " NAG S 1 " - " ASN B 803 " " NAG T 1 " - " ASN B1100 " " NAG U 1 " - " ASN B1136 " " NAG V 1 " - " ASN A 233 " " NAG W 1 " - " ASN A 719 " " NAG Y 1 " - " ASN A 803 " " NAG Z 1 " - " ASN A1100 " " NAG a 1 " - " ASN A1136 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 3.7 seconds 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 63 sheets defined 18.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.803A pdb=" N LEU C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 739 through 745 removed outlier: 3.737A pdb=" N TYR C 743 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 757 removed outlier: 3.922A pdb=" N ASN C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 756 " --> pdb=" O SER C 752 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN C 757 " --> pdb=" O ASN C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 785 removed outlier: 4.191A pdb=" N ASP C 777 " --> pdb=" O ALA C 773 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 781 " --> pdb=" O ASP C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 828 removed outlier: 3.768A pdb=" N LEU C 823 " --> pdb=" O PRO C 819 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 826 " --> pdb=" O ASP C 822 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 876 removed outlier: 3.521A pdb=" N ALA C 873 " --> pdb=" O ASP C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 892 removed outlier: 3.643A pdb=" N GLY C 891 " --> pdb=" O TRP C 888 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 892 " --> pdb=" O THR C 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 888 through 892' Processing helix chain 'C' and resid 899 through 910 removed outlier: 4.318A pdb=" N ALA C 905 " --> pdb=" O PRO C 901 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 906 " --> pdb=" O MET C 902 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN C 909 " --> pdb=" O ALA C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 3.641A pdb=" N TYR C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 941 removed outlier: 3.517A pdb=" N ALA C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 938 " --> pdb=" O GLY C 934 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 941 " --> pdb=" O GLN C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 966 removed outlier: 4.019A pdb=" N VAL C 953 " --> pdb=" O LYS C 949 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 957 " --> pdb=" O VAL C 953 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS C 966 " --> pdb=" O ASN C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 removed outlier: 3.865A pdb=" N ILE C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 978 through 983' Processing helix chain 'C' and resid 987 through 1034 removed outlier: 3.631A pdb=" N GLU C 992 " --> pdb=" O PRO C 988 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL C 993 " --> pdb=" O PRO C 989 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 996 " --> pdb=" O GLU C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 998 " --> pdb=" O GLN C 994 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C1004 " --> pdb=" O THR C1000 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C1009 " --> pdb=" O SER C1005 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C1015 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1147 removed outlier: 3.925A pdb=" N GLU C1146 " --> pdb=" O PRO C1142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1142 through 1147' Processing helix chain 'C' and resid 1147 through 1152 removed outlier: 3.549A pdb=" N LYS C1151 " --> pdb=" O LEU C1147 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C1152 " --> pdb=" O ASP C1148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1147 through 1152' Processing helix chain 'C' and resid 1152 through 1163 removed outlier: 4.221A pdb=" N LYS C1156 " --> pdb=" O GLU C1152 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR C1157 " --> pdb=" O GLU C1153 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C1158 " --> pdb=" O LEU C1154 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS C1159 " --> pdb=" O ASP C1155 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C1160 " --> pdb=" O LYS C1156 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS C1161 " --> pdb=" O TYR C1157 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C1162 " --> pdb=" O PHE C1158 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1152 through 1163' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.982A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.925A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 306 removed outlier: 3.593A pdb=" N LYS B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 removed outlier: 3.745A pdb=" N VAL B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.026A pdb=" N VAL B 369 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.637A pdb=" N LEU B 389 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN B 390 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 392 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.383A pdb=" N ARG B 410 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 removed outlier: 3.911A pdb=" N TYR B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 424' Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.809A pdb=" N TYR B 638 " --> pdb=" O TRP B 635 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 639 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 746 removed outlier: 3.530A pdb=" N ILE B 744 " --> pdb=" O CYS B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 757 removed outlier: 3.856A pdb=" N ASN B 753 " --> pdb=" O THR B 749 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU B 754 " --> pdb=" O GLU B 750 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 755 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 757 " --> pdb=" O ASN B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 779 removed outlier: 3.531A pdb=" N ASP B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 778 " --> pdb=" O VAL B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 828 removed outlier: 3.899A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 881 removed outlier: 3.513A pdb=" N SER B 877 " --> pdb=" O ALA B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 892 removed outlier: 3.575A pdb=" N ALA B 892 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 909 removed outlier: 3.691A pdb=" N MET B 904 " --> pdb=" O PHE B 900 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA B 905 " --> pdb=" O PRO B 901 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 909 " --> pdb=" O ALA B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.901A pdb=" N TYR B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 removed outlier: 3.641A pdb=" N GLY B 934 " --> pdb=" O ASN B 930 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 935 " --> pdb=" O SER B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 940 removed outlier: 3.632A pdb=" N SER B 939 " --> pdb=" O LYS B 935 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 940 " --> pdb=" O ILE B 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 935 through 940' Processing helix chain 'B' and resid 947 through 967 removed outlier: 3.666A pdb=" N VAL B 953 " --> pdb=" O LYS B 949 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 970 No H-bonds generated for 'chain 'B' and resid 968 through 970' Processing helix chain 'B' and resid 979 through 986 removed outlier: 4.156A pdb=" N PHE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1034 removed outlier: 3.747A pdb=" N GLN B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 998 " --> pdb=" O GLN B 994 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER B1032 " --> pdb=" O ALA B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1120 No H-bonds generated for 'chain 'B' and resid 1118 through 1120' Processing helix chain 'B' and resid 1143 through 1148 Processing helix chain 'B' and resid 1150 through 1158 removed outlier: 3.599A pdb=" N TYR B1157 " --> pdb=" O GLU B1153 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE B1158 " --> pdb=" O LEU B1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 407 through 410 removed outlier: 3.800A pdb=" N ARG A 410 " --> pdb=" O ASP A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.589A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 746 removed outlier: 3.928A pdb=" N ILE A 744 " --> pdb=" O CYS A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.588A pdb=" N ASN A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.715A pdb=" N GLN A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 775 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 776 " --> pdb=" O ILE A 772 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 777 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 778 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 828 removed outlier: 3.734A pdb=" N LEU A 823 " --> pdb=" O PRO A 819 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.528A pdb=" N SER A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 880 " --> pdb=" O THR A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.520A pdb=" N ALA A 892 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 910 removed outlier: 4.545A pdb=" N ALA A 905 " --> pdb=" O PRO A 901 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 908 " --> pdb=" O MET A 904 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 910 " --> pdb=" O TYR A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.577A pdb=" N TYR A 919 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 921 through 941 removed outlier: 3.538A pdb=" N ILE A 925 " --> pdb=" O ASN A 921 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 966 removed outlier: 3.529A pdb=" N ASP A 952 " --> pdb=" O GLY A 948 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 957 " --> pdb=" O VAL A 953 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 970 removed outlier: 3.577A pdb=" N SER A 970 " --> pdb=" O GLN A 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 970' Processing helix chain 'A' and resid 990 through 1033 removed outlier: 3.547A pdb=" N ARG A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A1015 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1146 Processing helix chain 'A' and resid 1147 through 1163 removed outlier: 3.837A pdb=" N LYS A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU A1152 " --> pdb=" O ASP A1148 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A1157 " --> pdb=" O GLU A1153 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A1158 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS A1161 " --> pdb=" O TYR A1157 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.807A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.882A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.368A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN C 61 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR C 271 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 266 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 226 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.781A pdb=" N ASP C 289 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.585A pdb=" N ARG C 236 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 107 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 105 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314 removed outlier: 3.747A pdb=" N THR C 601 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 358 through 360 removed outlier: 3.512A pdb=" N LYS C 358 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 399 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 360 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C 396 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 518 " --> pdb=" O ASN C 396 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL C 513 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE C 436 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 515 " --> pdb=" O CYS C 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 404 through 405 Processing sheet with id=AA7, first strand: chain 'C' and resid 454 through 456 Processing sheet with id=AA8, first strand: chain 'C' and resid 553 through 556 removed outlier: 3.585A pdb=" N VAL C 553 " --> pdb=" O THR C 590 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR C 590 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 645 through 646 Processing sheet with id=AB1, first strand: chain 'C' and resid 656 through 657 removed outlier: 6.146A pdb=" N GLU C 656 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR C 698 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 695 " --> pdb=" O SER C 675 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 672 " --> pdb=" O ILE C 668 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 666 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 715 through 717 Processing sheet with id=AB3, first strand: chain 'C' and resid 720 through 721 Processing sheet with id=AB4, first strand: chain 'C' and resid 724 through 730 removed outlier: 3.584A pdb=" N GLU C 727 " --> pdb=" O PHE C1064 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 737 through 738 Processing sheet with id=AB6, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 3.785A pdb=" N VAL C1096 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1083 through 1084 removed outlier: 3.564A pdb=" N CYS C1084 " --> pdb=" O VAL C1135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1088 through 1092 removed outlier: 4.599A pdb=" N ALA C1089 " --> pdb=" O SER C1125 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C1125 " --> pdb=" O ALA C1089 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AC1, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.998A pdb=" N SER H 59 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.707A pdb=" N SER L 64 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 45 through 49 removed outlier: 4.305A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP L 36 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA L 91 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL L 102 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.961A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR B 63 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 269 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.879A pdb=" N ASP B 289 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'B' and resid 90 through 96 removed outlier: 3.937A pdb=" N GLU B 188 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 226 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.696A pdb=" N GLU B 132 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 313 through 321 removed outlier: 5.410A pdb=" N ILE B 314 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR B 601 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN B 316 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 599 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER B 318 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 597 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 596 " --> pdb=" O GLN B 615 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 645 " --> pdb=" O LEU B 652 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AD3, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.606A pdb=" N ASN B 336 " --> pdb=" O VAL B 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 356 through 360 removed outlier: 4.221A pdb=" N ASN B 356 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 401 " --> pdb=" O ASN B 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 358 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 360 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 397 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP B 400 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AD6, first strand: chain 'B' and resid 553 through 556 removed outlier: 3.548A pdb=" N THR B 590 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 588 " --> pdb=" O THR B 555 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 656 through 657 removed outlier: 6.129A pdb=" N GLU B 656 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR B 698 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 673 " --> pdb=" O TYR B 697 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 713 through 717 removed outlier: 4.052A pdb=" N VAL B1096 " --> pdb=" O THR B1107 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR B1107 " --> pdb=" O VAL B1096 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 720 through 730 removed outlier: 3.515A pdb=" N GLU B 727 " --> pdb=" O PHE B1064 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B1067 " --> pdb=" O LEU B1051 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 720 through 730 removed outlier: 3.515A pdb=" N GLU B 727 " --> pdb=" O PHE B1064 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1122 through 1127 removed outlier: 4.703A pdb=" N ALA B1089 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B1084 " --> pdb=" O VAL B1135 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.817A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASN A 61 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A 271 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 266 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.838A pdb=" N ASP A 289 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.806A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 313 through 316 removed outlier: 3.953A pdb=" N THR A 601 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 652 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 645 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 356 through 359 removed outlier: 4.260A pdb=" N ASN A 356 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 401 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 511 " --> pdb=" O TRP A 438 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 438 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 454 through 456 Processing sheet with id=AF1, first strand: chain 'A' and resid 475 through 476 Processing sheet with id=AF2, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AF3, first strand: chain 'A' and resid 656 through 657 removed outlier: 5.794A pdb=" N GLU A 656 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N THR A 698 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 693 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 677 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 695 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA A 674 " --> pdb=" O PRO A 667 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 715 through 717 removed outlier: 3.530A pdb=" N LYS A1075 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 720 through 721 Processing sheet with id=AF6, first strand: chain 'A' and resid 724 through 730 removed outlier: 3.798A pdb=" N GLU A 727 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AF8, first strand: chain 'A' and resid 1083 through 1084 removed outlier: 3.630A pdb=" N CYS A1084 " --> pdb=" O VAL A1135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AG1, first strand: chain 'G' and resid 18 through 23 removed outlier: 3.724A pdb=" N CYS G 22 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 57 through 60 removed outlier: 3.629A pdb=" N ILE G 50 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.968A pdb=" N CYS I 22 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 45 through 51 removed outlier: 6.177A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AG6, first strand: chain 'J' and resid 46 through 47 removed outlier: 3.864A pdb=" N LYS J 46 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN J 38 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 46 through 47 removed outlier: 3.864A pdb=" N LYS J 46 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN J 38 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR J 87 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR J 107 " --> pdb=" O TYR J 87 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG9, first strand: chain 'K' and resid 34 through 39 removed outlier: 3.820A pdb=" N ASP K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2121 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: 12.28 Time building geometry restraints manager: 9.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5666 1.33 - 1.45: 9394 1.45 - 1.58: 17426 1.58 - 1.71: 0 1.71 - 1.84: 171 Bond restraints: 32657 Sorted by residual: bond pdb=" C PHE A 761 " pdb=" O PHE A 761 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.22e-02 6.72e+03 2.70e+01 bond pdb=" C ALA C 374 " pdb=" N PRO C 375 " ideal model delta sigma weight residual 1.337 1.387 -0.051 9.80e-03 1.04e+04 2.66e+01 bond pdb=" N VAL C 329 " pdb=" CA VAL C 329 " ideal model delta sigma weight residual 1.457 1.513 -0.056 1.15e-02 7.56e+03 2.39e+01 bond pdb=" C1 NAG A1205 " pdb=" O5 NAG A1205 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C1 NAG B1207 " pdb=" O5 NAG B1207 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 32652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 43504 2.94 - 5.88: 817 5.88 - 8.81: 93 8.81 - 11.75: 20 11.75 - 14.69: 24 Bond angle restraints: 44458 Sorted by residual: angle pdb=" CA PRO B 988 " pdb=" N PRO B 988 " pdb=" CD PRO B 988 " ideal model delta sigma weight residual 112.00 99.16 12.84 1.40e+00 5.10e-01 8.41e+01 angle pdb=" CA PRO B 944 " pdb=" N PRO B 944 " pdb=" CD PRO B 944 " ideal model delta sigma weight residual 112.00 99.25 12.75 1.40e+00 5.10e-01 8.29e+01 angle pdb=" CA PRO A 988 " pdb=" N PRO A 988 " pdb=" CD PRO A 988 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.25e+01 angle pdb=" CA PRO C 944 " pdb=" N PRO C 944 " pdb=" CD PRO C 944 " ideal model delta sigma weight residual 112.00 99.33 12.67 1.40e+00 5.10e-01 8.19e+01 angle pdb=" CA PRO A 944 " pdb=" N PRO A 944 " pdb=" CD PRO A 944 " ideal model delta sigma weight residual 112.00 99.35 12.65 1.40e+00 5.10e-01 8.17e+01 ... (remaining 44453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.62: 19044 26.62 - 53.23: 998 53.23 - 79.85: 161 79.85 - 106.47: 82 106.47 - 133.09: 22 Dihedral angle restraints: 20307 sinusoidal: 8781 harmonic: 11526 Sorted by residual: dihedral pdb=" CA ASN C 333 " pdb=" C ASN C 333 " pdb=" N ILE C 334 " pdb=" CA ILE C 334 " ideal model delta harmonic sigma weight residual 180.00 46.91 133.09 0 5.00e+00 4.00e-02 7.08e+02 dihedral pdb=" C ASN B 145 " pdb=" N ASN B 145 " pdb=" CA ASN B 145 " pdb=" CB ASN B 145 " ideal model delta harmonic sigma weight residual -122.60 -145.49 22.89 0 2.50e+00 1.60e-01 8.39e+01 dihedral pdb=" CB CYS C 664 " pdb=" SG CYS C 664 " pdb=" SG CYS C 673 " pdb=" CB CYS C 673 " ideal model delta sinusoidal sigma weight residual -86.00 -6.92 -79.08 1 1.00e+01 1.00e-02 7.78e+01 ... (remaining 20304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 5037 0.158 - 0.317: 104 0.317 - 0.475: 19 0.475 - 0.633: 3 0.633 - 0.792: 2 Chirality restraints: 5165 Sorted by residual: chirality pdb=" CA ASN B 145 " pdb=" N ASN B 145 " pdb=" C ASN B 145 " pdb=" CB ASN B 145 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA ASN B 146 " pdb=" N ASN B 146 " pdb=" C ASN B 146 " pdb=" CB ASN B 146 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 145 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -3.02 0.62 2.00e-01 2.50e+01 9.68e+00 ... (remaining 5162 not shown) Planarity restraints: 5690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 900 " 0.099 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO A 901 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO A 901 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 901 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 900 " -0.096 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO C 901 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO C 901 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 901 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 893 " 0.095 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO B 894 " -0.229 5.00e-02 4.00e+02 pdb=" CA PRO B 894 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 894 " 0.068 5.00e-02 4.00e+02 ... (remaining 5687 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 44 2.37 - 3.00: 16304 3.00 - 3.63: 44263 3.63 - 4.27: 66183 4.27 - 4.90: 109782 Nonbonded interactions: 236576 Sorted by model distance: nonbonded pdb=" OG SER A 818 " pdb=" CD PRO A 819 " model vdw 1.732 3.440 nonbonded pdb=" OG1 THR A 943 " pdb=" CD PRO A 944 " model vdw 1.739 3.440 nonbonded pdb=" OG SER C 818 " pdb=" CD PRO C 819 " model vdw 1.805 3.440 nonbonded pdb=" O GLN B 806 " pdb=" CD PRO B 819 " model vdw 1.934 3.440 nonbonded pdb=" OD1 ASP A 987 " pdb=" CD PRO A 988 " model vdw 1.977 3.440 ... (remaining 236571 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 'B' and (resid 14 through 1164 or resid 1201 through 1209)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 'N' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 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: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 67.820 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.190 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.117 32771 Z= 0.339 Angle : 1.031 15.575 44731 Z= 0.602 Chirality : 0.066 0.792 5165 Planarity : 0.009 0.138 5653 Dihedral : 17.393 133.086 12780 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.01 % Favored : 91.53 % Rotamer: Outliers : 1.20 % Allowed : 1.37 % Favored : 97.43 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % 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: -2.94 (0.12), residues: 3933 helix: -3.24 (0.14), residues: 607 sheet: -0.36 (0.18), residues: 878 loop : -2.33 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 111 HIS 0.005 0.001 HIS H 35 PHE 0.050 0.002 PHE C 340 TYR 0.046 0.001 TYR C 28 ARG 0.009 0.000 ARG A 468 Details of bonding type rmsd link_NAG-ASN : bond 0.02123 ( 37) link_NAG-ASN : angle 4.38308 ( 111) link_BETA1-4 : bond 0.00660 ( 24) link_BETA1-4 : angle 1.54078 ( 72) hydrogen bonds : bond 0.25464 ( 780) hydrogen bonds : angle 8.95210 ( 2121) SS BOND : bond 0.00806 ( 45) SS BOND : angle 1.95666 ( 90) covalent geometry : bond 0.00559 (32657) covalent geometry : angle 1.00466 (44458) Misc. bond : bond 0.00927 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 3.603 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: H 50 ILE cc_start: 0.6259 (tp) cc_final: 0.5992 (tp) REVERT: B 144 LYS cc_start: 0.5221 (OUTLIER) cc_final: 0.4731 (mmmt) REVERT: B 153 GLU cc_start: 0.1280 (OUTLIER) cc_final: 0.0596 (pm20) REVERT: B 450 ASN cc_start: 0.7766 (m-40) cc_final: 0.7305 (p0) REVERT: A 155 ARG cc_start: 0.6681 (mmp80) cc_final: 0.6412 (ttp80) REVERT: A 174 MET cc_start: 0.2213 (mpp) cc_final: 0.1888 (mpp) REVERT: I 48 MET cc_start: 0.6529 (ppp) cc_final: 0.6165 (ppp) REVERT: J 87 TYR cc_start: 0.7745 (m-80) cc_final: 0.7453 (m-10) outliers start: 41 outliers final: 20 residues processed: 238 average time/residue: 0.4569 time to fit residues: 180.0967 Evaluate side-chains 179 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 149 TRP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 PRO Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain K residue 94 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 199 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 354 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 566 GLN C 582 GLN C1090 HIS H 35 HIS L 32 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN B 903 GLN A 957 ASN G 65 GLN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.155471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.112730 restraints weight = 76970.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.109429 restraints weight = 57783.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.109537 restraints weight = 54895.849| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32771 Z= 0.128 Angle : 0.673 12.082 44731 Z= 0.332 Chirality : 0.047 0.428 5165 Planarity : 0.005 0.070 5653 Dihedral : 13.775 114.799 5779 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 0.93 % Allowed : 7.79 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % 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: -2.23 (0.13), residues: 3933 helix: -1.30 (0.19), residues: 629 sheet: -0.32 (0.17), residues: 930 loop : -2.12 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 36 HIS 0.003 0.001 HIS C1066 PHE 0.021 0.001 PHE A 431 TYR 0.017 0.001 TYR B1069 ARG 0.005 0.000 ARG L 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 37) link_NAG-ASN : angle 3.05907 ( 111) link_BETA1-4 : bond 0.00686 ( 24) link_BETA1-4 : angle 1.80286 ( 72) hydrogen bonds : bond 0.05427 ( 780) hydrogen bonds : angle 6.10363 ( 2121) SS BOND : bond 0.00218 ( 45) SS BOND : angle 1.26132 ( 90) covalent geometry : bond 0.00276 (32657) covalent geometry : angle 0.65118 (44458) Misc. bond : bond 0.00335 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 234 ILE cc_start: 0.8041 (mm) cc_final: 0.7750 (tt) REVERT: C 340 PHE cc_start: 0.4615 (m-80) cc_final: 0.4345 (m-80) REVERT: C 976 SER cc_start: 0.8418 (t) cc_final: 0.7966 (m) REVERT: B 144 LYS cc_start: 0.4707 (OUTLIER) cc_final: 0.4310 (mmmm) REVERT: B 450 ASN cc_start: 0.7749 (m-40) cc_final: 0.7260 (p0) REVERT: B 758 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7446 (t80) REVERT: A 155 ARG cc_start: 0.6799 (mmp80) cc_final: 0.6555 (ttp80) REVERT: A 573 ASP cc_start: 0.7202 (m-30) cc_final: 0.6926 (m-30) REVERT: J 87 TYR cc_start: 0.7830 (m-80) cc_final: 0.7439 (m-10) REVERT: J 88 TYR cc_start: 0.7567 (m-10) cc_final: 0.7206 (m-10) REVERT: K 36 TRP cc_start: -0.0338 (m-90) cc_final: -0.0625 (m-90) outliers start: 32 outliers final: 23 residues processed: 212 average time/residue: 0.4219 time to fit residues: 148.4991 Evaluate side-chains 188 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 332 PRO Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain J residue 59 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 167 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 149 optimal weight: 0.0000 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 307 optimal weight: 0.5980 chunk 185 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 377 optimal weight: 30.0000 overall best weight: 1.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.152616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.106196 restraints weight = 77117.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102758 restraints weight = 54236.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103510 restraints weight = 54651.585| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32771 Z= 0.130 Angle : 0.648 11.550 44731 Z= 0.312 Chirality : 0.046 0.414 5165 Planarity : 0.004 0.060 5653 Dihedral : 11.067 108.563 5765 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.02 % Favored : 92.91 % Rotamer: Outliers : 1.28 % Allowed : 11.24 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.03 % 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: -2.00 (0.13), residues: 3933 helix: -0.51 (0.21), residues: 628 sheet: -0.27 (0.18), residues: 901 loop : -2.08 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP H 107 HIS 0.005 0.001 HIS C1066 PHE 0.018 0.001 PHE C 106 TYR 0.019 0.001 TYR B1069 ARG 0.005 0.000 ARG L 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 37) link_NAG-ASN : angle 2.87148 ( 111) link_BETA1-4 : bond 0.00569 ( 24) link_BETA1-4 : angle 1.87440 ( 72) hydrogen bonds : bond 0.04480 ( 780) hydrogen bonds : angle 5.54736 ( 2121) SS BOND : bond 0.00218 ( 45) SS BOND : angle 1.07666 ( 90) covalent geometry : bond 0.00304 (32657) covalent geometry : angle 0.62707 (44458) Misc. bond : bond 0.00371 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 3.244 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: C 234 ILE cc_start: 0.8160 (mm) cc_final: 0.7863 (tt) REVERT: C 455 TYR cc_start: 0.4691 (p90) cc_final: 0.4227 (p90) REVERT: C 976 SER cc_start: 0.8452 (t) cc_final: 0.8054 (m) REVERT: B 144 LYS cc_start: 0.4551 (OUTLIER) cc_final: 0.4161 (mmmm) REVERT: B 150 MET cc_start: 0.6056 (mmm) cc_final: 0.5346 (tpt) REVERT: B 450 ASN cc_start: 0.7925 (m-40) cc_final: 0.7372 (p0) REVERT: B 758 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7633 (t80) REVERT: A 155 ARG cc_start: 0.6770 (mmp80) cc_final: 0.6511 (ttp80) REVERT: A 427 LEU cc_start: 0.6886 (mp) cc_final: 0.6189 (pt) REVERT: A 573 ASP cc_start: 0.7578 (m-30) cc_final: 0.7363 (m-30) REVERT: J 63 PHE cc_start: 0.7724 (m-10) cc_final: 0.7518 (m-10) REVERT: J 87 TYR cc_start: 0.7957 (m-80) cc_final: 0.7580 (m-10) outliers start: 44 outliers final: 26 residues processed: 207 average time/residue: 0.4515 time to fit residues: 155.6812 Evaluate side-chains 187 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain J residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.0020 chunk 351 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 284 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 GLN B 962 ASN ** J 32 ASN ** 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 = 0.4416 r_free = 0.4416 target = 0.153360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.107032 restraints weight = 77412.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104741 restraints weight = 53173.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104737 restraints weight = 53816.707| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32771 Z= 0.106 Angle : 0.611 11.323 44731 Z= 0.294 Chirality : 0.045 0.408 5165 Planarity : 0.004 0.056 5653 Dihedral : 9.715 108.451 5755 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer: Outliers : 1.52 % Allowed : 13.31 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.80 (0.13), residues: 3933 helix: -0.08 (0.22), residues: 627 sheet: -0.17 (0.18), residues: 894 loop : -2.01 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 36 HIS 0.006 0.001 HIS C 507 PHE 0.019 0.001 PHE B 183 TYR 0.016 0.001 TYR B1069 ARG 0.004 0.000 ARG B 985 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 37) link_NAG-ASN : angle 2.75535 ( 111) link_BETA1-4 : bond 0.00569 ( 24) link_BETA1-4 : angle 1.86420 ( 72) hydrogen bonds : bond 0.03767 ( 780) hydrogen bonds : angle 5.28022 ( 2121) SS BOND : bond 0.00226 ( 45) SS BOND : angle 1.16870 ( 90) covalent geometry : bond 0.00242 (32657) covalent geometry : angle 0.59041 (44458) Misc. bond : bond 0.00380 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.5641 (OUTLIER) cc_final: 0.4138 (p90) REVERT: C 234 ILE cc_start: 0.8154 (mm) cc_final: 0.7799 (tt) REVERT: C 333 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6500 (p0) REVERT: C 976 SER cc_start: 0.8343 (t) cc_final: 0.8050 (m) REVERT: C 1019 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 144 LYS cc_start: 0.4650 (OUTLIER) cc_final: 0.4135 (mttt) REVERT: B 150 MET cc_start: 0.6194 (mmm) cc_final: 0.5508 (tpt) REVERT: B 450 ASN cc_start: 0.7926 (m-40) cc_final: 0.7380 (p0) REVERT: B 758 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.7643 (t80) REVERT: A 155 ARG cc_start: 0.6778 (mmp80) cc_final: 0.6530 (ttp80) REVERT: A 427 LEU cc_start: 0.6892 (mp) cc_final: 0.6282 (pt) REVERT: I 48 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.5983 (tmm) REVERT: J 87 TYR cc_start: 0.8047 (m-80) cc_final: 0.7697 (m-10) outliers start: 52 outliers final: 29 residues processed: 214 average time/residue: 0.4064 time to fit residues: 146.4316 Evaluate side-chains 202 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain J residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 40.0000 chunk 46 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 416 GLN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 GLN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN A 930 ASN ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** 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 = 0.4396 r_free = 0.4396 target = 0.151135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108244 restraints weight = 76537.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.103537 restraints weight = 63265.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103850 restraints weight = 60439.647| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 32771 Z= 0.249 Angle : 0.725 11.072 44731 Z= 0.355 Chirality : 0.049 0.444 5165 Planarity : 0.005 0.057 5653 Dihedral : 9.466 108.518 5753 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.72 % Favored : 91.15 % Rotamer: Outliers : 2.04 % Allowed : 14.65 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.00 (0.13), residues: 3933 helix: -0.31 (0.21), residues: 620 sheet: -0.35 (0.18), residues: 868 loop : -2.08 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 36 HIS 0.010 0.001 HIS C1066 PHE 0.039 0.002 PHE C 106 TYR 0.026 0.002 TYR B1069 ARG 0.005 0.000 ARG G 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 37) link_NAG-ASN : angle 3.04450 ( 111) link_BETA1-4 : bond 0.00522 ( 24) link_BETA1-4 : angle 1.82893 ( 72) hydrogen bonds : bond 0.05035 ( 780) hydrogen bonds : angle 5.54903 ( 2121) SS BOND : bond 0.00476 ( 45) SS BOND : angle 1.42369 ( 90) covalent geometry : bond 0.00613 (32657) covalent geometry : angle 0.70396 (44458) Misc. bond : bond 0.00351 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 159 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.5144 (p90) REVERT: C 117 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6712 (tt) REVERT: C 333 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6295 (p0) REVERT: C 578 VAL cc_start: -0.2881 (OUTLIER) cc_final: -0.3140 (t) REVERT: C 976 SER cc_start: 0.8678 (t) cc_final: 0.8177 (m) REVERT: B 144 LYS cc_start: 0.4606 (OUTLIER) cc_final: 0.4390 (mttt) REVERT: B 150 MET cc_start: 0.6087 (mmm) cc_final: 0.4854 (tpt) REVERT: B 758 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.7546 (t80) REVERT: A 155 ARG cc_start: 0.6702 (mmp80) cc_final: 0.6426 (ttp80) REVERT: A 427 LEU cc_start: 0.6786 (mp) cc_final: 0.6168 (pt) REVERT: I 48 MET cc_start: 0.6253 (tmm) cc_final: 0.5965 (tmm) outliers start: 70 outliers final: 43 residues processed: 219 average time/residue: 0.3832 time to fit residues: 143.0304 Evaluate side-chains 201 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 911 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 76 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 348 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 chunk 310 optimal weight: 0.1980 chunk 379 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 311 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** J 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** 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 = 0.4426 r_free = 0.4426 target = 0.157197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3849 r_free = 0.3849 target = 0.111969 restraints weight = 79129.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.107312 restraints weight = 61563.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107520 restraints weight = 54019.975| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32771 Z= 0.110 Angle : 0.620 11.202 44731 Z= 0.300 Chirality : 0.046 0.408 5165 Planarity : 0.004 0.049 5653 Dihedral : 8.706 104.391 5750 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 1.84 % Allowed : 15.76 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.74 (0.13), residues: 3933 helix: 0.11 (0.22), residues: 617 sheet: -0.12 (0.18), residues: 888 loop : -2.01 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 438 HIS 0.003 0.001 HIS A1050 PHE 0.023 0.001 PHE C 379 TYR 0.015 0.001 TYR B1069 ARG 0.005 0.000 ARG B 985 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 37) link_NAG-ASN : angle 2.78672 ( 111) link_BETA1-4 : bond 0.00532 ( 24) link_BETA1-4 : angle 1.80089 ( 72) hydrogen bonds : bond 0.03747 ( 780) hydrogen bonds : angle 5.20403 ( 2121) SS BOND : bond 0.00284 ( 45) SS BOND : angle 1.10282 ( 90) covalent geometry : bond 0.00250 (32657) covalent geometry : angle 0.60004 (44458) Misc. bond : bond 0.00382 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.4600 (p90) REVERT: C 333 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6478 (p0) REVERT: C 455 TYR cc_start: 0.6281 (p90) cc_final: 0.4991 (p90) REVERT: C 976 SER cc_start: 0.8570 (t) cc_final: 0.8187 (m) REVERT: B 144 LYS cc_start: 0.4457 (OUTLIER) cc_final: 0.4032 (mttt) REVERT: B 150 MET cc_start: 0.6181 (mmm) cc_final: 0.5486 (tpt) REVERT: B 758 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.7576 (t80) REVERT: B 875 TYR cc_start: 0.8552 (m-80) cc_final: 0.8245 (m-80) REVERT: A 155 ARG cc_start: 0.6716 (mmp80) cc_final: 0.6436 (ttp80) REVERT: A 174 MET cc_start: 0.0325 (mmt) cc_final: 0.0039 (mmt) REVERT: A 427 LEU cc_start: 0.6751 (mp) cc_final: 0.6202 (pt) REVERT: A 985 ARG cc_start: 0.8309 (ptt180) cc_final: 0.8109 (ptt90) REVERT: A 1035 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7706 (p) REVERT: J 87 TYR cc_start: 0.7633 (m-80) cc_final: 0.7341 (m-10) outliers start: 63 outliers final: 39 residues processed: 220 average time/residue: 0.4008 time to fit residues: 149.5725 Evaluate side-chains 202 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 770 THR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 330 optimal weight: 9.9990 chunk 198 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 372 optimal weight: 20.0000 chunk 311 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN ** J 52 ASN ** 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 = 0.4425 r_free = 0.4425 target = 0.153219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108771 restraints weight = 76606.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105579 restraints weight = 55614.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105981 restraints weight = 48709.341| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32771 Z= 0.129 Angle : 0.627 10.868 44731 Z= 0.303 Chirality : 0.046 0.415 5165 Planarity : 0.004 0.047 5653 Dihedral : 8.269 100.242 5750 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.53 % Favored : 92.42 % Rotamer: Outliers : 1.75 % Allowed : 16.46 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.72 (0.13), residues: 3933 helix: 0.19 (0.22), residues: 619 sheet: -0.19 (0.18), residues: 862 loop : -1.96 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 36 HIS 0.004 0.001 HIS C1066 PHE 0.024 0.001 PHE C 340 TYR 0.017 0.001 TYR B1069 ARG 0.004 0.000 ARG C 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 37) link_NAG-ASN : angle 2.79557 ( 111) link_BETA1-4 : bond 0.00512 ( 24) link_BETA1-4 : angle 1.86073 ( 72) hydrogen bonds : bond 0.03804 ( 780) hydrogen bonds : angle 5.12678 ( 2121) SS BOND : bond 0.00308 ( 45) SS BOND : angle 1.14250 ( 90) covalent geometry : bond 0.00308 (32657) covalent geometry : angle 0.60625 (44458) Misc. bond : bond 0.00376 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.4616 (p90) REVERT: C 333 ASN cc_start: 0.7107 (OUTLIER) cc_final: 0.6510 (p0) REVERT: C 455 TYR cc_start: 0.6293 (p90) cc_final: 0.5025 (p90) REVERT: C 976 SER cc_start: 0.8569 (t) cc_final: 0.8176 (m) REVERT: B 150 MET cc_start: 0.6195 (mmm) cc_final: 0.4965 (tpt) REVERT: B 758 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 875 TYR cc_start: 0.8584 (m-80) cc_final: 0.8222 (m-80) REVERT: A 155 ARG cc_start: 0.6697 (mmp80) cc_final: 0.6420 (ttp80) REVERT: A 427 LEU cc_start: 0.6662 (mp) cc_final: 0.6174 (pt) REVERT: A 985 ARG cc_start: 0.8336 (ptt180) cc_final: 0.8118 (ptt90) REVERT: A 1035 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7844 (p) REVERT: J 87 TYR cc_start: 0.7756 (m-80) cc_final: 0.7460 (m-10) outliers start: 60 outliers final: 49 residues processed: 210 average time/residue: 0.4318 time to fit residues: 155.6507 Evaluate side-chains 207 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain J residue 59 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 128 optimal weight: 30.0000 chunk 318 optimal weight: 0.0000 chunk 204 optimal weight: 3.9990 chunk 82 optimal weight: 0.0470 chunk 293 optimal weight: 0.9980 chunk 320 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 227 optimal weight: 0.3980 chunk 230 optimal weight: 0.7980 chunk 217 optimal weight: 0.0000 overall best weight: 0.2486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 ASN B 143 HIS ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN ** J 52 ASN ** 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 = 0.4449 r_free = 0.4449 target = 0.154960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.111772 restraints weight = 77287.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.108775 restraints weight = 54289.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109058 restraints weight = 49695.586| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 32771 Z= 0.098 Angle : 0.602 11.073 44731 Z= 0.290 Chirality : 0.045 0.402 5165 Planarity : 0.004 0.047 5653 Dihedral : 7.595 92.461 5745 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 1.43 % Allowed : 16.81 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.54 (0.13), residues: 3933 helix: 0.50 (0.22), residues: 628 sheet: -0.07 (0.18), residues: 858 loop : -1.91 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 36 HIS 0.003 0.000 HIS A1050 PHE 0.027 0.001 PHE C 340 TYR 0.022 0.001 TYR A 367 ARG 0.007 0.000 ARG B 985 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 37) link_NAG-ASN : angle 2.67076 ( 111) link_BETA1-4 : bond 0.00530 ( 24) link_BETA1-4 : angle 1.91268 ( 72) hydrogen bonds : bond 0.03123 ( 780) hydrogen bonds : angle 4.89172 ( 2121) SS BOND : bond 0.00227 ( 45) SS BOND : angle 0.91346 ( 90) covalent geometry : bond 0.00219 (32657) covalent geometry : angle 0.58203 (44458) Misc. bond : bond 0.00378 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.5712 (OUTLIER) cc_final: 0.4301 (p90) REVERT: C 117 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6951 (tt) REVERT: C 333 ASN cc_start: 0.6720 (OUTLIER) cc_final: 0.6150 (p0) REVERT: C 455 TYR cc_start: 0.6225 (p90) cc_final: 0.5020 (p90) REVERT: C 904 MET cc_start: 0.9053 (tpt) cc_final: 0.8847 (tpt) REVERT: C 976 SER cc_start: 0.8442 (t) cc_final: 0.8134 (m) REVERT: B 150 MET cc_start: 0.5924 (mmm) cc_final: 0.4837 (tmm) REVERT: B 758 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7611 (t80) REVERT: B 875 TYR cc_start: 0.8557 (m-80) cc_final: 0.8245 (m-80) REVERT: A 155 ARG cc_start: 0.6694 (mmp80) cc_final: 0.6467 (ttp80) REVERT: A 427 LEU cc_start: 0.6583 (mp) cc_final: 0.6180 (pt) REVERT: A 983 PHE cc_start: 0.8228 (m-80) cc_final: 0.8025 (m-80) REVERT: J 87 TYR cc_start: 0.7542 (m-80) cc_final: 0.7255 (m-10) outliers start: 49 outliers final: 33 residues processed: 211 average time/residue: 0.4227 time to fit residues: 151.4123 Evaluate side-chains 196 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1141 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 76 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 14 optimal weight: 0.7980 chunk 357 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 364 optimal weight: 0.9980 chunk 290 optimal weight: 0.3980 chunk 374 optimal weight: 9.9990 chunk 368 optimal weight: 30.0000 chunk 349 optimal weight: 20.0000 chunk 174 optimal weight: 0.0000 chunk 213 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.153959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.110450 restraints weight = 76909.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.106699 restraints weight = 58635.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106970 restraints weight = 54348.417| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32771 Z= 0.120 Angle : 0.622 10.881 44731 Z= 0.298 Chirality : 0.045 0.413 5165 Planarity : 0.004 0.048 5653 Dihedral : 7.322 86.971 5745 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.88 % Rotamer: Outliers : 1.49 % Allowed : 17.10 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.53 (0.13), residues: 3933 helix: 0.50 (0.22), residues: 627 sheet: -0.07 (0.18), residues: 863 loop : -1.90 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 36 HIS 0.003 0.001 HIS C1066 PHE 0.017 0.001 PHE C 65 TYR 0.023 0.001 TYR A 367 ARG 0.003 0.000 ARG G 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 37) link_NAG-ASN : angle 2.72732 ( 111) link_BETA1-4 : bond 0.00494 ( 24) link_BETA1-4 : angle 1.96210 ( 72) hydrogen bonds : bond 0.03462 ( 780) hydrogen bonds : angle 4.92456 ( 2121) SS BOND : bond 0.00240 ( 45) SS BOND : angle 1.37819 ( 90) covalent geometry : bond 0.00287 (32657) covalent geometry : angle 0.60016 (44458) Misc. bond : bond 0.00361 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.4603 (p90) REVERT: C 117 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6982 (tt) REVERT: C 333 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.6125 (p0) REVERT: C 455 TYR cc_start: 0.6261 (p90) cc_final: 0.5044 (p90) REVERT: C 904 MET cc_start: 0.9120 (tpt) cc_final: 0.8823 (tpt) REVERT: C 976 SER cc_start: 0.8494 (t) cc_final: 0.8156 (m) REVERT: B 52 GLN cc_start: 0.7583 (tp40) cc_final: 0.7379 (tp40) REVERT: B 149 TRP cc_start: 0.2794 (OUTLIER) cc_final: 0.2264 (t60) REVERT: B 150 MET cc_start: 0.5959 (mmm) cc_final: 0.5242 (tmm) REVERT: B 758 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 875 TYR cc_start: 0.8600 (m-80) cc_final: 0.8254 (m-80) REVERT: A 155 ARG cc_start: 0.6685 (mmp80) cc_final: 0.6437 (ttp80) REVERT: A 427 LEU cc_start: 0.6583 (mp) cc_final: 0.6218 (pt) REVERT: A 983 PHE cc_start: 0.8241 (m-80) cc_final: 0.8032 (m-80) REVERT: I 48 MET cc_start: 0.6038 (tmm) cc_final: 0.5788 (tmm) REVERT: J 87 TYR cc_start: 0.7722 (m-80) cc_final: 0.7460 (m-10) outliers start: 51 outliers final: 41 residues processed: 201 average time/residue: 0.4159 time to fit residues: 141.8035 Evaluate side-chains 204 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 279 optimal weight: 10.0000 chunk 230 optimal weight: 0.0870 chunk 253 optimal weight: 0.6980 chunk 376 optimal weight: 10.0000 chunk 379 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 806 GLN B 238 GLN A 238 GLN A 424 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 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 = 0.4368 r_free = 0.4368 target = 0.149760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.103012 restraints weight = 76947.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.100156 restraints weight = 54312.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100540 restraints weight = 48821.377| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 32771 Z= 0.196 Angle : 0.688 10.628 44731 Z= 0.335 Chirality : 0.048 0.436 5165 Planarity : 0.004 0.050 5653 Dihedral : 7.345 81.628 5745 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.85 % Favored : 91.08 % Rotamer: Outliers : 1.66 % Allowed : 16.96 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.73 (0.13), residues: 3933 helix: 0.16 (0.22), residues: 627 sheet: -0.20 (0.18), residues: 852 loop : -1.97 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 36 HIS 0.008 0.001 HIS C1066 PHE 0.030 0.002 PHE C 106 TYR 0.023 0.001 TYR B1069 ARG 0.009 0.000 ARG B 985 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 37) link_NAG-ASN : angle 2.93598 ( 111) link_BETA1-4 : bond 0.00434 ( 24) link_BETA1-4 : angle 2.04186 ( 72) hydrogen bonds : bond 0.04452 ( 780) hydrogen bonds : angle 5.27066 ( 2121) SS BOND : bond 0.00338 ( 45) SS BOND : angle 1.60508 ( 90) covalent geometry : bond 0.00478 (32657) covalent geometry : angle 0.66523 (44458) Misc. bond : bond 0.00352 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7866 Ramachandran restraints generated. 3933 Oldfield, 0 Emsley, 3933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 106 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.5444 (p90) REVERT: C 117 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6969 (tt) REVERT: C 234 ILE cc_start: 0.8384 (mm) cc_final: 0.8081 (tt) REVERT: C 333 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6224 (p0) REVERT: C 976 SER cc_start: 0.8729 (t) cc_final: 0.8215 (m) REVERT: L 36 TRP cc_start: 0.1526 (t-100) cc_final: 0.1057 (m100) REVERT: B 150 MET cc_start: 0.5924 (mmm) cc_final: 0.5087 (tmm) REVERT: B 758 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7625 (t80) REVERT: B 875 TYR cc_start: 0.8678 (m-80) cc_final: 0.8311 (m-80) REVERT: A 155 ARG cc_start: 0.6711 (mmp80) cc_final: 0.6417 (ttp80) REVERT: A 427 LEU cc_start: 0.6639 (mp) cc_final: 0.6246 (pt) REVERT: A 983 PHE cc_start: 0.8343 (m-80) cc_final: 0.8127 (m-80) REVERT: I 48 MET cc_start: 0.6107 (tmm) cc_final: 0.5833 (tmm) outliers start: 57 outliers final: 47 residues processed: 206 average time/residue: 0.4063 time to fit residues: 140.6293 Evaluate side-chains 204 residues out of total 3447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 517 PHE Chi-restraints excluded: chain C residue 592 CYS Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 940 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 149 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain J residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 323 optimal weight: 0.7980 chunk 345 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.0020 chunk 339 optimal weight: 0.9980 chunk 124 optimal weight: 40.0000 chunk 273 optimal weight: 9.9990 chunk 336 optimal weight: 0.8980 chunk 383 optimal weight: 20.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 424 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.153461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.109550 restraints weight = 76675.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105919 restraints weight = 57033.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.106656 restraints weight = 50629.977| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32771 Z= 0.112 Angle : 0.635 12.166 44731 Z= 0.305 Chirality : 0.046 0.534 5165 Planarity : 0.004 0.068 5653 Dihedral : 6.990 82.654 5745 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.76 % Favored : 93.16 % Rotamer: Outliers : 1.28 % Allowed : 17.69 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.55 (0.13), residues: 3933 helix: 0.45 (0.22), residues: 627 sheet: -0.05 (0.18), residues: 838 loop : -1.89 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 36 HIS 0.005 0.001 HIS A1050 PHE 0.020 0.001 PHE H 108 TYR 0.019 0.001 TYR A 367 ARG 0.009 0.000 ARG B 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 37) link_NAG-ASN : angle 2.74562 ( 111) link_BETA1-4 : bond 0.00461 ( 24) link_BETA1-4 : angle 2.00397 ( 72) hydrogen bonds : bond 0.03493 ( 780) hydrogen bonds : angle 4.97584 ( 2121) SS BOND : bond 0.00243 ( 45) SS BOND : angle 1.33093 ( 90) covalent geometry : bond 0.00258 (32657) covalent geometry : angle 0.61357 (44458) Misc. bond : bond 0.00828 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11293.89 seconds wall clock time: 200 minutes 43.47 seconds (12043.47 seconds total)