Starting phenix.real_space_refine on Tue Dec 31 22:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vtt_21383/12_2024/6vtt_21383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vtt_21383/12_2024/6vtt_21383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vtt_21383/12_2024/6vtt_21383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vtt_21383/12_2024/6vtt_21383.map" model { file = "/net/cci-nas-00/data/ceres_data/6vtt_21383/12_2024/6vtt_21383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vtt_21383/12_2024/6vtt_21383.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.071 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 110 5.16 5 C 10385 2.51 5 N 2712 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16607 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3400 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Chain: "E" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3410 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 22, 'TRANS': 408} Chain breaks: 5 Chain: "G" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3448 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 5 Chain: "H" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1026 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1012 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 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: "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: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "F" 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: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 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 Time building chain proxies: 10.53, per 1000 atoms: 0.63 Number of scatterers: 16607 At special positions: 0 Unit cell: (128.244, 128.244, 167.703, 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 110 16.00 O 3400 8.00 N 2712 7.00 C 10385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100A" - pdb=" SG CYS H 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN b 4 " - " MAN b 5 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 6 " " MAN V 4 " - " MAN V 5 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 5 " " BMA b 3 " - " MAN b 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1611 " - " ASN A 611 " " NAG A1637 " - " ASN A 637 " " NAG B1611 " - " ASN B 611 " " NAG B1637 " - " ASN B 637 " " NAG C1611 " - " ASN C 611 " " NAG C1637 " - " ASN C 637 " " NAG D 1 " - " ASN F 130 " " NAG E1088 " - " ASN E 88 " " NAG E1130 " - " ASN E 130 " " NAG E1156 " - " ASN E 156 " " NAG E1160 " - " ASN E 160 " " NAG E1230 " - " ASN E 230 " " NAG E1241 " - " ASN E 241 " " NAG E1276 " - " ASN E 276 " " NAG E1289 " - " ASN E 289 " " NAG E1301 " - " ASN E 301 " " NAG E1332 " - " ASN E 332 " " NAG E1356 " - " ASN E 356 " " NAG E1362 " - " ASN E 362 " " NAG E1442 " - " ASN E 442 " " NAG E1443 " - " ASN E 448 " " NAG E1502 " - " ASN E 502 " " NAG F1088 " - " ASN F 88 " " NAG F1234 " - " ASN F 234 " " NAG F1289 " - " ASN F 289 " " NAG F1301 " - " ASN F 301 " " NAG F1356 " - " ASN F 356 " " NAG F1362 " - " ASN F 362 " " NAG F1386 " - " ASN F 386 " " NAG F1442 " - " ASN F 442 " " NAG F1448 " - " ASN F 448 " " NAG F1502 " - " ASN F 502 " " NAG G1088 " - " ASN G 88 " " NAG G1234 " - " ASN G 234 " " NAG G1276 " - " ASN G 276 " " NAG G1301 " - " ASN G 301 " " NAG G1356 " - " ASN G 356 " " NAG G1362 " - " ASN G 362 " " NAG G1386 " - " ASN G 386 " " NAG G1442 " - " ASN G 442 " " NAG G1448 " - " ASN G 448 " " NAG G1502 " - " ASN G 502 " " NAG I 1 " - " ASN F 156 " " NAG J 1 " - " ASN F 160 " " NAG K 1 " - " ASN F 197 " " NAG M 1 " - " ASN F 230 " " NAG N 1 " - " ASN F 241 " " NAG O 1 " - " ASN F 262 " " NAG P 1 " - " ASN F 276 " " NAG Q 1 " - " ASN F 332 " " NAG R 1 " - " ASN E 197 " " NAG S 1 " - " ASN E 234 " " NAG T 1 " - " ASN E 262 " " NAG U 1 " - " ASN E 386 " " NAG V 1 " - " ASN G 130 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 230 " " NAG a 1 " - " ASN G 241 " " NAG b 1 " - " ASN G 262 " " NAG c 1 " - " ASN G 289 " " NAG d 1 " - " ASN G 332 " Time building additional restraints: 5.30 Conformation dependent library (CDL) restraints added in 2.1 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 38 sheets defined 21.2% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.569A pdb=" N HIS F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 109 " --> pdb=" O HIS F 105 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 349 removed outlier: 3.649A pdb=" N THR F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 353 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.565A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU F 429 " --> pdb=" O MET F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 429' Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.959A pdb=" N SER E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.718A pdb=" N LYS E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 349 removed outlier: 3.575A pdb=" N SER E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.781A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.603A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.686A pdb=" N GLU G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 356 removed outlier: 3.910A pdb=" N ARG G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU G 347 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 349 " --> pdb=" O VAL G 345 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG G 350 " --> pdb=" O SER G 346 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.858A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.737A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.944A pdb=" N TRP H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.962A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.582A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU L 83 " --> pdb=" O THR L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.936A pdb=" N PHE A 519 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 521 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A 522 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 removed outlier: 3.507A pdb=" N ALA A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 529 through 542 removed outlier: 4.306A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.710A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.925A pdb=" N ILE A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 623 " --> pdb=" O TYR A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 623' Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.530A pdb=" N ASP A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 633 " --> pdb=" O MET A 629 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.855A pdb=" N LYS A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 655 " --> pdb=" O PHE A 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 4.338A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 539 " --> pdb=" O ASN B 535 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.735A pdb=" N GLU B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.067A pdb=" N ILE B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP B 623 " --> pdb=" O TYR B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 623' Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.548A pdb=" N ASP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 640 through 658 removed outlier: 3.654A pdb=" N LYS B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 520 removed outlier: 3.689A pdb=" N PHE C 519 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 520 " --> pdb=" O GLY C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 514 through 520' Processing helix chain 'C' and resid 532 through 543 removed outlier: 3.935A pdb=" N LEU C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL C 539 " --> pdb=" O ASN C 535 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 595 removed outlier: 3.558A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 593 " --> pdb=" O VAL C 589 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.577A pdb=" N TRP C 623 " --> pdb=" O TYR C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 633 removed outlier: 3.606A pdb=" N ARG C 633 " --> pdb=" O MET C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 659 removed outlier: 3.620A pdb=" N LEU C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.592A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 92 through 93 removed outlier: 3.926A pdb=" N GLY F 237 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 181 through 185 removed outlier: 7.452A pdb=" N GLU F 190 " --> pdb=" O LEU F 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.864A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 259 through 260 removed outlier: 6.942A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N LYS F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N VAL F 292 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 259 through 260 removed outlier: 6.942A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N THR F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N ILE F 294 " --> pdb=" O THR F 444 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N LYS F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N VAL F 292 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.974A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS F 385 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 304 through 312 removed outlier: 3.507A pdb=" N PHE F 317 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 309 " --> pdb=" O GLN F 315 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 358 through 361 Processing sheet with id=AB3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.074A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.655A pdb=" N THR E 244 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 93 removed outlier: 4.387A pdb=" N PHE E 93 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 121 removed outlier: 4.016A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AB8, first strand: chain 'E' and resid 181 through 185 removed outlier: 7.842A pdb=" N GLU E 190 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 271 through 273 Processing sheet with id=AC1, first strand: chain 'E' and resid 292 through 297 removed outlier: 3.975A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS E 296 " --> pdb=" O CYS E 445 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.900A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS E 305 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR E 318 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 330 through 331 Processing sheet with id=AC4, first strand: chain 'E' and resid 376 through 378 Processing sheet with id=AC5, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC6, first strand: chain 'G' and resid 494 through 499 removed outlier: 4.944A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'G' and resid 91 through 92 Processing sheet with id=AC9, first strand: chain 'G' and resid 132 through 133 removed outlier: 4.725A pdb=" N ARG G 171 " --> pdb=" O GLU H 100B" (cutoff:3.500A) removed outlier: 8.532A pdb=" N GLU H 100B" --> pdb=" O ARG G 171 " (cutoff:3.500A) removed outlier: 14.969A pdb=" N TYR G 173 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 19.152A pdb=" N GLU H 100 " --> pdb=" O TYR G 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS H 100A" --> pdb=" O SER H 100T" (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER H 100T" --> pdb=" O CYS H 100A" (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU H 100C" --> pdb=" O ALA H 100R" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'G' and resid 201 through 203 Processing sheet with id=AD3, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.630A pdb=" N ILE G 271 " --> pdb=" O HIS G 287 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 377 through 378 removed outlier: 3.641A pdb=" N CYS G 378 " --> pdb=" O GLU G 381 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS G 296 " --> pdb=" O CYS G 445 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS G 445 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.421A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY H 10 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY H 10 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS H 94 " --> pdb=" O ASN H 102 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 19 through 24 removed outlier: 4.410A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 45 through 48 removed outlier: 5.966A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 45 through 48 removed outlier: 5.966A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1152 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: 5.83 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5123 1.34 - 1.47: 4326 1.47 - 1.60: 7326 1.60 - 1.73: 2 1.73 - 1.86: 144 Bond restraints: 16921 Sorted by residual: bond pdb=" O2 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.461 1.635 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.543 0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.548 0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" N GLU H 100C" pdb=" CA GLU H 100C" ideal model delta sigma weight residual 1.460 1.486 -0.026 1.17e-02 7.31e+03 5.03e+00 ... (remaining 16916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.74: 22922 5.74 - 11.48: 27 11.48 - 17.21: 3 17.21 - 22.95: 3 22.95 - 28.69: 4 Bond angle restraints: 22959 Sorted by residual: angle pdb=" O2 TYS H 100H" pdb=" S TYS H 100H" pdb=" O3 TYS H 100H" ideal model delta sigma weight residual 115.38 86.69 28.69 3.00e+00 1.11e-01 9.14e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 115.16 86.70 28.46 3.00e+00 1.11e-01 9.00e+01 angle pdb=" O1 TYS H 100I" pdb=" S TYS H 100I" pdb=" O2 TYS H 100I" ideal model delta sigma weight residual 114.11 85.86 28.25 3.00e+00 1.11e-01 8.86e+01 angle pdb=" O1 TYS H 100H" pdb=" S TYS H 100H" pdb=" O2 TYS H 100H" ideal model delta sigma weight residual 114.11 86.76 27.35 3.00e+00 1.11e-01 8.31e+01 angle pdb=" OH TYS H 100I" pdb=" S TYS H 100I" pdb=" O3 TYS H 100I" ideal model delta sigma weight residual 100.21 119.65 -19.44 3.00e+00 1.11e-01 4.20e+01 ... (remaining 22954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 10786 22.40 - 44.80: 495 44.80 - 67.20: 108 67.20 - 89.60: 46 89.60 - 112.00: 28 Dihedral angle restraints: 11463 sinusoidal: 5922 harmonic: 5541 Sorted by residual: dihedral pdb=" C ARG F 192 " pdb=" N ARG F 192 " pdb=" CA ARG F 192 " pdb=" CB ARG F 192 " ideal model delta harmonic sigma weight residual -122.60 -105.76 -16.84 0 2.50e+00 1.60e-01 4.54e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual -86.00 -133.75 47.75 1 1.00e+01 1.00e-02 3.15e+01 dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 11460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2678 0.095 - 0.189: 179 0.189 - 0.284: 17 0.284 - 0.378: 3 0.378 - 0.473: 3 Chirality restraints: 2880 Sorted by residual: chirality pdb=" C1 MAN V 6 " pdb=" O3 BMA V 3 " pdb=" C2 MAN V 6 " pdb=" O5 MAN V 6 " both_signs ideal model delta sigma weight residual False 2.40 1.99 0.41 2.00e-02 2.50e+03 4.24e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 MAN V 4 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.88e+01 ... (remaining 2877 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " -0.367 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG V 2 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " -0.102 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " 0.558 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G1088 " -0.120 2.00e-02 2.50e+03 9.65e-02 1.16e+02 pdb=" C7 NAG G1088 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG G1088 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG G1088 " 0.149 2.00e-02 2.50e+03 pdb=" O7 NAG G1088 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 87 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C GLU G 87 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU G 87 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN G 88 " -0.013 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1922 2.75 - 3.29: 15557 3.29 - 3.83: 24992 3.83 - 4.36: 28809 4.36 - 4.90: 50112 Nonbonded interactions: 121392 Sorted by model distance: nonbonded pdb=" O4 MAN V 6 " pdb=" O6 MAN V 6 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR F 37 " pdb=" O CYS A 604 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN F 258 " pdb=" OG1 THR F 387 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLN E 363 " pdb=" OG SER E 388 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLU E 164 " pdb=" CB ASN G 197 " model vdw 2.271 3.440 ... (remaining 121387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 513 through 566 or resid 568 through 660 or resid 1611 thr \ ough 1637)) selection = (chain 'C' and (resid 513 through 544 or resid 568 through 660 or resid 1611 thr \ ough 1637)) } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 34 through 60 or resid 65 through 135 or resid 152 through \ 186 or resid 189 through 394 or resid 411 through 504 or resid 1130 through 133 \ 2)) selection = (chain 'F' and (resid 34 through 60 or resid 65 through 186 or resid 189 through \ 459 or resid 464 through 504 or resid 1234 through 1502)) selection = (chain 'G' and (resid 34 through 135 or resid 152 through 394 or resid 411 throu \ gh 459 or resid 464 through 504 or resid 1088 through 1448)) } ncs_group { reference = chain 'K' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'V' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.870 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.005 0.174 16921 Z= 0.294 Angle : 0.825 28.688 22959 Z= 0.351 Chirality : 0.052 0.473 2880 Planarity : 0.007 0.315 2776 Dihedral : 14.724 112.005 7782 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.15), residues: 1872 helix: -4.20 (0.13), residues: 330 sheet: -2.46 (0.21), residues: 433 loop : -3.05 (0.15), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 338 HIS 0.002 0.000 HIS E 374 PHE 0.008 0.001 PHE F 233 TYR 0.004 0.001 TYR G 484 ARG 0.003 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.7974 (p0) cc_final: 0.7636 (p0) REVERT: F 217 TYR cc_start: 0.7698 (m-10) cc_final: 0.7463 (m-10) REVERT: E 107 ASP cc_start: 0.7943 (t0) cc_final: 0.7533 (t0) REVERT: E 258 GLN cc_start: 0.8273 (mt0) cc_final: 0.8054 (mt0) REVERT: H 28 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7662 (ptp90) REVERT: H 30 ASP cc_start: 0.8593 (p0) cc_final: 0.8103 (p0) REVERT: H 32 TYR cc_start: 0.6782 (m-80) cc_final: 0.6176 (m-10) REVERT: H 34 MET cc_start: 0.8396 (mmm) cc_final: 0.7953 (mpp) REVERT: H 38 ARG cc_start: 0.6893 (ptt180) cc_final: 0.5756 (ptp-170) REVERT: H 39 GLN cc_start: 0.7360 (tt0) cc_final: 0.6746 (tt0) REVERT: H 48 VAL cc_start: 0.5732 (t) cc_final: 0.5486 (t) REVERT: H 51 ILE cc_start: 0.9073 (tt) cc_final: 0.8407 (mm) REVERT: H 64 TRP cc_start: 0.6877 (m-10) cc_final: 0.6364 (m-90) REVERT: H 101 ILE cc_start: 0.8644 (mm) cc_final: 0.8404 (pt) REVERT: L 50 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7970 (tm-30) REVERT: L 87 TYR cc_start: 0.5341 (m-80) cc_final: 0.4553 (m-80) REVERT: B 584 GLU cc_start: 0.8215 (tp30) cc_final: 0.7999 (mm-30) REVERT: B 595 MET cc_start: 0.7380 (mtm) cc_final: 0.7063 (mtm) REVERT: C 607 ASN cc_start: 0.8543 (t0) cc_final: 0.8247 (t0) REVERT: C 620 ASN cc_start: 0.8115 (t0) cc_final: 0.7747 (t0) REVERT: C 657 GLU cc_start: 0.9039 (tp30) cc_final: 0.8812 (tt0) REVERT: C 658 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8154 (mptt) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3862 time to fit residues: 107.5610 Evaluate side-chains 128 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 148 optimal weight: 0.0000 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 216 HIS G 66 HIS ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16921 Z= 0.206 Angle : 0.612 9.716 22959 Z= 0.296 Chirality : 0.046 0.257 2880 Planarity : 0.004 0.033 2776 Dihedral : 12.834 92.056 4176 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.65 % Allowed : 8.20 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.17), residues: 1872 helix: -2.16 (0.23), residues: 334 sheet: -1.99 (0.22), residues: 475 loop : -2.61 (0.16), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 35 HIS 0.003 0.001 HIS E 374 PHE 0.012 0.001 PHE F 376 TYR 0.022 0.001 TYR L 36 ARG 0.004 0.000 ARG E 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.8047 (p0) cc_final: 0.7783 (p0) REVERT: E 192 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7152 (ttm170) REVERT: G 302 MET cc_start: 0.8579 (mmt) cc_final: 0.8292 (mmp) REVERT: H 30 ASP cc_start: 0.8680 (p0) cc_final: 0.8283 (p0) REVERT: H 38 ARG cc_start: 0.7272 (ptt180) cc_final: 0.6460 (ptp90) REVERT: H 39 GLN cc_start: 0.7060 (tt0) cc_final: 0.6810 (tt0) REVERT: H 51 ILE cc_start: 0.9019 (tt) cc_final: 0.8411 (mm) REVERT: H 64 TRP cc_start: 0.6913 (m-10) cc_final: 0.6426 (m-90) REVERT: H 108 MET cc_start: 0.8175 (tpp) cc_final: 0.7931 (tpp) REVERT: L 32 PHE cc_start: 0.7678 (m-80) cc_final: 0.7182 (m-80) REVERT: L 50 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8076 (tm-30) REVERT: L 87 TYR cc_start: 0.6008 (m-80) cc_final: 0.5753 (m-80) REVERT: C 607 ASN cc_start: 0.8471 (t0) cc_final: 0.8250 (t0) REVERT: C 619 TYR cc_start: 0.8058 (t80) cc_final: 0.7704 (t80) outliers start: 11 outliers final: 4 residues processed: 142 average time/residue: 0.3165 time to fit residues: 68.2245 Evaluate side-chains 119 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain B residue 539 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 chunk 153 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16921 Z= 0.147 Angle : 0.563 9.853 22959 Z= 0.267 Chirality : 0.046 0.251 2880 Planarity : 0.004 0.076 2776 Dihedral : 11.164 84.999 4176 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.83 % Allowed : 10.27 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.18), residues: 1872 helix: -1.17 (0.26), residues: 333 sheet: -1.75 (0.22), residues: 482 loop : -2.29 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 35 HIS 0.003 0.001 HIS F 216 PHE 0.012 0.001 PHE L 98 TYR 0.015 0.001 TYR C 638 ARG 0.008 0.000 ARG E 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 97 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (ptmt) REVERT: F 195 ASN cc_start: 0.8080 (p0) cc_final: 0.7782 (p0) REVERT: G 302 MET cc_start: 0.8653 (mmt) cc_final: 0.8356 (mmp) REVERT: H 39 GLN cc_start: 0.7219 (tt0) cc_final: 0.6757 (tt0) REVERT: H 51 ILE cc_start: 0.8982 (tt) cc_final: 0.8264 (mm) REVERT: H 64 TRP cc_start: 0.6952 (m-10) cc_final: 0.6481 (m-90) REVERT: H 91 TYR cc_start: 0.7711 (m-80) cc_final: 0.7463 (m-80) REVERT: H 108 MET cc_start: 0.8247 (tpp) cc_final: 0.7946 (tpp) REVERT: L 32 PHE cc_start: 0.7695 (m-80) cc_final: 0.6672 (m-80) REVERT: L 87 TYR cc_start: 0.6369 (m-80) cc_final: 0.6081 (m-80) REVERT: C 607 ASN cc_start: 0.8480 (t0) cc_final: 0.8264 (t0) REVERT: C 619 TYR cc_start: 0.8111 (t80) cc_final: 0.7748 (t80) outliers start: 14 outliers final: 5 residues processed: 138 average time/residue: 0.3035 time to fit residues: 64.1362 Evaluate side-chains 121 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain B residue 655 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 0.2980 chunk 172 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 90 optimal weight: 0.0470 chunk 163 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16921 Z= 0.209 Angle : 0.581 10.587 22959 Z= 0.275 Chirality : 0.046 0.260 2880 Planarity : 0.003 0.036 2776 Dihedral : 9.835 77.097 4176 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.42 % Allowed : 11.86 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.18), residues: 1872 helix: -0.61 (0.29), residues: 333 sheet: -1.59 (0.22), residues: 472 loop : -2.04 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 35 HIS 0.004 0.001 HIS E 374 PHE 0.020 0.002 PHE B 651 TYR 0.014 0.001 TYR C 638 ARG 0.005 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 195 ASN cc_start: 0.8144 (p0) cc_final: 0.7899 (p0) REVERT: E 170 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7503 (ttp80) REVERT: G 434 MET cc_start: 0.8368 (ptp) cc_final: 0.8080 (ptp) REVERT: H 38 ARG cc_start: 0.7114 (ptt180) cc_final: 0.6740 (ptp90) REVERT: H 39 GLN cc_start: 0.7372 (tt0) cc_final: 0.7119 (tt0) REVERT: H 51 ILE cc_start: 0.8991 (tt) cc_final: 0.8295 (mm) REVERT: H 64 TRP cc_start: 0.6943 (m-10) cc_final: 0.6440 (m-90) REVERT: H 91 TYR cc_start: 0.7634 (m-80) cc_final: 0.7243 (m-80) REVERT: H 98 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: H 100 GLU cc_start: 0.8969 (pt0) cc_final: 0.8758 (pt0) REVERT: L 87 TYR cc_start: 0.6433 (m-80) cc_final: 0.6062 (m-80) REVERT: C 607 ASN cc_start: 0.8487 (t0) cc_final: 0.8216 (t0) REVERT: C 612 SER cc_start: 0.8715 (m) cc_final: 0.8201 (t) REVERT: C 619 TYR cc_start: 0.8199 (t80) cc_final: 0.7799 (t80) REVERT: C 659 ASP cc_start: 0.5124 (m-30) cc_final: 0.4345 (p0) outliers start: 24 outliers final: 14 residues processed: 138 average time/residue: 0.2840 time to fit residues: 61.4202 Evaluate side-chains 129 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 632 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 67 ASN F 246 GLN F 392 ASN F 425 ASN H 39 GLN L 38 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16921 Z= 0.396 Angle : 0.689 11.086 22959 Z= 0.330 Chirality : 0.049 0.277 2880 Planarity : 0.004 0.046 2776 Dihedral : 9.614 69.202 4176 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.89 % Allowed : 13.51 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 1872 helix: -0.52 (0.29), residues: 327 sheet: -1.67 (0.22), residues: 476 loop : -2.00 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 427 HIS 0.006 0.002 HIS E 374 PHE 0.020 0.002 PHE G 391 TYR 0.013 0.001 TYR C 638 ARG 0.003 0.001 ARG F 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9075 (p) REVERT: F 302 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8229 (mmp) REVERT: E 170 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7474 (ttp80) REVERT: G 125 LEU cc_start: 0.9316 (tp) cc_final: 0.9064 (tp) REVERT: G 302 MET cc_start: 0.8717 (mmt) cc_final: 0.8435 (mmp) REVERT: H 38 ARG cc_start: 0.7105 (ptt180) cc_final: 0.6677 (ptp90) REVERT: H 51 ILE cc_start: 0.9002 (tt) cc_final: 0.8354 (mm) REVERT: H 64 TRP cc_start: 0.6877 (m-10) cc_final: 0.6357 (m-10) REVERT: H 91 TYR cc_start: 0.7572 (m-80) cc_final: 0.7265 (m-80) REVERT: H 98 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: H 99 ASP cc_start: 0.7678 (p0) cc_final: 0.7462 (p0) REVERT: C 607 ASN cc_start: 0.8676 (t0) cc_final: 0.8287 (t0) REVERT: C 612 SER cc_start: 0.8931 (m) cc_final: 0.8457 (t) outliers start: 32 outliers final: 20 residues processed: 139 average time/residue: 0.3041 time to fit residues: 63.6573 Evaluate side-chains 128 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 0.0870 chunk 45 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16921 Z= 0.193 Angle : 0.584 10.038 22959 Z= 0.276 Chirality : 0.046 0.268 2880 Planarity : 0.003 0.036 2776 Dihedral : 8.939 61.198 4176 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.71 % Allowed : 14.45 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.19), residues: 1872 helix: -0.26 (0.30), residues: 330 sheet: -1.55 (0.22), residues: 472 loop : -1.91 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 571 HIS 0.003 0.001 HIS F 216 PHE 0.015 0.001 PHE L 32 TYR 0.012 0.001 TYR C 638 ARG 0.005 0.000 ARG G 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9070 (p) REVERT: F 302 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8204 (mmp) REVERT: E 170 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7499 (ttp80) REVERT: E 290 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6828 (pp20) REVERT: G 125 LEU cc_start: 0.9256 (tp) cc_final: 0.9032 (tp) REVERT: H 38 ARG cc_start: 0.7025 (ptt180) cc_final: 0.6507 (ptp90) REVERT: H 51 ILE cc_start: 0.9016 (tt) cc_final: 0.8370 (mm) REVERT: H 64 TRP cc_start: 0.6892 (m-10) cc_final: 0.6376 (m-10) REVERT: H 91 TYR cc_start: 0.7581 (m-80) cc_final: 0.7186 (m-80) REVERT: H 98 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7441 (mm-30) REVERT: H 99 ASP cc_start: 0.7735 (p0) cc_final: 0.7513 (p0) REVERT: H 100 GLU cc_start: 0.8970 (pt0) cc_final: 0.8294 (pt0) REVERT: C 607 ASN cc_start: 0.8642 (t0) cc_final: 0.8279 (t0) REVERT: C 612 SER cc_start: 0.8884 (m) cc_final: 0.8373 (t) outliers start: 29 outliers final: 17 residues processed: 137 average time/residue: 0.3062 time to fit residues: 63.9948 Evaluate side-chains 132 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16921 Z= 0.163 Angle : 0.563 10.364 22959 Z= 0.265 Chirality : 0.045 0.266 2880 Planarity : 0.003 0.040 2776 Dihedral : 8.279 60.808 4176 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.18 % Allowed : 14.69 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.19), residues: 1872 helix: 0.00 (0.30), residues: 324 sheet: -1.46 (0.22), residues: 491 loop : -1.82 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP C 571 HIS 0.003 0.001 HIS F 216 PHE 0.014 0.001 PHE L 32 TYR 0.017 0.001 TYR L 36 ARG 0.005 0.000 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9073 (p) REVERT: F 302 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8200 (mmp) REVERT: E 170 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7576 (ttp80) REVERT: E 290 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: G 125 LEU cc_start: 0.9235 (tp) cc_final: 0.9027 (tp) REVERT: H 38 ARG cc_start: 0.6984 (ptt180) cc_final: 0.6528 (ptp90) REVERT: H 51 ILE cc_start: 0.9027 (tt) cc_final: 0.8382 (mm) REVERT: H 64 TRP cc_start: 0.6893 (m-10) cc_final: 0.6389 (m-10) REVERT: H 91 TYR cc_start: 0.7523 (m-80) cc_final: 0.7061 (m-80) REVERT: H 98 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: H 99 ASP cc_start: 0.7731 (p0) cc_final: 0.7497 (p0) REVERT: H 100 GLU cc_start: 0.8981 (pt0) cc_final: 0.8311 (pt0) REVERT: L 46 LEU cc_start: 0.8767 (pt) cc_final: 0.8188 (tt) REVERT: C 607 ASN cc_start: 0.8604 (t0) cc_final: 0.8264 (t0) REVERT: C 612 SER cc_start: 0.8854 (m) cc_final: 0.8314 (t) outliers start: 37 outliers final: 24 residues processed: 153 average time/residue: 0.2990 time to fit residues: 70.8946 Evaluate side-chains 143 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16921 Z= 0.300 Angle : 0.629 10.926 22959 Z= 0.298 Chirality : 0.047 0.277 2880 Planarity : 0.004 0.040 2776 Dihedral : 8.263 64.367 4176 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.60 % Allowed : 14.93 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.19), residues: 1872 helix: -0.01 (0.30), residues: 324 sheet: -1.47 (0.22), residues: 491 loop : -1.81 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 571 HIS 0.005 0.001 HIS E 374 PHE 0.022 0.002 PHE H 67 TYR 0.010 0.001 TYR L 36 ARG 0.006 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9067 (p) REVERT: F 302 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8224 (mmp) REVERT: E 170 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7515 (ttp80) REVERT: E 290 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6839 (pp20) REVERT: G 125 LEU cc_start: 0.9300 (tp) cc_final: 0.9078 (tp) REVERT: H 38 ARG cc_start: 0.6979 (ptt180) cc_final: 0.6463 (ptp90) REVERT: H 51 ILE cc_start: 0.9079 (tt) cc_final: 0.8414 (mm) REVERT: H 64 TRP cc_start: 0.6755 (m-10) cc_final: 0.6269 (m-10) REVERT: H 91 TYR cc_start: 0.7486 (m-80) cc_final: 0.7084 (m-80) REVERT: H 98 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7442 (mm-30) REVERT: H 99 ASP cc_start: 0.7721 (p0) cc_final: 0.7475 (p0) REVERT: L 46 LEU cc_start: 0.8778 (pt) cc_final: 0.8193 (tt) REVERT: C 607 ASN cc_start: 0.8652 (t0) cc_final: 0.8266 (t0) REVERT: C 612 SER cc_start: 0.8921 (m) cc_final: 0.8426 (t) outliers start: 44 outliers final: 28 residues processed: 149 average time/residue: 0.2832 time to fit residues: 65.7129 Evaluate side-chains 144 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 478 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16921 Z= 0.276 Angle : 0.627 10.884 22959 Z= 0.297 Chirality : 0.047 0.280 2880 Planarity : 0.003 0.040 2776 Dihedral : 8.165 64.681 4176 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.12 % Allowed : 15.93 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.19), residues: 1872 helix: 0.01 (0.30), residues: 325 sheet: -1.42 (0.23), residues: 479 loop : -1.78 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 571 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.002 PHE E 53 TYR 0.012 0.001 TYR L 36 ARG 0.004 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9068 (p) REVERT: F 302 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8223 (mmp) REVERT: E 170 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7479 (ttp80) REVERT: E 290 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: H 38 ARG cc_start: 0.6967 (ptt180) cc_final: 0.6452 (ptp90) REVERT: H 51 ILE cc_start: 0.9073 (tt) cc_final: 0.8445 (mm) REVERT: H 64 TRP cc_start: 0.6789 (m-10) cc_final: 0.6251 (m-10) REVERT: H 91 TYR cc_start: 0.7496 (m-80) cc_final: 0.7088 (m-80) REVERT: H 98 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: H 99 ASP cc_start: 0.7667 (p0) cc_final: 0.7452 (p0) REVERT: L 46 LEU cc_start: 0.8764 (pt) cc_final: 0.8223 (tt) REVERT: L 50 GLU cc_start: 0.8760 (tp30) cc_final: 0.7802 (tm-30) REVERT: C 607 ASN cc_start: 0.8658 (t0) cc_final: 0.8257 (t0) REVERT: C 612 SER cc_start: 0.8925 (m) cc_final: 0.8420 (t) outliers start: 36 outliers final: 30 residues processed: 142 average time/residue: 0.2709 time to fit residues: 60.0941 Evaluate side-chains 145 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.0270 chunk 119 optimal weight: 1.9990 chunk 159 optimal weight: 0.1980 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16921 Z= 0.178 Angle : 0.587 10.741 22959 Z= 0.276 Chirality : 0.046 0.323 2880 Planarity : 0.003 0.041 2776 Dihedral : 7.873 62.179 4176 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.01 % Allowed : 16.11 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.19), residues: 1872 helix: 0.14 (0.30), residues: 330 sheet: -1.31 (0.23), residues: 469 loop : -1.69 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 35 HIS 0.003 0.001 HIS F 216 PHE 0.014 0.001 PHE E 210 TYR 0.013 0.001 TYR L 36 ARG 0.004 0.000 ARG H 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 295 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9063 (p) REVERT: F 302 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8209 (mmp) REVERT: E 170 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7591 (ttp80) REVERT: E 290 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: H 32 TYR cc_start: 0.6915 (m-80) cc_final: 0.5622 (m-10) REVERT: H 38 ARG cc_start: 0.7056 (ptt180) cc_final: 0.6520 (ptp90) REVERT: H 51 ILE cc_start: 0.9067 (tt) cc_final: 0.8415 (mm) REVERT: H 64 TRP cc_start: 0.6751 (m-10) cc_final: 0.6282 (m-10) REVERT: H 91 TYR cc_start: 0.7483 (m-80) cc_final: 0.7015 (m-80) REVERT: H 98 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7279 (mm-30) REVERT: H 99 ASP cc_start: 0.7609 (p0) cc_final: 0.7390 (p0) REVERT: L 46 LEU cc_start: 0.8879 (pt) cc_final: 0.8392 (tt) REVERT: C 530 MET cc_start: 0.8363 (mmm) cc_final: 0.7950 (mmt) REVERT: C 607 ASN cc_start: 0.8628 (t0) cc_final: 0.8248 (t0) REVERT: C 612 SER cc_start: 0.8900 (m) cc_final: 0.8366 (t) outliers start: 34 outliers final: 28 residues processed: 150 average time/residue: 0.2824 time to fit residues: 66.3894 Evaluate side-chains 148 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 362 ASN Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 150 optimal weight: 40.0000 chunk 62 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.093178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072496 restraints weight = 42808.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074830 restraints weight = 24001.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.076401 restraints weight = 16533.773| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16921 Z= 0.229 Angle : 0.615 14.381 22959 Z= 0.290 Chirality : 0.046 0.395 2880 Planarity : 0.003 0.040 2776 Dihedral : 7.881 63.606 4176 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.18 % Allowed : 16.34 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.19), residues: 1872 helix: 0.19 (0.30), residues: 331 sheet: -1.29 (0.23), residues: 477 loop : -1.67 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 35 HIS 0.004 0.001 HIS E 374 PHE 0.014 0.001 PHE E 53 TYR 0.007 0.001 TYR C 638 ARG 0.004 0.000 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2765.78 seconds wall clock time: 52 minutes 23.13 seconds (3143.13 seconds total)