Starting phenix.real_space_refine on Wed May 21 12:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atz_43838/05_2025/9atz_43838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atz_43838/05_2025/9atz_43838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9atz_43838/05_2025/9atz_43838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atz_43838/05_2025/9atz_43838.map" model { file = "/net/cci-nas-00/data/ceres_data/9atz_43838/05_2025/9atz_43838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atz_43838/05_2025/9atz_43838.cif" } resolution = 3.4 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= 0.000 sd= 0.002 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 99 5.16 5 C 13090 2.51 5 N 3789 2.21 5 O 4212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21190 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 539 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 107} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 558 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 110} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 622 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 122} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3443 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 4 Chain: "E" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "F" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 539 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 107} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 558 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 110} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "H" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 622 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 122} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "I" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3443 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 4 Chain: "J" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "K" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 558 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 110} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 622 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 122} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "M" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3443 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 24, 'TRANS': 406} Chain breaks: 4 Chain: "N" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 539 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 107} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "O" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1014 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "Q" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1021 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "R" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 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: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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: "I" 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: "M" 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 Time building chain proxies: 15.01, per 1000 atoms: 0.71 Number of scatterers: 21190 At special positions: 0 Unit cell: (128.535, 128.535, 179.74, 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 99 16.00 O 4212 8.00 N 3789 7.00 C 13090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=1.90 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 375 " - pdb=" SG CYS D 442 " distance=1.54 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 415 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 73 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.11 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 329 " distance=2.03 Simple disulfide: pdb=" SG CYS I 375 " - pdb=" SG CYS I 442 " distance=2.01 Simple disulfide: pdb=" SG CYS I 382 " - pdb=" SG CYS I 415 " distance=2.03 Simple disulfide: pdb=" SG CYS I 498 " - pdb=" SG CYS Q 602 " distance=2.03 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 73 " distance=2.03 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 196 " distance=2.05 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.03 Simple disulfide: pdb=" SG CYS M 228 " - pdb=" SG CYS M 239 " distance=2.15 Simple disulfide: pdb=" SG CYS M 296 " - pdb=" SG CYS M 329 " distance=2.77 Simple disulfide: pdb=" SG CYS M 375 " - pdb=" SG CYS M 442 " distance=2.03 Simple disulfide: pdb=" SG CYS M 382 " - pdb=" SG CYS M 415 " distance=2.03 Simple disulfide: pdb=" SG CYS O 595 " - pdb=" SG CYS O 601 " distance=2.03 Simple disulfide: pdb=" SG CYS P 595 " - pdb=" SG CYS P 601 " distance=2.22 Simple disulfide: pdb=" SG CYS Q 595 " - pdb=" SG CYS Q 601 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " " BMA a 3 " - " MAN a 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG D 601 " - " ASN D 187 " " NAG D 602 " - " ASN D 301 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 230 " " NAG D 605 " - " ASN D 234 " " NAG D 606 " - " ASN D 276 " " NAG D 607 " - " ASN D 389 " " NAG D 608 " - " ASN D 439 " " NAG D 609 " - " ASN D 445 " " NAG I 601 " - " ASN I 187 " " NAG I 602 " - " ASN I 301 " " NAG I 603 " - " ASN I 156 " " NAG I 604 " - " ASN I 160 " " NAG I 605 " - " ASN I 230 " " NAG I 606 " - " ASN I 234 " " NAG I 607 " - " ASN I 276 " " NAG I 608 " - " ASN I 389 " " NAG I 609 " - " ASN I 197 " " NAG I 610 " - " ASN I 445 " " NAG M 601 " - " ASN M 187 " " NAG M 602 " - " ASN M 301 " " NAG M 603 " - " ASN M 160 " " NAG M 604 " - " ASN M 276 " " NAG M 605 " - " ASN M 389 " " NAG M 606 " - " ASN M 197 " " NAG M 607 " - " ASN M 241 " " NAG M 608 " - " ASN M 234 " " NAG M 609 " - " ASN M 230 " " NAG M 610 " - " ASN M 445 " " NAG S 1 " - " ASN D 156 " " NAG T 1 " - " ASN D 197 " " NAG U 1 " - " ASN D 241 " " NAG V 1 " - " ASN D 262 " " NAG W 1 " - " ASN D 289 " " NAG X 1 " - " ASN D 357 " " NAG Y 1 " - " ASN D 383 " " NAG Z 1 " - " ASN I 241 " " NAG a 1 " - " ASN I 262 " " NAG b 1 " - " ASN I 289 " " NAG c 1 " - " ASN I 357 " " NAG d 1 " - " ASN I 383 " " NAG e 1 " - " ASN M 262 " " NAG f 1 " - " ASN M 289 " " NAG g 1 " - " ASN M 357 " " NAG h 1 " - " ASN M 383 " " NAG i 1 " - " ASN M 156 " Time building additional restraints: 6.07 Conformation dependent library (CDL) restraints added in 2.0 seconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5842 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 29.7% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'B' and resid 60 through 63 removed outlier: 3.679A pdb=" N UNK B 63 " --> pdb=" O UNK B 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 60 through 63' Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'C' and resid 84 through 87 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.687A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 351 Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.501A pdb=" N ILE D 368 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 387 Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.807A pdb=" N UNK E 84 " --> pdb=" O UNK E 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 63 removed outlier: 3.670A pdb=" N UNK G 63 " --> pdb=" O UNK G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 60 through 63' Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.834A pdb=" N UNK G 85 " --> pdb=" O UNK G 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 62 removed outlier: 3.596A pdb=" N UNK H 62 " --> pdb=" O UNK H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 62' Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 98 through 117 removed outlier: 3.655A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 333 through 351 Processing helix chain 'I' and resid 365 through 370 removed outlier: 3.575A pdb=" N THR I 370 " --> pdb=" O LEU I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 387 Processing helix chain 'I' and resid 472 through 481 removed outlier: 3.522A pdb=" N TRP I 476 " --> pdb=" O MET I 472 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU I 479 " --> pdb=" O ASN I 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.822A pdb=" N UNK J 84 " --> pdb=" O UNK J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 63 removed outlier: 3.599A pdb=" N UNK K 63 " --> pdb=" O UNK K 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 63' Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.820A pdb=" N UNK K 85 " --> pdb=" O UNK K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 62 removed outlier: 3.600A pdb=" N UNK L 62 " --> pdb=" O UNK L 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 59 through 62' Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.767A pdb=" N UNK L 88 " --> pdb=" O UNK L 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 Processing helix chain 'M' and resid 98 through 117 removed outlier: 3.669A pdb=" N GLU M 102 " --> pdb=" O ASN M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 333 through 351 Processing helix chain 'M' and resid 384 through 387 Processing helix chain 'M' and resid 422 through 426 removed outlier: 4.314A pdb=" N GLN M 425 " --> pdb=" O ASN M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 481 removed outlier: 3.572A pdb=" N GLU M 479 " --> pdb=" O ASN M 475 " (cutoff:3.500A) Processing helix chain 'O' and resid 526 through 542 Processing helix chain 'O' and resid 567 through 593 removed outlier: 3.787A pdb=" N LEU O 573 " --> pdb=" O GLY O 569 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA O 579 " --> pdb=" O THR O 575 " (cutoff:3.500A) Processing helix chain 'O' and resid 624 through 633 Processing helix chain 'O' and resid 635 through 657 Processing helix chain 'P' and resid 526 through 542 removed outlier: 3.695A pdb=" N THR P 535 " --> pdb=" O SER P 531 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL P 536 " --> pdb=" O ILE P 532 " (cutoff:3.500A) Processing helix chain 'P' and resid 560 through 565 Processing helix chain 'P' and resid 567 through 593 Processing helix chain 'P' and resid 624 through 632 Processing helix chain 'P' and resid 635 through 658 removed outlier: 3.762A pdb=" N LEU P 658 " --> pdb=" O GLU P 654 " (cutoff:3.500A) Processing helix chain 'Q' and resid 529 through 541 removed outlier: 4.219A pdb=" N THR Q 533 " --> pdb=" O ALA Q 529 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG Q 539 " --> pdb=" O THR Q 535 " (cutoff:3.500A) Processing helix chain 'Q' and resid 561 through 565 removed outlier: 3.588A pdb=" N ASP Q 565 " --> pdb=" O HIS Q 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 561 through 565' Processing helix chain 'Q' and resid 567 through 593 Processing helix chain 'Q' and resid 624 through 632 Processing helix chain 'Q' and resid 635 through 658 Processing helix chain 'R' and resid 80 through 84 removed outlier: 3.640A pdb=" N UNK R 84 " --> pdb=" O UNK R 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.301A pdb=" N UNK A 36 " --> pdb=" O UNK A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.686A pdb=" N UNK B 35 " --> pdb=" O UNK B 47 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N UNK B 49 " --> pdb=" O UNK B 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N UNK B 34 " --> pdb=" O UNK B 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 5.667A pdb=" N UNK C 16 " --> pdb=" O UNK C 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 11 through 12 current: chain 'C' and resid 44 through 51 removed outlier: 3.608A pdb=" N UNK C 54 " --> pdb=" O UNK C 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 54 through 57 current: chain 'C' and resid 104 through 113 Processing sheet with id=AA7, first strand: chain 'D' and resid 491 through 496 removed outlier: 5.206A pdb=" N VAL O 605 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL D 38 " --> pdb=" O THR O 603 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR O 603 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N TYR D 40 " --> pdb=" O CYS O 601 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N CYS O 601 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.657A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 177 removed outlier: 7.058A pdb=" N LYS D 190 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.422A pdb=" N THR D 202 " --> pdb=" O TYR D 432 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 259 through 261 current: chain 'D' and resid 284 through 298 removed outlier: 6.076A pdb=" N GLU D 293 " --> pdb=" O LYS D 332 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 327 through 332 current: chain 'D' and resid 379 through 382 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 379 through 382 current: chain 'D' and resid 462 through 467 Processing sheet with id=AB5, first strand: chain 'D' and resid 301 through 310 removed outlier: 4.242A pdb=" N ASN D 301 " --> pdb=" O ILE D 321A" (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS D 305 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR D 318 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE D 307 " --> pdb=" O TYR D 316 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR D 316 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE D 309 " --> pdb=" O TRP D 314 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP D 314 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 13 current: chain 'E' and resid 46 through 51 removed outlier: 6.672A pdb=" N UNK E 54 " --> pdb=" O UNK E 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 55 current: chain 'E' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'F' and resid 46 through 49 removed outlier: 6.319A pdb=" N UNK F 36 " --> pdb=" O UNK F 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 34 through 38 removed outlier: 7.172A pdb=" N UNK G 34 " --> pdb=" O UNK G 49 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N UNK G 49 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N UNK G 35 " --> pdb=" O UNK G 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 56 through 58 current: chain 'G' and resid 97 through 101 Processing sheet with id=AC3, first strand: chain 'H' and resid 4 through 7 removed outlier: 5.694A pdb=" N UNK H 16 " --> pdb=" O UNK H 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK H 82 " --> pdb=" O UNK H 16 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 44 through 50 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 55 through 57 current: chain 'H' and resid 104 through 113 Processing sheet with id=AC5, first strand: chain 'I' and resid 492 through 496 removed outlier: 5.274A pdb=" N VAL Q 605 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL I 38 " --> pdb=" O THR Q 603 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR Q 603 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.637A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'I' and resid 91 through 92 Processing sheet with id=AC9, first strand: chain 'I' and resid 169 through 177 removed outlier: 7.102A pdb=" N LYS I 190 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.409A pdb=" N THR I 202 " --> pdb=" O TYR I 432 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 292 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 292 current: chain 'I' and resid 390 through 392 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 390 through 392 current: chain 'I' and resid 462 through 467 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 294 through 308 removed outlier: 4.230A pdb=" N ASN I 301 " --> pdb=" O ILE I 321A" (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS I 305 " --> pdb=" O THR I 318 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N THR I 318 " --> pdb=" O LYS I 305 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE I 307 " --> pdb=" O TYR I 316 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR I 316 " --> pdb=" O ILE I 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 314 through 321A current: chain 'I' and resid 378 through 382 removed outlier: 4.112A pdb=" N PHE I 379 " --> pdb=" O LYS I 418 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 13 current: chain 'J' and resid 46 through 51 removed outlier: 6.650A pdb=" N UNK J 54 " --> pdb=" O UNK J 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 54 through 55 current: chain 'J' and resid 101 through 102 Processing sheet with id=AD6, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.876A pdb=" N UNK K 34 " --> pdb=" O UNK K 49 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N UNK K 49 " --> pdb=" O UNK K 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N UNK K 35 " --> pdb=" O UNK K 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 56 through 58 current: chain 'K' and resid 97 through 99 Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.662A pdb=" N UNK L 16 " --> pdb=" O UNK L 82 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 11 through 12 current: chain 'L' and resid 44 through 51 removed outlier: 3.625A pdb=" N UNK L 54 " --> pdb=" O UNK L 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 54 through 57 current: chain 'L' and resid 104 through 113 Processing sheet with id=AE1, first strand: chain 'M' and resid 492 through 496 removed outlier: 5.673A pdb=" N VAL P 605 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL M 38 " --> pdb=" O THR P 603 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR P 603 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 45 through 47 removed outlier: 4.603A pdb=" N VAL M 242 " --> pdb=" O LEU M 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'M' and resid 91 through 93 Processing sheet with id=AE5, first strand: chain 'M' and resid 129 through 131 Processing sheet with id=AE6, first strand: chain 'M' and resid 154 through 162 Processing sheet with id=AE7, first strand: chain 'M' and resid 201 through 203 removed outlier: 6.424A pdb=" N THR M 202 " --> pdb=" O TYR M 432 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 259 through 261 current: chain 'M' and resid 284 through 310 removed outlier: 4.321A pdb=" N ASN M 301 " --> pdb=" O ILE M 321A" (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS M 305 " --> pdb=" O THR M 318 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N THR M 318 " --> pdb=" O LYS M 305 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE M 307 " --> pdb=" O TYR M 316 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N TYR M 316 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE M 309 " --> pdb=" O TRP M 314 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TRP M 314 " --> pdb=" O ILE M 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 313 through 321A current: chain 'M' and resid 378 through 382 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 378 through 382 current: chain 'M' and resid 462 through 467 Processing sheet with id=AE9, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.339A pdb=" N UNK N 36 " --> pdb=" O UNK N 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'R' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 10 through 14 current: chain 'R' and resid 46 through 51 removed outlier: 6.642A pdb=" N UNK R 54 " --> pdb=" O UNK R 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 54 through 55 current: chain 'R' and resid 101 through 102 701 hydrogen bonds defined for protein. 1884 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: 7.94 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6933 1.34 - 1.46: 3382 1.46 - 1.58: 11015 1.58 - 1.70: 1 1.70 - 1.81: 129 Bond restraints: 21460 Sorted by residual: bond pdb=" C1 MAN a 4 " pdb=" C2 MAN a 4 " ideal model delta sigma weight residual 1.526 1.621 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" N ILE M 181 " pdb=" CA ILE M 181 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N ILE D 440 " pdb=" CA ILE D 440 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" N GLU M 185B" pdb=" CA GLU M 185B" ideal model delta sigma weight residual 1.453 1.494 -0.040 1.27e-02 6.20e+03 1.00e+01 bond pdb=" N CYS I 442 " pdb=" CA CYS I 442 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.27e-02 6.20e+03 8.71e+00 ... (remaining 21455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 27337 1.71 - 3.43: 1820 3.43 - 5.14: 186 5.14 - 6.85: 32 6.85 - 8.57: 8 Bond angle restraints: 29383 Sorted by residual: angle pdb=" CA GLY D 438 " pdb=" C GLY D 438 " pdb=" O GLY D 438 " ideal model delta sigma weight residual 122.57 118.19 4.38 9.20e-01 1.18e+00 2.26e+01 angle pdb=" C ARG D 376 " pdb=" CA ARG D 376 " pdb=" CB ARG D 376 " ideal model delta sigma weight residual 116.63 111.51 5.12 1.16e+00 7.43e-01 1.95e+01 angle pdb=" CA GLU M 185A" pdb=" C GLU M 185A" pdb=" O GLU M 185A" ideal model delta sigma weight residual 121.55 117.72 3.83 1.06e+00 8.90e-01 1.31e+01 angle pdb=" CA ILE I 194 " pdb=" C ILE I 194 " pdb=" O ILE I 194 " ideal model delta sigma weight residual 121.98 117.67 4.31 1.21e+00 6.83e-01 1.27e+01 angle pdb=" CA GLU M 185B" pdb=" C GLU M 185B" pdb=" O GLU M 185B" ideal model delta sigma weight residual 121.88 117.89 3.99 1.13e+00 7.83e-01 1.24e+01 ... (remaining 29378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 13405 22.26 - 44.52: 297 44.52 - 66.78: 74 66.78 - 89.04: 29 89.04 - 111.29: 14 Dihedral angle restraints: 13819 sinusoidal: 4912 harmonic: 8907 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual -86.00 2.03 -88.03 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS I 375 " pdb=" SG CYS I 375 " pdb=" SG CYS I 442 " pdb=" CB CYS I 442 " ideal model delta sinusoidal sigma weight residual -86.00 -158.60 72.60 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS M 126 " pdb=" SG CYS M 126 " pdb=" SG CYS M 196 " pdb=" CB CYS M 196 " ideal model delta sinusoidal sigma weight residual -86.00 -125.25 39.25 1 1.00e+01 1.00e-02 2.17e+01 ... (remaining 13816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3491 0.098 - 0.195: 269 0.195 - 0.293: 18 0.293 - 0.391: 0 0.391 - 0.489: 2 Chirality restraints: 3780 Sorted by residual: chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.81e+01 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.59e+01 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN M 383 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 3777 not shown) Planarity restraints: 3841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG h 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 607 " 0.346 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG M 607 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG M 607 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG M 607 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG M 607 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 1 " -0.332 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG h 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG h 1 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG h 1 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG h 1 " -0.189 2.00e-02 2.50e+03 ... (remaining 3838 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 35 2.48 - 3.08: 14934 3.08 - 3.69: 29875 3.69 - 4.29: 43084 4.29 - 4.90: 72522 Nonbonded interactions: 160450 Sorted by model distance: nonbonded pdb=" O3 NAG I 609 " pdb=" O7 NAG I 609 " model vdw 1.872 3.040 nonbonded pdb=" OD1 ASP M 335 " pdb=" NH2 ARG M 338 " model vdw 2.252 3.120 nonbonded pdb=" O3 NAG T 1 " pdb=" O7 NAG T 1 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 496 " model vdw 2.267 3.040 nonbonded pdb=" NH2 ARG I 298 " pdb=" O GLY I 438 " model vdw 2.294 3.120 ... (remaining 160445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name O )) or resid 9 through 35 or (resid 36 through 37 and (name N or name CA \ or name C or name O )) or resid 38 through 69 or (resid 70 and (name N or name \ CA or name C or name O )) or resid 71 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O )))) selection = (chain 'B' and (resid 6 through 12 or (resid 13 and (name N or name CA or name C \ or name O )) or resid 14 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O )) or resid 42 through 73 or (resid 74 and (name N or na \ me CA or name C or name O )) or resid 75 through 84 or (resid 85 and (name N or \ name CA or name C or name O )) or resid 86 through 110)) selection = (chain 'C' and (resid 19 through 51B or (resid 52 and (name N or name CA or name \ C or name O )) or resid 53 through 97 or (resid 98 and (name N or name CA or na \ me C or name O )) or resid 99 through 122 or (resid 123 and (name N or name CA o \ r name C or name O )))) selection = (chain 'E' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O )) or resid 12 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O )) or resid 41 through 72 or (resid 73 and (name N or na \ me CA or name C or name O )) or resid 74 through 85 or (resid 86 and (name N or \ name CA or name C or name O )) or resid 87 through 110 or (resid 111 and (name N \ or name CA or name C or name O )))) selection = (chain 'F' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name O )) or resid 9 through 35 or (resid 36 through 37 and (name N or name CA \ or name C or name O )) or resid 38 through 69 or (resid 70 and (name N or name \ CA or name C or name O )) or resid 71 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O )))) selection = (chain 'G' and (resid 6 through 12 or (resid 13 and (name N or name CA or name C \ or name O )) or resid 14 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O )) or resid 42 through 73 or (resid 74 and (name N or na \ me CA or name C or name O )) or resid 75 through 84 or (resid 85 and (name N or \ name CA or name C or name O )) or resid 86 through 110)) selection = (chain 'H' and (resid 19 through 51B or (resid 52 and (name N or name CA or name \ C or name O )) or resid 53 through 97 or (resid 98 and (name N or name CA or na \ me C or name O )) or resid 99 through 122 or (resid 123 and (name N or name CA o \ r name C or name O )))) selection = (chain 'J' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O )) or resid 12 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O )) or resid 41 through 72 or (resid 73 and (name N or na \ me CA or name C or name O )) or resid 74 through 85 or (resid 86 and (name N or \ name CA or name C or name O )) or resid 87 through 110 or (resid 111 and (name N \ or name CA or name C or name O )))) selection = (chain 'K' and (resid 6 through 12 or (resid 13 and (name N or name CA or name C \ or name O )) or resid 14 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O )) or resid 42 through 73 or (resid 74 and (name N or na \ me CA or name C or name O )) or resid 75 through 84 or (resid 85 and (name N or \ name CA or name C or name O )) or resid 86 through 110)) selection = (chain 'L' and (resid 19 through 51B or (resid 52 and (name N or name CA or name \ C or name O )) or resid 53 through 97 or (resid 98 and (name N or name CA or na \ me C or name O )) or resid 99 through 122 or (resid 123 and (name N or name CA o \ r name C or name O )))) selection = (chain 'N' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name O )) or resid 9 through 35 or (resid 36 through 37 and (name N or name CA \ or name C or name O )) or resid 38 through 69 or (resid 70 and (name N or name \ CA or name C or name O )) or resid 71 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O )))) selection = (chain 'R' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O )) or resid 12 through 38 or (resid 39 through 40 and (name N or name \ CA or name C or name O )) or resid 41 through 72 or (resid 73 and (name N or na \ me CA or name C or name O )) or resid 74 through 85 or (resid 86 and (name N or \ name CA or name C or name O )) or resid 87 through 110 or (resid 111 and (name N \ or name CA or name C or name O )))) } ncs_group { reference = chain 'D' selection = (chain 'I' and (resid 34 through 501 or resid 601 through 609)) selection = (chain 'M' and (resid 34 through 501 or resid 601 through 609)) } ncs_group { reference = chain 'O' selection = (chain 'P' and (resid 518 through 559 or resid 561 through 658)) selection = (chain 'Q' and (resid 518 through 545 or resid 560 through 658)) } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'V' selection = chain 'a' selection = chain 'e' } 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 individual isotropic 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 50.640 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.160 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.742 21559 Z= 0.447 Angle : 1.058 58.574 29653 Z= 0.536 Chirality : 0.051 0.489 3780 Planarity : 0.012 0.304 3795 Dihedral : 11.744 111.294 7896 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.13 % Allowed : 1.87 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1634 helix: 0.76 (0.26), residues: 424 sheet: -1.06 (0.21), residues: 471 loop : -0.59 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 96 HIS 0.004 0.001 HIS D 105 PHE 0.022 0.002 PHE I 53 TYR 0.018 0.001 TYR D 191 ARG 0.004 0.000 ARG O 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 46) link_NAG-ASN : angle 2.56593 ( 138) link_ALPHA1-6 : bond 0.00317 ( 3) link_ALPHA1-6 : angle 2.09104 ( 9) link_BETA1-4 : bond 0.01033 ( 20) link_BETA1-4 : angle 4.26778 ( 60) link_ALPHA1-3 : bond 0.01883 ( 3) link_ALPHA1-3 : angle 5.86076 ( 9) hydrogen bonds : bond 0.13086 ( 701) hydrogen bonds : angle 6.54780 ( 1884) SS BOND : bond 0.18021 ( 27) SS BOND : angle 10.92898 ( 54) covalent geometry : bond 0.00544 (21460) covalent geometry : angle 0.91148 (29383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8099 (mm-30) REVERT: D 231 LYS cc_start: 0.7966 (mttt) cc_final: 0.7479 (mptt) REVERT: D 424 TRP cc_start: 0.8376 (m-90) cc_final: 0.8120 (m-90) REVERT: D 472 MET cc_start: 0.9168 (mmm) cc_final: 0.8909 (tpp) REVERT: I 88 ASN cc_start: 0.7513 (m-40) cc_final: 0.7268 (m-40) REVERT: I 472 MET cc_start: 0.9283 (mmm) cc_final: 0.9028 (tpp) REVERT: M 130 GLU cc_start: 0.8631 (tt0) cc_final: 0.8423 (tt0) REVERT: M 231 LYS cc_start: 0.7741 (mttt) cc_final: 0.6983 (mttp) REVERT: P 638 THR cc_start: 0.8797 (m) cc_final: 0.8468 (p) REVERT: Q 543 SER cc_start: 0.5585 (t) cc_final: 0.5061 (p) REVERT: Q 587 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8505 (mm110) REVERT: Q 616 HIS cc_start: 0.6447 (m-70) cc_final: 0.6024 (m-70) outliers start: 2 outliers final: 1 residues processed: 361 average time/residue: 0.3781 time to fit residues: 197.6767 Evaluate side-chains 192 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 185 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 232 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN D 371 HIS I 103 GLN I 287 HIS I 341 GLN I 371 HIS ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN M 195 ASN M 287 HIS M 371 HIS M 422 ASN O 587 GLN P 537 GLN P 627 GLN P 637 ASN ** Q 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 627 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108612 restraints weight = 35027.260| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.75 r_work: 0.3111 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 21559 Z= 0.402 Angle : 1.046 11.731 29653 Z= 0.464 Chirality : 0.057 0.558 3780 Planarity : 0.004 0.050 3795 Dihedral : 10.304 83.796 4646 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.47 % Allowed : 7.81 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1634 helix: 0.77 (0.25), residues: 424 sheet: -1.11 (0.22), residues: 489 loop : -1.03 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 568 HIS 0.009 0.002 HIS O 616 PHE 0.027 0.003 PHE I 53 TYR 0.017 0.002 TYR O 635 ARG 0.009 0.001 ARG M 477 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 46) link_NAG-ASN : angle 2.66698 ( 138) link_ALPHA1-6 : bond 0.00910 ( 3) link_ALPHA1-6 : angle 2.48883 ( 9) link_BETA1-4 : bond 0.00743 ( 20) link_BETA1-4 : angle 3.67077 ( 60) link_ALPHA1-3 : bond 0.02517 ( 3) link_ALPHA1-3 : angle 3.96960 ( 9) hydrogen bonds : bond 0.05551 ( 701) hydrogen bonds : angle 5.59526 ( 1884) SS BOND : bond 0.00905 ( 27) SS BOND : angle 1.38591 ( 54) covalent geometry : bond 0.00918 (21460) covalent geometry : angle 1.01601 (29383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8461 (ttp) REVERT: D 88 ASN cc_start: 0.8154 (m-40) cc_final: 0.7949 (m-40) REVERT: D 102 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8454 (mm-30) REVERT: I 231 LYS cc_start: 0.8563 (mptt) cc_final: 0.7814 (mmtm) REVERT: I 489 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8721 (mtmt) REVERT: O 632 ILE cc_start: 0.9053 (pt) cc_final: 0.8693 (tt) REVERT: P 632 ILE cc_start: 0.9203 (pt) cc_final: 0.8969 (tt) REVERT: Q 543 SER cc_start: 0.5975 (t) cc_final: 0.5490 (p) REVERT: Q 585 LYS cc_start: 0.8881 (tptt) cc_final: 0.8421 (mttt) REVERT: Q 658 LEU cc_start: 0.7723 (mp) cc_final: 0.7473 (mp) outliers start: 37 outliers final: 21 residues processed: 211 average time/residue: 0.3575 time to fit residues: 113.0078 Evaluate side-chains 178 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 321 ILE Chi-restraints excluded: chain I residue 339 THR Chi-restraints excluded: chain I residue 341 GLN Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 443 LYS Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain P residue 545 ILE Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain Q residue 546 VAL Chi-restraints excluded: chain Q residue 648 ASN Chi-restraints excluded: chain Q residue 650 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 99 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN D 114 GLN I 341 GLN M 88 ASN M 195 ASN M 341 GLN M 422 ASN ** O 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 540 GLN P 637 ASN P 648 ASN P 649 GLN Q 537 GLN ** Q 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 637 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111693 restraints weight = 34625.176| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.77 r_work: 0.3197 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21559 Z= 0.147 Angle : 0.673 10.668 29653 Z= 0.300 Chirality : 0.043 0.263 3780 Planarity : 0.003 0.036 3795 Dihedral : 9.015 77.441 4646 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.87 % Allowed : 10.41 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1634 helix: 1.27 (0.26), residues: 422 sheet: -0.95 (0.22), residues: 489 loop : -0.89 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 628 HIS 0.005 0.001 HIS Q 616 PHE 0.014 0.001 PHE M 53 TYR 0.015 0.001 TYR Q 635 ARG 0.007 0.001 ARG I 342 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 46) link_NAG-ASN : angle 1.90069 ( 138) link_ALPHA1-6 : bond 0.00285 ( 3) link_ALPHA1-6 : angle 1.71972 ( 9) link_BETA1-4 : bond 0.00943 ( 20) link_BETA1-4 : angle 2.99239 ( 60) link_ALPHA1-3 : bond 0.02553 ( 3) link_ALPHA1-3 : angle 3.57945 ( 9) hydrogen bonds : bond 0.04288 ( 701) hydrogen bonds : angle 4.93037 ( 1884) SS BOND : bond 0.00429 ( 27) SS BOND : angle 0.82533 ( 54) covalent geometry : bond 0.00323 (21460) covalent geometry : angle 0.64432 (29383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8138 (mm-30) REVERT: D 472 MET cc_start: 0.9055 (mmm) cc_final: 0.8785 (mmm) REVERT: M 49 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8476 (mt-10) REVERT: O 632 ILE cc_start: 0.8955 (pt) cc_final: 0.8447 (tt) REVERT: P 614 LYS cc_start: 0.7661 (mtmm) cc_final: 0.7304 (ttmt) REVERT: P 632 ILE cc_start: 0.9220 (pt) cc_final: 0.8994 (tt) REVERT: Q 525 SER cc_start: 0.7817 (p) cc_final: 0.6996 (m) REVERT: Q 585 LYS cc_start: 0.8736 (tptt) cc_final: 0.8484 (ttmt) REVERT: Q 644 GLU cc_start: 0.7405 (pt0) cc_final: 0.7168 (pt0) REVERT: Q 658 LEU cc_start: 0.7767 (mp) cc_final: 0.7458 (mp) outliers start: 28 outliers final: 16 residues processed: 191 average time/residue: 0.3237 time to fit residues: 95.0956 Evaluate side-chains 178 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 443 LYS Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain P residue 545 ILE Chi-restraints excluded: chain P residue 626 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 22 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 231 optimal weight: 0.0170 chunk 295 optimal weight: 5.9990 overall best weight: 3.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN D 425 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN P 574 GLN P 637 ASN Q 616 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108769 restraints weight = 35335.984| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.75 r_work: 0.3133 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21559 Z= 0.288 Angle : 0.830 11.504 29653 Z= 0.366 Chirality : 0.048 0.398 3780 Planarity : 0.003 0.038 3795 Dihedral : 9.033 79.078 4646 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 11.47 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1634 helix: 1.02 (0.25), residues: 441 sheet: -1.04 (0.22), residues: 489 loop : -1.02 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 568 HIS 0.004 0.001 HIS D 105 PHE 0.020 0.002 PHE I 53 TYR 0.015 0.002 TYR O 635 ARG 0.006 0.001 ARG I 477 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 46) link_NAG-ASN : angle 2.10865 ( 138) link_ALPHA1-6 : bond 0.00372 ( 3) link_ALPHA1-6 : angle 2.13738 ( 9) link_BETA1-4 : bond 0.00832 ( 20) link_BETA1-4 : angle 3.25742 ( 60) link_ALPHA1-3 : bond 0.02121 ( 3) link_ALPHA1-3 : angle 3.57824 ( 9) hydrogen bonds : bond 0.04682 ( 701) hydrogen bonds : angle 5.10535 ( 1884) SS BOND : bond 0.00682 ( 27) SS BOND : angle 0.95642 ( 54) covalent geometry : bond 0.00649 (21460) covalent geometry : angle 0.80364 (29383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 102 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8224 (mm-30) REVERT: D 472 MET cc_start: 0.9100 (mmm) cc_final: 0.8834 (mmm) REVERT: I 185 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: M 49 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: O 527 MET cc_start: 0.8064 (mtp) cc_final: 0.7850 (mtp) REVERT: O 542 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5541 (mt) REVERT: O 632 ILE cc_start: 0.8809 (pt) cc_final: 0.8425 (tt) REVERT: P 632 ILE cc_start: 0.9185 (pt) cc_final: 0.8920 (tt) REVERT: Q 543 SER cc_start: 0.6353 (t) cc_final: 0.6044 (p) outliers start: 38 outliers final: 23 residues processed: 192 average time/residue: 0.3201 time to fit residues: 94.6105 Evaluate side-chains 189 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 339 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 331 ILE Chi-restraints excluded: chain O residue 526 THR Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain P residue 545 ILE Chi-restraints excluded: chain P residue 648 ASN Chi-restraints excluded: chain Q residue 532 ILE Chi-restraints excluded: chain Q residue 546 VAL Chi-restraints excluded: chain Q residue 562 LEU Chi-restraints excluded: chain Q residue 648 ASN Chi-restraints excluded: chain Q residue 650 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 23 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 287 optimal weight: 7.9990 chunk 223 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 229 ASN P 637 ASN Q 616 HIS Q 637 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110925 restraints weight = 35195.928| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.86 r_work: 0.3190 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21559 Z= 0.112 Angle : 0.617 11.014 29653 Z= 0.276 Chirality : 0.041 0.251 3780 Planarity : 0.002 0.031 3795 Dihedral : 8.134 73.520 4646 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.80 % Allowed : 13.14 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1634 helix: 1.20 (0.25), residues: 440 sheet: -0.88 (0.22), residues: 489 loop : -0.92 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 628 HIS 0.003 0.001 HIS Q 567 PHE 0.013 0.001 PHE M 53 TYR 0.013 0.001 TYR Q 635 ARG 0.005 0.000 ARG M 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 46) link_NAG-ASN : angle 1.71719 ( 138) link_ALPHA1-6 : bond 0.00328 ( 3) link_ALPHA1-6 : angle 1.64885 ( 9) link_BETA1-4 : bond 0.00902 ( 20) link_BETA1-4 : angle 2.86175 ( 60) link_ALPHA1-3 : bond 0.02093 ( 3) link_ALPHA1-3 : angle 3.31076 ( 9) hydrogen bonds : bond 0.03794 ( 701) hydrogen bonds : angle 4.68319 ( 1884) SS BOND : bond 0.00348 ( 27) SS BOND : angle 0.64621 ( 54) covalent geometry : bond 0.00237 (21460) covalent geometry : angle 0.59076 (29383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 185 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7262 (pp20) REVERT: M 66 ARG cc_start: 0.6773 (mmp80) cc_final: 0.6562 (mmp80) REVERT: O 542 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5477 (mt) REVERT: O 632 ILE cc_start: 0.8858 (pt) cc_final: 0.8327 (tt) REVERT: P 632 ILE cc_start: 0.9189 (pt) cc_final: 0.8925 (tt) outliers start: 27 outliers final: 19 residues processed: 198 average time/residue: 0.3429 time to fit residues: 103.6297 Evaluate side-chains 182 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 49 GLU Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain P residue 545 ILE Chi-restraints excluded: chain Q residue 546 VAL Chi-restraints excluded: chain Q residue 644 GLU Chi-restraints excluded: chain Q residue 648 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 57 optimal weight: 7.9990 chunk 287 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN D 114 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN O 537 GLN P 637 ASN Q 616 HIS Q 637 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105068 restraints weight = 36165.619| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.80 r_work: 0.3074 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.072 21559 Z= 0.506 Angle : 1.094 12.339 29653 Z= 0.485 Chirality : 0.059 0.563 3780 Planarity : 0.004 0.041 3795 Dihedral : 9.496 83.622 4646 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.67 % Allowed : 13.74 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1634 helix: 0.64 (0.25), residues: 443 sheet: -1.15 (0.22), residues: 465 loop : -1.02 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP I 96 HIS 0.009 0.002 HIS I 105 PHE 0.024 0.003 PHE I 53 TYR 0.015 0.003 TYR I 223 ARG 0.009 0.001 ARG M 477 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 46) link_NAG-ASN : angle 2.53563 ( 138) link_ALPHA1-6 : bond 0.01096 ( 3) link_ALPHA1-6 : angle 2.43847 ( 9) link_BETA1-4 : bond 0.00731 ( 20) link_BETA1-4 : angle 3.68551 ( 60) link_ALPHA1-3 : bond 0.02013 ( 3) link_ALPHA1-3 : angle 3.10489 ( 9) hydrogen bonds : bond 0.05450 ( 701) hydrogen bonds : angle 5.59825 ( 1884) SS BOND : bond 0.00932 ( 27) SS BOND : angle 1.15639 ( 54) covalent geometry : bond 0.01149 (21460) covalent geometry : angle 1.06888 (29383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 185 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8072 (pp20) REVERT: O 527 MET cc_start: 0.8142 (mtp) cc_final: 0.7851 (mtp) REVERT: O 540 GLN cc_start: 0.7126 (tt0) cc_final: 0.6507 (tp40) REVERT: O 542 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5874 (mt) REVERT: O 632 ILE cc_start: 0.8892 (pt) cc_final: 0.8306 (tt) REVERT: P 614 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7680 (ttmt) REVERT: P 632 ILE cc_start: 0.9193 (pt) cc_final: 0.8803 (tt) REVERT: Q 543 SER cc_start: 0.6906 (t) cc_final: 0.6301 (p) REVERT: Q 632 ILE cc_start: 0.9191 (pt) cc_final: 0.8629 (tt) outliers start: 40 outliers final: 28 residues processed: 191 average time/residue: 0.3652 time to fit residues: 104.4939 Evaluate side-chains 188 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 321 ILE Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 339 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 331 ILE Chi-restraints excluded: chain O residue 526 THR Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain O residue 638 THR Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 614 LYS Chi-restraints excluded: chain P residue 648 ASN Chi-restraints excluded: chain Q residue 532 ILE Chi-restraints excluded: chain Q residue 546 VAL Chi-restraints excluded: chain Q residue 648 ASN Chi-restraints excluded: chain Q residue 650 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 235 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 216 optimal weight: 0.0770 chunk 265 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 209 optimal weight: 0.0060 chunk 148 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 overall best weight: 0.5154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN O 561 HIS ** O 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 588 GLN P 616 HIS P 637 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114056 restraints weight = 34799.223| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.63 r_work: 0.3216 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21559 Z= 0.118 Angle : 0.642 11.420 29653 Z= 0.290 Chirality : 0.040 0.241 3780 Planarity : 0.003 0.034 3795 Dihedral : 8.071 72.206 4646 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.67 % Allowed : 14.88 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1634 helix: 1.11 (0.25), residues: 435 sheet: -0.84 (0.21), residues: 528 loop : -1.02 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 628 HIS 0.004 0.001 HIS Q 561 PHE 0.014 0.001 PHE D 53 TYR 0.011 0.001 TYR Q 635 ARG 0.007 0.000 ARG M 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 46) link_NAG-ASN : angle 1.73924 ( 138) link_ALPHA1-6 : bond 0.00699 ( 3) link_ALPHA1-6 : angle 1.42771 ( 9) link_BETA1-4 : bond 0.00920 ( 20) link_BETA1-4 : angle 2.89746 ( 60) link_ALPHA1-3 : bond 0.02158 ( 3) link_ALPHA1-3 : angle 3.07240 ( 9) hydrogen bonds : bond 0.03778 ( 701) hydrogen bonds : angle 4.79597 ( 1884) SS BOND : bond 0.00289 ( 27) SS BOND : angle 0.68125 ( 54) covalent geometry : bond 0.00246 (21460) covalent geometry : angle 0.61681 (29383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 540 GLN cc_start: 0.6509 (tt0) cc_final: 0.5977 (tp40) REVERT: O 542 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5663 (mt) REVERT: O 561 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7363 (p90) REVERT: O 628 TRP cc_start: 0.8852 (t-100) cc_final: 0.8612 (t-100) REVERT: O 632 ILE cc_start: 0.8665 (pt) cc_final: 0.8342 (tt) REVERT: P 525 SER cc_start: 0.7212 (t) cc_final: 0.6992 (p) REVERT: P 540 GLN cc_start: 0.7159 (tt0) cc_final: 0.6729 (mt0) REVERT: P 632 ILE cc_start: 0.9165 (pt) cc_final: 0.8806 (tt) outliers start: 25 outliers final: 18 residues processed: 199 average time/residue: 0.3529 time to fit residues: 106.7496 Evaluate side-chains 196 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 561 HIS Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 648 ASN Chi-restraints excluded: chain Q residue 644 GLU Chi-restraints excluded: chain Q residue 648 ASN Chi-restraints excluded: chain Q residue 650 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 283 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 648 ASN P 637 ASN Q 637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105902 restraints weight = 35805.224| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.74 r_work: 0.3071 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.067 21559 Z= 0.469 Angle : 1.039 12.644 29653 Z= 0.461 Chirality : 0.057 0.536 3780 Planarity : 0.004 0.042 3795 Dihedral : 9.164 81.861 4646 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.47 % Allowed : 15.08 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1634 helix: 0.84 (0.25), residues: 443 sheet: -1.07 (0.22), residues: 459 loop : -1.03 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 568 HIS 0.008 0.002 HIS I 105 PHE 0.022 0.003 PHE I 53 TYR 0.015 0.002 TYR I 317 ARG 0.008 0.001 ARG M 477 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 46) link_NAG-ASN : angle 2.39602 ( 138) link_ALPHA1-6 : bond 0.00614 ( 3) link_ALPHA1-6 : angle 2.45043 ( 9) link_BETA1-4 : bond 0.00792 ( 20) link_BETA1-4 : angle 3.60348 ( 60) link_ALPHA1-3 : bond 0.01907 ( 3) link_ALPHA1-3 : angle 2.71991 ( 9) hydrogen bonds : bond 0.05248 ( 701) hydrogen bonds : angle 5.45271 ( 1884) SS BOND : bond 0.00866 ( 27) SS BOND : angle 1.11696 ( 54) covalent geometry : bond 0.01067 (21460) covalent geometry : angle 1.01445 (29383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.8564 (ttp) cc_final: 0.8315 (ttm) REVERT: I 185 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: O 527 MET cc_start: 0.8080 (mtp) cc_final: 0.7749 (mtp) REVERT: O 540 GLN cc_start: 0.6872 (tt0) cc_final: 0.6273 (tp40) REVERT: O 542 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6029 (mt) REVERT: O 632 ILE cc_start: 0.8820 (pt) cc_final: 0.8321 (tt) REVERT: P 525 SER cc_start: 0.7381 (t) cc_final: 0.7063 (m) REVERT: P 540 GLN cc_start: 0.7378 (tt0) cc_final: 0.6853 (mt0) REVERT: P 632 ILE cc_start: 0.9128 (pt) cc_final: 0.8764 (tt) REVERT: Q 632 ILE cc_start: 0.9187 (pt) cc_final: 0.8662 (tt) outliers start: 37 outliers final: 30 residues processed: 187 average time/residue: 0.3533 time to fit residues: 99.0980 Evaluate side-chains 191 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain I residue 339 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 244 THR Chi-restraints excluded: chain M residue 331 ILE Chi-restraints excluded: chain O residue 526 THR Chi-restraints excluded: chain O residue 532 ILE Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain O residue 613 ASN Chi-restraints excluded: chain O residue 648 ASN Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 648 ASN Chi-restraints excluded: chain Q residue 532 ILE Chi-restraints excluded: chain Q residue 546 VAL Chi-restraints excluded: chain Q residue 644 GLU Chi-restraints excluded: chain Q residue 648 ASN Chi-restraints excluded: chain Q residue 650 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 126 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN O 588 GLN P 616 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111930 restraints weight = 34903.040| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.56 r_work: 0.3221 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21559 Z= 0.141 Angle : 0.667 11.364 29653 Z= 0.301 Chirality : 0.042 0.254 3780 Planarity : 0.003 0.043 3795 Dihedral : 8.139 72.619 4646 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 1.73 % Allowed : 15.94 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1634 helix: 0.98 (0.25), residues: 441 sheet: -0.87 (0.22), residues: 528 loop : -1.05 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 628 HIS 0.006 0.001 HIS O 561 PHE 0.014 0.001 PHE D 53 TYR 0.010 0.001 TYR I 39 ARG 0.007 0.000 ARG M 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 46) link_NAG-ASN : angle 1.78254 ( 138) link_ALPHA1-6 : bond 0.00278 ( 3) link_ALPHA1-6 : angle 1.42781 ( 9) link_BETA1-4 : bond 0.00824 ( 20) link_BETA1-4 : angle 2.97154 ( 60) link_ALPHA1-3 : bond 0.01791 ( 3) link_ALPHA1-3 : angle 2.81757 ( 9) hydrogen bonds : bond 0.03959 ( 701) hydrogen bonds : angle 4.83031 ( 1884) SS BOND : bond 0.00372 ( 27) SS BOND : angle 0.71162 ( 54) covalent geometry : bond 0.00309 (21460) covalent geometry : angle 0.64203 (29383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 185 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7313 (pp20) REVERT: M 39 TYR cc_start: 0.8760 (m-80) cc_final: 0.8516 (m-80) REVERT: M 106 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8412 (mm-30) REVERT: O 540 GLN cc_start: 0.6379 (tt0) cc_final: 0.5805 (tp40) REVERT: O 542 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5605 (mt) REVERT: O 587 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8557 (mm110) REVERT: O 632 ILE cc_start: 0.8597 (pt) cc_final: 0.8335 (tt) REVERT: P 525 SER cc_start: 0.7259 (t) cc_final: 0.7041 (m) REVERT: P 540 GLN cc_start: 0.7159 (tt0) cc_final: 0.6796 (mt0) REVERT: P 632 ILE cc_start: 0.9130 (pt) cc_final: 0.8710 (tt) REVERT: Q 632 ILE cc_start: 0.9041 (pt) cc_final: 0.8584 (tp) outliers start: 26 outliers final: 21 residues processed: 200 average time/residue: 0.3375 time to fit residues: 102.9506 Evaluate side-chains 198 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain O residue 648 ASN Chi-restraints excluded: chain P residue 532 ILE Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 648 ASN Chi-restraints excluded: chain Q residue 532 ILE Chi-restraints excluded: chain Q residue 644 GLU Chi-restraints excluded: chain Q residue 648 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 234 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 290 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 616 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109111 restraints weight = 35526.795| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.74 r_work: 0.3136 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21559 Z= 0.243 Angle : 0.753 12.028 29653 Z= 0.336 Chirality : 0.046 0.362 3780 Planarity : 0.003 0.047 3795 Dihedral : 8.289 75.661 4646 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 1.80 % Allowed : 15.88 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1634 helix: 1.05 (0.25), residues: 441 sheet: -0.87 (0.21), residues: 528 loop : -1.04 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP O 628 HIS 0.004 0.001 HIS I 105 PHE 0.017 0.002 PHE I 53 TYR 0.010 0.001 TYR O 635 ARG 0.005 0.000 ARG I 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 46) link_NAG-ASN : angle 1.91552 ( 138) link_ALPHA1-6 : bond 0.00233 ( 3) link_ALPHA1-6 : angle 1.82206 ( 9) link_BETA1-4 : bond 0.00826 ( 20) link_BETA1-4 : angle 3.17024 ( 60) link_ALPHA1-3 : bond 0.01685 ( 3) link_ALPHA1-3 : angle 2.60880 ( 9) hydrogen bonds : bond 0.04271 ( 701) hydrogen bonds : angle 4.90726 ( 1884) SS BOND : bond 0.00568 ( 27) SS BOND : angle 0.79659 ( 54) covalent geometry : bond 0.00554 (21460) covalent geometry : angle 0.72793 (29383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.8583 (ttp) cc_final: 0.8352 (ttm) REVERT: I 185 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: M 106 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8720 (mm-30) REVERT: O 527 MET cc_start: 0.8090 (mtp) cc_final: 0.7764 (mtp) REVERT: O 540 GLN cc_start: 0.6595 (tt0) cc_final: 0.5958 (tp40) REVERT: O 542 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5743 (mt) REVERT: P 525 SER cc_start: 0.7252 (t) cc_final: 0.7005 (p) REVERT: P 540 GLN cc_start: 0.7323 (tt0) cc_final: 0.6889 (mt0) REVERT: P 632 ILE cc_start: 0.9143 (pt) cc_final: 0.8692 (tt) REVERT: Q 632 ILE cc_start: 0.9068 (pt) cc_final: 0.8580 (tp) outliers start: 27 outliers final: 24 residues processed: 181 average time/residue: 0.3406 time to fit residues: 93.4571 Evaluate side-chains 184 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 439 ASN Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 196 CYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 331 ILE Chi-restraints excluded: chain O residue 526 THR Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain P residue 532 ILE Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 648 ASN Chi-restraints excluded: chain Q residue 532 ILE Chi-restraints excluded: chain Q residue 644 GLU Chi-restraints excluded: chain Q residue 648 ASN Chi-restraints excluded: chain Q residue 650 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 90 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 281 optimal weight: 0.5980 chunk 205 optimal weight: 0.0270 chunk 275 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 616 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110466 restraints weight = 35476.885| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.77 r_work: 0.3152 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21559 Z= 0.179 Angle : 0.676 11.863 29653 Z= 0.304 Chirality : 0.043 0.292 3780 Planarity : 0.003 0.048 3795 Dihedral : 7.987 73.255 4646 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 1.93 % Allowed : 15.68 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1634 helix: 1.11 (0.25), residues: 441 sheet: -0.80 (0.22), residues: 528 loop : -0.98 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 628 HIS 0.007 0.001 HIS D 105 PHE 0.017 0.002 PHE D 53 TYR 0.009 0.001 TYR I 39 ARG 0.005 0.000 ARG I 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 46) link_NAG-ASN : angle 1.77770 ( 138) link_ALPHA1-6 : bond 0.00173 ( 3) link_ALPHA1-6 : angle 1.63064 ( 9) link_BETA1-4 : bond 0.00865 ( 20) link_BETA1-4 : angle 3.03454 ( 60) link_ALPHA1-3 : bond 0.01808 ( 3) link_ALPHA1-3 : angle 2.50044 ( 9) hydrogen bonds : bond 0.03981 ( 701) hydrogen bonds : angle 4.76378 ( 1884) SS BOND : bond 0.00432 ( 27) SS BOND : angle 0.71577 ( 54) covalent geometry : bond 0.00404 (21460) covalent geometry : angle 0.65123 (29383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9983.93 seconds wall clock time: 173 minutes 25.39 seconds (10405.39 seconds total)