Starting phenix.real_space_refine on Fri Sep 19 00:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atz_43838/09_2025/9atz_43838.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atz_43838/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9atz_43838/09_2025/9atz_43838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atz_43838/09_2025/9atz_43838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9atz_43838/09_2025/9atz_43838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atz_43838/09_2025/9atz_43838.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.27, per 1000 atoms: 0.20 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: 1.64 Conformation dependent library (CDL) restraints added in 584.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.64 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: 3.44 Time building geometry restraints manager: 2.11 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 609) selection = (chain 'M' and resid 34 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 16.930 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.000 ARG O 539 TYR 0.018 0.001 TYR D 191 PHE 0.022 0.002 PHE I 53 TRP 0.010 0.001 TRP D 96 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00544 (21460) covalent geometry : angle 0.91148 (29383) SS BOND : bond 0.18021 ( 27) SS BOND : angle 10.92898 ( 54) hydrogen bonds : bond 0.13086 ( 701) hydrogen bonds : angle 6.54780 ( 1884) link_ALPHA1-3 : bond 0.01883 ( 3) link_ALPHA1-3 : angle 5.86076 ( 9) 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_NAG-ASN : bond 0.00758 ( 46) link_NAG-ASN : angle 2.56593 ( 138) *********************** 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 : 0.792 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: 0.8119 (m-90) REVERT: D 472 MET cc_start: 0.9168 (mmm) cc_final: 0.8907 (tpp) REVERT: I 88 ASN cc_start: 0.7513 (m-40) cc_final: 0.7265 (m-40) REVERT: I 472 MET cc_start: 0.9283 (mmm) cc_final: 0.9028 (tpp) REVERT: M 231 LYS cc_start: 0.7741 (mttt) cc_final: 0.6983 (mttp) REVERT: O 647 GLN cc_start: 0.7975 (tp40) cc_final: 0.7609 (tp40) REVERT: P 638 THR cc_start: 0.8797 (m) cc_final: 0.8470 (p) REVERT: Q 543 SER cc_start: 0.5585 (t) cc_final: 0.5071 (p) REVERT: Q 587 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8504 (mm110) REVERT: Q 616 HIS cc_start: 0.6447 (m-70) cc_final: 0.6026 (m-70) outliers start: 2 outliers final: 1 residues processed: 361 average time/residue: 0.1659 time to fit residues: 87.2033 Evaluate side-chains 191 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 103 GLN I 371 HIS M 88 ASN M 195 ASN M 287 HIS M 371 HIS M 422 ASN O 587 GLN P 627 GLN P 637 ASN Q 574 GLN Q 627 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112010 restraints weight = 35037.514| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.83 r_work: 0.3194 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21559 Z= 0.239 Angle : 0.780 11.401 29653 Z= 0.349 Chirality : 0.047 0.326 3780 Planarity : 0.003 0.031 3795 Dihedral : 9.521 83.407 4646 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.00 % Allowed : 7.94 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1634 helix: 1.26 (0.26), residues: 420 sheet: -0.93 (0.21), residues: 486 loop : -0.84 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 473 TYR 0.015 0.002 TYR O 635 PHE 0.021 0.002 PHE I 53 TRP 0.015 0.002 TRP M 96 HIS 0.006 0.002 HIS O 616 Details of bonding type rmsd covalent geometry : bond 0.00544 (21460) covalent geometry : angle 0.74848 (29383) SS BOND : bond 0.00803 ( 27) SS BOND : angle 1.15728 ( 54) hydrogen bonds : bond 0.04906 ( 701) hydrogen bonds : angle 5.19405 ( 1884) link_ALPHA1-3 : bond 0.02502 ( 3) link_ALPHA1-3 : angle 4.06102 ( 9) link_ALPHA1-6 : bond 0.00560 ( 3) link_ALPHA1-6 : angle 2.17945 ( 9) link_BETA1-4 : bond 0.00749 ( 20) link_BETA1-4 : angle 3.30521 ( 60) link_NAG-ASN : bond 0.00410 ( 46) link_NAG-ASN : angle 2.21777 ( 138) *********************** 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 212 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 ASN cc_start: 0.7959 (m-40) cc_final: 0.7719 (m-40) REVERT: D 102 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8225 (mm-30) REVERT: I 88 ASN cc_start: 0.7889 (m-40) cc_final: 0.7659 (m-40) REVERT: I 255 VAL cc_start: 0.9348 (t) cc_final: 0.9027 (m) REVERT: O 630 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8048 (mtt180) REVERT: O 642 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8724 (mp) REVERT: O 647 GLN cc_start: 0.8334 (tp40) cc_final: 0.7665 (tp40) REVERT: Q 541 LEU cc_start: 0.7039 (tp) cc_final: 0.6817 (tt) REVERT: Q 585 LYS cc_start: 0.8731 (tptt) cc_final: 0.8282 (mttt) REVERT: Q 596 SER cc_start: 0.9235 (t) cc_final: 0.9033 (p) outliers start: 30 outliers final: 17 residues processed: 202 average time/residue: 0.1492 time to fit residues: 45.0709 Evaluate side-chains 176 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 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 O residue 520 LEU Chi-restraints excluded: chain O residue 630 ARG Chi-restraints excluded: chain O residue 642 LEU Chi-restraints excluded: chain P residue 545 ILE Chi-restraints excluded: chain Q residue 546 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 156 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 199 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN D 371 HIS ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 GLN P 537 GLN P 540 GLN P 637 ASN P 649 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109878 restraints weight = 35122.981| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.73 r_work: 0.3140 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21559 Z= 0.278 Angle : 0.814 11.308 29653 Z= 0.362 Chirality : 0.048 0.346 3780 Planarity : 0.003 0.044 3795 Dihedral : 9.240 80.659 4646 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.07 % Allowed : 9.07 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.20), residues: 1634 helix: 1.20 (0.26), residues: 422 sheet: -0.96 (0.22), residues: 489 loop : -0.95 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 497 TYR 0.017 0.002 TYR O 635 PHE 0.019 0.002 PHE I 53 TRP 0.017 0.002 TRP D 96 HIS 0.008 0.002 HIS O 616 Details of bonding type rmsd covalent geometry : bond 0.00632 (21460) covalent geometry : angle 0.78803 (29383) SS BOND : bond 0.00636 ( 27) SS BOND : angle 0.98956 ( 54) hydrogen bonds : bond 0.04853 ( 701) hydrogen bonds : angle 5.17429 ( 1884) link_ALPHA1-3 : bond 0.02519 ( 3) link_ALPHA1-3 : angle 3.53918 ( 9) link_ALPHA1-6 : bond 0.00311 ( 3) link_ALPHA1-6 : angle 1.80765 ( 9) link_BETA1-4 : bond 0.00755 ( 20) link_BETA1-4 : angle 3.20189 ( 60) link_NAG-ASN : bond 0.00428 ( 46) link_NAG-ASN : angle 2.08954 ( 138) *********************** 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 210 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 472 MET cc_start: 0.9109 (mmm) cc_final: 0.8895 (mmm) REVERT: I 88 ASN cc_start: 0.8147 (m-40) cc_final: 0.7937 (m-40) REVERT: M 39 TYR cc_start: 0.8828 (m-80) cc_final: 0.8607 (m-80) REVERT: O 630 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8003 (mtt180) REVERT: O 632 ILE cc_start: 0.8962 (pt) cc_final: 0.8563 (tt) REVERT: O 650 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: P 644 GLU cc_start: 0.7668 (pt0) cc_final: 0.7463 (pt0) REVERT: Q 543 SER cc_start: 0.6416 (t) cc_final: 0.6115 (p) outliers start: 46 outliers final: 22 residues processed: 194 average time/residue: 0.1436 time to fit residues: 42.9106 Evaluate side-chains 178 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 THR Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 443 LYS Chi-restraints excluded: chain M residue 38 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 M residue 244 THR Chi-restraints excluded: chain O residue 600 ILE Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain O residue 630 ARG Chi-restraints excluded: chain O residue 650 GLN Chi-restraints excluded: chain P residue 545 ILE Chi-restraints excluded: chain P residue 626 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 225 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 ASN M 229 ASN M 422 ASN P 574 GLN P 637 ASN P 648 ASN Q 616 HIS Q 637 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107758 restraints weight = 35878.844| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.78 r_work: 0.3132 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 21559 Z= 0.286 Angle : 0.813 11.443 29653 Z= 0.361 Chirality : 0.048 0.365 3780 Planarity : 0.003 0.030 3795 Dihedral : 8.886 78.521 4646 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.74 % Allowed : 10.94 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.20), residues: 1634 helix: 0.97 (0.25), residues: 443 sheet: -1.01 (0.22), residues: 489 loop : -1.04 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 473 TYR 0.018 0.002 TYR O 635 PHE 0.018 0.002 PHE I 53 TRP 0.014 0.002 TRP O 568 HIS 0.004 0.001 HIS M 287 Details of bonding type rmsd covalent geometry : bond 0.00652 (21460) covalent geometry : angle 0.78629 (29383) SS BOND : bond 0.00655 ( 27) SS BOND : angle 0.96586 ( 54) hydrogen bonds : bond 0.04616 ( 701) hydrogen bonds : angle 5.08534 ( 1884) link_ALPHA1-3 : bond 0.02177 ( 3) link_ALPHA1-3 : angle 3.52179 ( 9) link_ALPHA1-6 : bond 0.00334 ( 3) link_ALPHA1-6 : angle 2.09956 ( 9) link_BETA1-4 : bond 0.00800 ( 20) link_BETA1-4 : angle 3.19096 ( 60) link_NAG-ASN : bond 0.00390 ( 46) link_NAG-ASN : angle 2.08218 ( 138) *********************** 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 208 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 472 MET cc_start: 0.9087 (mmm) cc_final: 0.8776 (mmm) REVERT: I 88 ASN cc_start: 0.8047 (m-40) cc_final: 0.7843 (m-40) REVERT: I 231 LYS cc_start: 0.8311 (mptt) cc_final: 0.7994 (mmtm) REVERT: M 49 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: O 542 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5296 (mt) REVERT: O 562 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7882 (pp) REVERT: O 630 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7951 (mtt180) REVERT: O 650 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: P 632 ILE cc_start: 0.9179 (pt) cc_final: 0.8905 (tt) REVERT: Q 525 SER cc_start: 0.7758 (p) cc_final: 0.6957 (m) REVERT: Q 543 SER cc_start: 0.6480 (t) cc_final: 0.6268 (p) outliers start: 41 outliers final: 24 residues processed: 196 average time/residue: 0.1457 time to fit residues: 43.7219 Evaluate side-chains 186 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 444 SER Chi-restraints excluded: chain M residue 38 VAL 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 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 542 LEU Chi-restraints excluded: chain O residue 562 LEU Chi-restraints excluded: chain O residue 630 ARG Chi-restraints excluded: chain O residue 650 GLN Chi-restraints excluded: chain P residue 592 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 53 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 225 optimal weight: 0.1980 chunk 111 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 425 GLN ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 637 ASN Q 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110086 restraints weight = 35129.016| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.71 r_work: 0.3174 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21559 Z= 0.229 Angle : 0.742 11.462 29653 Z= 0.330 Chirality : 0.045 0.314 3780 Planarity : 0.003 0.029 3795 Dihedral : 8.528 76.775 4646 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.00 % Allowed : 12.47 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1634 helix: 0.97 (0.25), residues: 443 sheet: -0.96 (0.22), residues: 489 loop : -1.00 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 497 TYR 0.015 0.001 TYR Q 635 PHE 0.017 0.002 PHE I 53 TRP 0.013 0.001 TRP I 476 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00521 (21460) covalent geometry : angle 0.71565 (29383) SS BOND : bond 0.00559 ( 27) SS BOND : angle 0.85522 ( 54) hydrogen bonds : bond 0.04297 ( 701) hydrogen bonds : angle 4.93711 ( 1884) link_ALPHA1-3 : bond 0.02035 ( 3) link_ALPHA1-3 : angle 3.20511 ( 9) link_ALPHA1-6 : bond 0.00224 ( 3) link_ALPHA1-6 : angle 1.79123 ( 9) link_BETA1-4 : bond 0.00793 ( 20) link_BETA1-4 : angle 3.08828 ( 60) link_NAG-ASN : bond 0.00322 ( 46) link_NAG-ASN : angle 1.98593 ( 138) *********************** 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 210 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 472 MET cc_start: 0.9048 (mmm) cc_final: 0.8757 (mmm) REVERT: M 49 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: O 542 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5507 (mt) REVERT: O 562 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7796 (pp) REVERT: O 639 ILE cc_start: 0.9266 (mm) cc_final: 0.9030 (mt) REVERT: O 650 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: P 540 GLN cc_start: 0.7335 (tt0) cc_final: 0.6834 (mt0) REVERT: P 614 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7571 (ttmt) REVERT: P 623 MET cc_start: 0.7691 (ttp) cc_final: 0.6930 (ttp) REVERT: P 632 ILE cc_start: 0.9159 (pt) cc_final: 0.8824 (tt) REVERT: Q 525 SER cc_start: 0.7817 (p) cc_final: 0.7331 (m) outliers start: 45 outliers final: 24 residues processed: 197 average time/residue: 0.1455 time to fit residues: 43.9742 Evaluate side-chains 190 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain D residue 427 VAL 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 339 THR Chi-restraints excluded: chain M residue 38 VAL 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 M residue 331 ILE Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 562 LEU Chi-restraints excluded: chain O residue 650 GLN 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 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 Chi-restraints excluded: chain Q residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 275 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 274 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108260 restraints weight = 35865.077| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.76 r_work: 0.3126 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 21559 Z= 0.315 Angle : 0.841 12.974 29653 Z= 0.372 Chirality : 0.049 0.385 3780 Planarity : 0.003 0.031 3795 Dihedral : 8.763 78.667 4646 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.60 % Allowed : 13.41 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1634 helix: 0.86 (0.25), residues: 443 sheet: -0.97 (0.22), residues: 489 loop : -1.06 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 477 TYR 0.012 0.002 TYR D 223 PHE 0.018 0.002 PHE I 53 TRP 0.016 0.002 TRP O 568 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00717 (21460) covalent geometry : angle 0.81535 (29383) SS BOND : bond 0.00689 ( 27) SS BOND : angle 0.97380 ( 54) hydrogen bonds : bond 0.04593 ( 701) hydrogen bonds : angle 5.08091 ( 1884) link_ALPHA1-3 : bond 0.02003 ( 3) link_ALPHA1-3 : angle 3.01119 ( 9) link_ALPHA1-6 : bond 0.00297 ( 3) link_ALPHA1-6 : angle 2.11125 ( 9) link_BETA1-4 : bond 0.00849 ( 20) link_BETA1-4 : angle 3.28982 ( 60) link_NAG-ASN : bond 0.00413 ( 46) link_NAG-ASN : angle 2.12829 ( 138) *********************** 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 207 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 472 MET cc_start: 0.9098 (mmm) cc_final: 0.8796 (mmm) REVERT: I 185 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: M 49 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8506 (mt-10) REVERT: O 542 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.5846 (mt) REVERT: O 562 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7882 (pp) REVERT: O 650 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: P 540 GLN cc_start: 0.7397 (tt0) cc_final: 0.6897 (mt0) REVERT: P 632 ILE cc_start: 0.9127 (pt) cc_final: 0.8735 (tt) REVERT: Q 543 SER cc_start: 0.6641 (t) cc_final: 0.6404 (p) outliers start: 39 outliers final: 32 residues processed: 197 average time/residue: 0.1514 time to fit residues: 44.6827 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 : 0.446 ------------------------------------------------------------------------------- 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 339 THR Chi-restraints excluded: chain D residue 427 VAL 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 339 THR Chi-restraints excluded: chain I residue 390 SER Chi-restraints excluded: chain I residue 444 SER Chi-restraints excluded: chain M residue 38 VAL 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 185 GLU 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 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 562 LEU Chi-restraints excluded: chain O residue 602 CYS Chi-restraints excluded: chain O residue 650 GLN Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 648 ASN Chi-restraints excluded: chain Q residue 546 VAL Chi-restraints excluded: chain Q residue 562 LEU Chi-restraints excluded: chain Q residue 644 GLU Chi-restraints excluded: chain Q residue 648 ASN Chi-restraints excluded: chain Q residue 650 GLN Chi-restraints excluded: chain Q residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 239 optimal weight: 0.4980 chunk 241 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 229 ASN O 561 HIS O 588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113113 restraints weight = 35034.262| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.68 r_work: 0.3211 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21559 Z= 0.123 Angle : 0.631 11.527 29653 Z= 0.282 Chirality : 0.041 0.248 3780 Planarity : 0.002 0.038 3795 Dihedral : 7.989 73.076 4646 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.27 % Allowed : 13.94 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.21), residues: 1634 helix: 1.00 (0.25), residues: 445 sheet: -0.79 (0.22), residues: 489 loop : -0.94 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 353 TYR 0.011 0.001 TYR Q 635 PHE 0.014 0.001 PHE D 53 TRP 0.015 0.001 TRP Q 628 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00267 (21460) covalent geometry : angle 0.60515 (29383) SS BOND : bond 0.00373 ( 27) SS BOND : angle 0.67257 ( 54) hydrogen bonds : bond 0.03674 ( 701) hydrogen bonds : angle 4.65345 ( 1884) link_ALPHA1-3 : bond 0.01925 ( 3) link_ALPHA1-3 : angle 2.91928 ( 9) link_ALPHA1-6 : bond 0.00289 ( 3) link_ALPHA1-6 : angle 1.50464 ( 9) link_BETA1-4 : bond 0.00822 ( 20) link_BETA1-4 : angle 2.91877 ( 60) link_NAG-ASN : bond 0.00290 ( 46) link_NAG-ASN : angle 1.72836 ( 138) *********************** 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 214 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.8390 (ttp) cc_final: 0.8121 (ttm) REVERT: I 185 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: M 49 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: O 542 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5747 (mt) REVERT: O 562 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7771 (pp) REVERT: O 639 ILE cc_start: 0.9276 (mm) cc_final: 0.9055 (mt) REVERT: P 540 GLN cc_start: 0.7056 (tt0) cc_final: 0.6606 (mt0) REVERT: P 632 ILE cc_start: 0.9178 (pt) cc_final: 0.8837 (tt) REVERT: Q 525 SER cc_start: 0.7964 (p) cc_final: 0.7419 (m) REVERT: Q 623 MET cc_start: 0.7533 (ttp) cc_final: 0.6944 (ttp) REVERT: Q 632 ILE cc_start: 0.9130 (pt) cc_final: 0.8706 (tp) outliers start: 34 outliers final: 22 residues processed: 206 average time/residue: 0.1431 time to fit residues: 45.2643 Evaluate side-chains 197 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 427 VAL 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 390 SER Chi-restraints excluded: chain M residue 38 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 526 THR Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 562 LEU Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 603 THR Chi-restraints excluded: chain P residue 648 ASN 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 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 32 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 143 optimal weight: 0.0020 chunk 117 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111342 restraints weight = 35402.492| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.73 r_work: 0.3176 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21559 Z= 0.208 Angle : 0.708 11.814 29653 Z= 0.315 Chirality : 0.044 0.293 3780 Planarity : 0.003 0.040 3795 Dihedral : 8.100 74.782 4646 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.92 % Favored : 96.02 % Rotamer: Outliers : 2.07 % Allowed : 14.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.21), residues: 1634 helix: 1.01 (0.25), residues: 451 sheet: -0.81 (0.22), residues: 489 loop : -0.92 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 308 TYR 0.011 0.001 TYR O 635 PHE 0.015 0.002 PHE I 53 TRP 0.032 0.001 TRP O 628 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00470 (21460) covalent geometry : angle 0.68275 (29383) SS BOND : bond 0.00519 ( 27) SS BOND : angle 0.78854 ( 54) hydrogen bonds : bond 0.04000 ( 701) hydrogen bonds : angle 4.73201 ( 1884) link_ALPHA1-3 : bond 0.01767 ( 3) link_ALPHA1-3 : angle 2.73273 ( 9) link_ALPHA1-6 : bond 0.00205 ( 3) link_ALPHA1-6 : angle 1.78238 ( 9) link_BETA1-4 : bond 0.00828 ( 20) link_BETA1-4 : angle 3.06342 ( 60) link_NAG-ASN : bond 0.00323 ( 46) link_NAG-ASN : angle 1.83519 ( 138) *********************** 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 196 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 MET cc_start: 0.8473 (ttp) cc_final: 0.8256 (ttm) REVERT: I 185 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7391 (pp20) REVERT: O 542 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5827 (mt) REVERT: O 562 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7809 (pp) REVERT: O 632 ILE cc_start: 0.8925 (mm) cc_final: 0.8676 (mm) REVERT: O 639 ILE cc_start: 0.9308 (mm) cc_final: 0.9047 (mt) REVERT: P 540 GLN cc_start: 0.7031 (tt0) cc_final: 0.6592 (mt0) REVERT: P 632 ILE cc_start: 0.9164 (pt) cc_final: 0.8774 (tt) REVERT: Q 632 ILE cc_start: 0.9135 (pt) cc_final: 0.8640 (tp) outliers start: 31 outliers final: 26 residues processed: 188 average time/residue: 0.1538 time to fit residues: 43.9612 Evaluate side-chains 190 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 427 VAL 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 390 SER Chi-restraints excluded: chain M residue 38 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 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 561 HIS Chi-restraints excluded: chain O residue 562 LEU Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 603 THR Chi-restraints excluded: chain P residue 648 ASN 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 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 195 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 279 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 271 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 283 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 ASN P 637 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107834 restraints weight = 35703.331| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.76 r_work: 0.3123 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 21559 Z= 0.319 Angle : 0.845 12.215 29653 Z= 0.375 Chirality : 0.049 0.390 3780 Planarity : 0.003 0.042 3795 Dihedral : 8.553 77.820 4646 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.33 % Allowed : 14.48 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.21), residues: 1634 helix: 0.91 (0.25), residues: 450 sheet: -0.90 (0.23), residues: 462 loop : -0.86 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 308 TYR 0.012 0.002 TYR I 223 PHE 0.018 0.002 PHE I 53 TRP 0.021 0.002 TRP O 628 HIS 0.006 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00725 (21460) covalent geometry : angle 0.81990 (29383) SS BOND : bond 0.00688 ( 27) SS BOND : angle 0.97970 ( 54) hydrogen bonds : bond 0.04528 ( 701) hydrogen bonds : angle 5.06751 ( 1884) link_ALPHA1-3 : bond 0.01763 ( 3) link_ALPHA1-3 : angle 2.50364 ( 9) link_ALPHA1-6 : bond 0.00352 ( 3) link_ALPHA1-6 : angle 2.00269 ( 9) link_BETA1-4 : bond 0.00808 ( 20) link_BETA1-4 : angle 3.30350 ( 60) link_NAG-ASN : bond 0.00435 ( 46) link_NAG-ASN : angle 2.10614 ( 138) *********************** 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 193 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 185 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: M 49 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8518 (mt-10) REVERT: O 542 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6074 (mt) REVERT: O 562 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7841 (pp) REVERT: O 632 ILE cc_start: 0.8876 (mm) cc_final: 0.8650 (mm) REVERT: O 639 ILE cc_start: 0.9332 (mm) cc_final: 0.9061 (mt) REVERT: P 540 GLN cc_start: 0.7368 (tt0) cc_final: 0.6358 (tp40) REVERT: P 629 ASP cc_start: 0.9053 (t70) cc_final: 0.8850 (t0) REVERT: P 632 ILE cc_start: 0.9091 (pt) cc_final: 0.8717 (tt) REVERT: Q 632 ILE cc_start: 0.9141 (pt) cc_final: 0.8651 (tp) outliers start: 35 outliers final: 27 residues processed: 183 average time/residue: 0.1393 time to fit residues: 38.7502 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 : 0.624 ------------------------------------------------------------------------------- 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 427 VAL 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 198 THR Chi-restraints excluded: chain I residue 339 THR Chi-restraints excluded: chain I residue 444 SER Chi-restraints excluded: chain M residue 38 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 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 562 LEU Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 603 THR Chi-restraints excluded: chain P residue 648 ASN 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 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 106 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106767 restraints weight = 35444.099| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.83 r_work: 0.3094 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 21559 Z= 0.342 Angle : 0.876 12.692 29653 Z= 0.389 Chirality : 0.051 0.412 3780 Planarity : 0.003 0.047 3795 Dihedral : 8.800 78.443 4646 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 2.40 % Allowed : 14.88 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.21), residues: 1634 helix: 0.72 (0.25), residues: 455 sheet: -1.03 (0.23), residues: 465 loop : -0.95 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 308 TYR 0.013 0.002 TYR I 223 PHE 0.018 0.003 PHE I 53 TRP 0.053 0.002 TRP O 628 HIS 0.019 0.002 HIS O 616 Details of bonding type rmsd covalent geometry : bond 0.00779 (21460) covalent geometry : angle 0.85100 (29383) SS BOND : bond 0.00709 ( 27) SS BOND : angle 0.98395 ( 54) hydrogen bonds : bond 0.04677 ( 701) hydrogen bonds : angle 5.14652 ( 1884) link_ALPHA1-3 : bond 0.01670 ( 3) link_ALPHA1-3 : angle 2.41813 ( 9) link_ALPHA1-6 : bond 0.00379 ( 3) link_ALPHA1-6 : angle 1.98742 ( 9) link_BETA1-4 : bond 0.00802 ( 20) link_BETA1-4 : angle 3.41132 ( 60) link_NAG-ASN : bond 0.00461 ( 46) link_NAG-ASN : angle 2.17776 ( 138) ********************** 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 190 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 185 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: M 49 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8611 (mt-10) REVERT: O 534 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7541 (pp) REVERT: O 542 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6115 (mt) REVERT: O 562 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7789 (pp) REVERT: O 632 ILE cc_start: 0.8858 (mm) cc_final: 0.8544 (mm) REVERT: O 639 ILE cc_start: 0.9351 (mm) cc_final: 0.9078 (mt) REVERT: P 540 GLN cc_start: 0.7369 (tt0) cc_final: 0.6388 (tp40) REVERT: P 632 ILE cc_start: 0.9137 (pt) cc_final: 0.8761 (tt) REVERT: Q 632 ILE cc_start: 0.9135 (pt) cc_final: 0.8612 (tp) outliers start: 36 outliers final: 26 residues processed: 183 average time/residue: 0.1338 time to fit residues: 37.9395 Evaluate side-chains 179 residues out of total 1499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 427 VAL 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 I residue 444 SER Chi-restraints excluded: chain M residue 38 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 M residue 331 ILE Chi-restraints excluded: chain O residue 526 THR Chi-restraints excluded: chain O residue 534 LEU Chi-restraints excluded: chain O residue 542 LEU Chi-restraints excluded: chain O residue 562 LEU Chi-restraints excluded: chain P residue 592 ILE Chi-restraints excluded: chain P residue 603 THR Chi-restraints excluded: chain P residue 648 ASN 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 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 245 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 637 ASN 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 = 0.128856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108247 restraints weight = 35622.300| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.76 r_work: 0.3126 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21559 Z= 0.220 Angle : 0.745 12.175 29653 Z= 0.332 Chirality : 0.046 0.314 3780 Planarity : 0.003 0.050 3795 Dihedral : 8.422 74.933 4646 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % Rotamer: Outliers : 2.27 % Allowed : 15.08 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1634 helix: 0.87 (0.25), residues: 450 sheet: -0.96 (0.23), residues: 465 loop : -0.90 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 308 TYR 0.011 0.001 TYR I 223 PHE 0.016 0.002 PHE I 53 TRP 0.051 0.002 TRP O 628 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00502 (21460) covalent geometry : angle 0.71864 (29383) SS BOND : bond 0.00473 ( 27) SS BOND : angle 1.15179 ( 54) hydrogen bonds : bond 0.04164 ( 701) hydrogen bonds : angle 4.89109 ( 1884) link_ALPHA1-3 : bond 0.01611 ( 3) link_ALPHA1-3 : angle 2.36148 ( 9) link_ALPHA1-6 : bond 0.00175 ( 3) link_ALPHA1-6 : angle 1.69725 ( 9) link_BETA1-4 : bond 0.00818 ( 20) link_BETA1-4 : angle 3.19590 ( 60) link_NAG-ASN : bond 0.00347 ( 46) link_NAG-ASN : angle 1.93338 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.97 seconds wall clock time: 77 minutes 39.08 seconds (4659.08 seconds total)