Starting phenix.real_space_refine on Sat Jul 4 00:24:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fl1_29264/07_2026/8fl1_29264.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.048 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 117 5.16 5 C 10538 2.51 5 N 2808 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16951 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3543 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1094 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} 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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 801 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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 chiralities: 6 Chain: "K" 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 chiralities: 2 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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 chiralities: 5 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 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 chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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 chiralities: 6 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 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 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 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 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 chiralities: 2 Chain: "d" 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 chiralities: 5 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 3.55, per 1000 atoms: 0.21 Number of scatterers: 16951 At special positions: 0 Unit cell: (132.126, 129.96, 168.948, 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 117 16.00 O 3488 8.00 N 2808 7.00 C 10538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " 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 I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 J 4 " - " MAN J 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 6 " " BMA d 3 " - " MAN d 5 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG C 611 " - " ASN C 137 " " NAG D 1 " - " ASN C 160 " " NAG E 1 " - " ASN C 197 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 137 " " NAG G 611 " - " ASN G 276 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG I 610 " - " ASN I 462 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 276 " " NAG M 1 " - " ASN C 295 " " NAG N 1 " - " ASN C 363 " " NAG O 1 " - " ASN C 386 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 363 " " NAG T 1 " - " ASN G 386 " " NAG U 1 " - " ASN G 448 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 156 " " NAG e 1 " - " ASN I 160 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 789.0 milliseconds 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 29 sheets defined 23.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.530A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 542' Processing helix chain 'A' and resid 570 through 596 removed outlier: 3.626A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.647A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.508A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.077A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.556A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.767A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.810A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.927A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.580A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.697A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.248A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 352 removed outlier: 3.736A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.390A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 536 through 543' Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.987A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.562A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.594A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 98 through 116 removed outlier: 4.163A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.575A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.541A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 474 through 481 removed outlier: 4.174A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.521A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 59 through 64' Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.634A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 3.837A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.613A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 484 removed outlier: 4.329A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.796A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 28 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.614A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.528A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP G 35 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.650A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.932A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.154A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA8, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 309 removed outlier: 6.700A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 309 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'F' and resid 603 through 609 removed outlier: 4.549A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.316A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 55 through 56 removed outlier: 3.611A pdb=" N SER G 56 " --> pdb=" O VAL G 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.081A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.505A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 330 through 334 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 330 through 334 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.862A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AB8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.577A pdb=" N LYS I 46 " --> pdb=" O LYS I 490 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'I' and resid 92 through 94 removed outlier: 3.786A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 130 through 133 removed outlier: 7.024A pdb=" N LYS I 169 " --> pdb=" O TYS H 100H" (cutoff:3.500A) removed outlier: 7.943A pdb=" N PHE H 100J" --> pdb=" O LYS I 169 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS I 171 " --> pdb=" O PHE H 100J" (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'I' and resid 202 through 203 removed outlier: 7.178A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 298 removed outlier: 3.685A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 329 through 333 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 466 through 470 Processing sheet with id=AC6, first strand: chain 'I' and resid 302 through 312 removed outlier: 6.664A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.752A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER H 25 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.045A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 39 removed outlier: 7.088A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AD1, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 46 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.526A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 75 " --> pdb=" O ILE L 19 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 1.74 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: 5004 1.34 - 1.46: 4416 1.46 - 1.59: 7694 1.59 - 1.71: 1 1.71 - 1.83: 154 Bond restraints: 17269 Sorted by residual: bond pdb=" O3 TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.458 1.635 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" OH TYS H 100H" pdb=" S TYS H 100H" ideal model delta sigma weight residual 1.679 1.535 0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" OH TYS H 100G" pdb=" S TYS H 100G" ideal model delta sigma weight residual 1.679 1.546 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 1.408 1.474 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CZ TYS H 100G" pdb=" OH TYS H 100G" ideal model delta sigma weight residual 1.371 1.425 -0.054 2.00e-02 2.50e+03 7.28e+00 ... (remaining 17264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 22939 2.20 - 4.40: 414 4.40 - 6.60: 80 6.60 - 8.80: 1 8.80 - 11.00: 3 Bond angle restraints: 23437 Sorted by residual: angle pdb=" CA TYS H 100G" pdb=" C TYS H 100G" pdb=" O TYS H 100G" ideal model delta sigma weight residual 120.80 113.83 6.97 1.70e+00 3.46e-01 1.68e+01 angle pdb=" C CYS I 218 " pdb=" N ALA I 219 " pdb=" CA ALA I 219 " ideal model delta sigma weight residual 120.97 131.74 -10.77 2.84e+00 1.24e-01 1.44e+01 angle pdb=" C2 MAN e 4 " pdb=" C3 MAN e 4 " pdb=" O3 MAN e 4 " ideal model delta sigma weight residual 107.58 118.58 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" OH TYS H 100H" pdb=" S TYS H 100H" pdb=" O3 TYS H 100H" ideal model delta sigma weight residual 100.21 109.42 -9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" CA GLY G 354 " pdb=" C GLY G 354 " pdb=" O GLY G 354 " ideal model delta sigma weight residual 122.24 119.79 2.45 8.70e-01 1.32e+00 7.91e+00 ... (remaining 23432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8546 17.93 - 35.86: 802 35.86 - 53.79: 155 53.79 - 71.72: 27 71.72 - 89.66: 20 Dihedral angle restraints: 9550 sinusoidal: 3870 harmonic: 5680 Sorted by residual: dihedral pdb=" CB CYS A 605 " pdb=" SG CYS A 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -150.38 64.38 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS I 378 " pdb=" SG CYS I 378 " pdb=" SG CYS I 445 " pdb=" CB CYS I 445 " ideal model delta sinusoidal sigma weight residual -86.00 -146.05 60.05 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 9547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2480 0.061 - 0.123: 420 0.123 - 0.184: 32 0.184 - 0.246: 0 0.246 - 0.307: 9 Chirality restraints: 2941 Sorted by residual: chirality pdb=" C1 NAG G 608 " pdb=" ND2 ASN G 355 " pdb=" C2 NAG G 608 " pdb=" O5 NAG G 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3 MAN e 4 " pdb=" C2 MAN e 4 " pdb=" C4 MAN e 4 " pdb=" O3 MAN e 4 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2938 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 3 " -0.109 9.50e-02 1.11e+02 4.88e-02 1.47e+00 pdb=" NE ARG H 3 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG H 3 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG H 3 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG H 3 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 448 " 0.011 2.00e-02 2.50e+03 9.82e-03 1.21e+00 pdb=" CG ASN C 448 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 448 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 448 " -0.011 2.00e-02 2.50e+03 pdb=" C1 NAG C 610 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL I 75 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO I 76 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO I 76 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO I 76 " 0.015 5.00e-02 4.00e+02 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3537 2.79 - 3.32: 15367 3.32 - 3.84: 25820 3.84 - 4.37: 30107 4.37 - 4.90: 52026 Nonbonded interactions: 126857 Sorted by model distance: nonbonded pdb=" OD1 ASN C 137 " pdb=" N2 NAG C 611 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG G 298 " pdb=" OD1 ASN G 302 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR G 163 " pdb=" OE1 GLU G 164 " model vdw 2.274 3.040 nonbonded pdb=" OG SER L 14 " pdb=" OE1 GLN L 17 " model vdw 2.278 3.040 nonbonded pdb=" O LEU L 4 " pdb=" OG1 THR L 100 " model vdw 2.280 3.040 ... (remaining 126852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 519 through 702) selection = chain 'B' selection = (chain 'F' and (resid 519 through 546 or resid 569 through 702)) } ncs_group { reference = (chain 'C' and resid 33 through 610) selection = (chain 'G' and (resid 33 through 185 or resid 189 through 610)) selection = (chain 'I' and resid 33 through 610) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'X' and (resid 1 or resid 4 through 6)) selection = (chain 'e' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.760 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 0.177 17415 Z= 0.249 Angle : 0.702 10.997 23837 Z= 0.297 Chirality : 0.048 0.307 2941 Planarity : 0.003 0.049 2846 Dihedral : 14.351 89.655 5768 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1934 helix: 0.41 (0.28), residues: 362 sheet: 1.01 (0.24), residues: 490 loop : -0.31 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 588 TYR 0.008 0.001 TYR L 49 PHE 0.010 0.001 PHE C 223 TRP 0.006 0.001 TRP H 103 HIS 0.003 0.000 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.25 (17269) covalent geometry : angle 0.67685 / 0.29 (23437) SS BOND : bond 0.00266 / 0.18 ( 38) SS BOND : angle 1.37668 / 0.89 ( 76) hydrogen bonds : bond 0.28822 / 18.89 ( 408) hydrogen bonds : angle 8.50327 / 6.29 ( 1149) link_ALPHA1-2 : bond 0.00714 / 0.33 ( 3) link_ALPHA1-2 : angle 1.59062 / 0.81 ( 9) link_ALPHA1-3 : bond 0.00622 / 0.30 ( 7) link_ALPHA1-3 : angle 2.75689 / 1.59 ( 21) link_ALPHA1-6 : bond 0.00400 / 0.19 ( 6) link_ALPHA1-6 : angle 1.45372 / 0.85 ( 18) link_BETA1-4 : bond 0.00467 / 0.24 ( 29) link_BETA1-4 : angle 1.13501 / 0.82 ( 87) link_NAG-ASN : bond 0.00364 / 0.22 ( 63) link_NAG-ASN : angle 1.67990 / 1.17 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7468 (ptmm) REVERT: B 579 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8674 (ttm170) REVERT: B 612 SER cc_start: 0.8931 (m) cc_final: 0.8403 (p) REVERT: B 615 SER cc_start: 0.8688 (t) cc_final: 0.8352 (m) REVERT: C 128 THR cc_start: 0.8773 (m) cc_final: 0.8484 (p) REVERT: C 271 MET cc_start: 0.7697 (mmt) cc_final: 0.7497 (mmm) REVERT: F 617 ARG cc_start: 0.6330 (ttm110) cc_final: 0.6119 (ttm110) REVERT: G 97 LYS cc_start: 0.7919 (mttp) cc_final: 0.7624 (mttp) REVERT: G 246 GLN cc_start: 0.6151 (mp10) cc_final: 0.5516 (mp10) REVERT: G 277 ILE cc_start: 0.8144 (mm) cc_final: 0.7881 (mm) REVERT: I 121 LYS cc_start: 0.8141 (mttp) cc_final: 0.7898 (tttm) REVERT: I 474 ASP cc_start: 0.6285 (t0) cc_final: 0.6079 (t0) REVERT: H 34 MET cc_start: 0.6912 (mmt) cc_final: 0.6341 (mmt) REVERT: H 52 LYS cc_start: 0.7686 (mtpt) cc_final: 0.6705 (mtpp) REVERT: H 70 SER cc_start: 0.8258 (t) cc_final: 0.7942 (p) REVERT: H 100 ASP cc_start: 0.8659 (t0) cc_final: 0.8443 (t70) REVERT: H 100 MET cc_start: 0.8044 (mtt) cc_final: 0.7684 (mtp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1202 time to fit residues: 73.2427 Evaluate side-chains 231 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN C 67 ASN C 85 HIS C 195 ASN C 249 HIS C 258 GLN F 656 ASN G 249 HIS ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118300 restraints weight = 25237.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123619 restraints weight = 17667.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124607 restraints weight = 12687.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124662 restraints weight = 11031.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.124983 restraints weight = 10986.262| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17415 Z= 0.240 Angle : 0.779 17.415 23837 Z= 0.366 Chirality : 0.050 0.405 2941 Planarity : 0.004 0.041 2846 Dihedral : 4.218 30.309 2107 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.00 % Allowed : 10.21 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1934 helix: 0.18 (0.26), residues: 373 sheet: 0.40 (0.23), residues: 540 loop : -0.36 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 38 TYR 0.021 0.002 TYR L 36 PHE 0.033 0.002 PHE C 382 TRP 0.021 0.002 TRP I 479 HIS 0.005 0.002 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (17269) covalent geometry : angle 0.71615 / 0.35 (23437) SS BOND : bond 0.00525 / 0.33 ( 38) SS BOND : angle 1.57455 / 1.05 ( 76) hydrogen bonds : bond 0.06945 / 4.63 ( 408) hydrogen bonds : angle 5.84770 / 4.28 ( 1149) link_ALPHA1-2 : bond 0.00748 / 0.35 ( 3) link_ALPHA1-2 : angle 1.93675 / 0.93 ( 9) link_ALPHA1-3 : bond 0.00642 / 0.31 ( 7) link_ALPHA1-3 : angle 2.96643 / 1.66 ( 21) link_ALPHA1-6 : bond 0.00376 / 0.18 ( 6) link_ALPHA1-6 : angle 1.67410 / 1.02 ( 18) link_BETA1-4 : bond 0.00400 / 0.22 ( 29) link_BETA1-4 : angle 1.23577 / 0.88 ( 87) link_NAG-ASN : bond 0.00663 / 0.34 ( 63) link_NAG-ASN : angle 3.12982 / 2.34 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 LEU cc_start: 0.9347 (mt) cc_final: 0.9140 (mt) REVERT: A 655 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7678 (ptmm) REVERT: B 607 ASN cc_start: 0.7869 (p0) cc_final: 0.7433 (p0) REVERT: B 615 SER cc_start: 0.8738 (t) cc_final: 0.8440 (m) REVERT: B 616 ASN cc_start: 0.8142 (p0) cc_final: 0.7816 (p0) REVERT: B 655 LYS cc_start: 0.7998 (ptpt) cc_final: 0.7654 (pptt) REVERT: C 434 MET cc_start: 0.7647 (tmm) cc_final: 0.7253 (tmm) REVERT: C 449 ILE cc_start: 0.8907 (mt) cc_final: 0.8701 (mt) REVERT: F 590 GLN cc_start: 0.9207 (tp40) cc_final: 0.8890 (tp40) REVERT: G 97 LYS cc_start: 0.8242 (mttp) cc_final: 0.7812 (mttp) REVERT: I 39 TYR cc_start: 0.8988 (m-80) cc_final: 0.8783 (m-80) REVERT: I 104 MET cc_start: 0.8511 (ttt) cc_final: 0.8284 (ttt) REVERT: I 121 LYS cc_start: 0.8273 (mttp) cc_final: 0.7959 (tttm) REVERT: H 32 GLN cc_start: 0.7151 (mt0) cc_final: 0.6881 (mt0) REVERT: H 52 LYS cc_start: 0.8388 (mtpt) cc_final: 0.8156 (mtmt) REVERT: H 56 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7946 (pp20) REVERT: H 89 THR cc_start: 0.7462 (t) cc_final: 0.7250 (t) REVERT: H 100 ASP cc_start: 0.8769 (t0) cc_final: 0.8473 (t0) REVERT: H 100 MET cc_start: 0.8356 (mtt) cc_final: 0.8140 (mtp) outliers start: 52 outliers final: 35 residues processed: 270 average time/residue: 0.1107 time to fit residues: 44.9654 Evaluate side-chains 245 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 132 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 0.0270 chunk 90 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 640 GLN B 653 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN H 39 GLN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134812 restraints weight = 26029.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136664 restraints weight = 22151.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138523 restraints weight = 17858.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.141209 restraints weight = 13749.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141455 restraints weight = 12529.283| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 17415 Z= 0.131 Angle : 0.658 16.763 23837 Z= 0.306 Chirality : 0.046 0.529 2941 Planarity : 0.003 0.041 2846 Dihedral : 3.939 25.322 2107 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.54 % Allowed : 14.02 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1934 helix: 0.64 (0.27), residues: 376 sheet: 0.46 (0.24), residues: 490 loop : -0.30 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 166 TYR 0.019 0.001 TYR B 638 PHE 0.020 0.001 PHE C 382 TRP 0.029 0.001 TRP L 35 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17269) covalent geometry : angle 0.58776 / 0.29 (23437) SS BOND : bond 0.00365 / 0.24 ( 38) SS BOND : angle 1.57005 / 0.99 ( 76) hydrogen bonds : bond 0.05691 / 3.75 ( 408) hydrogen bonds : angle 5.26471 / 3.85 ( 1149) link_ALPHA1-2 : bond 0.00873 / 0.40 ( 3) link_ALPHA1-2 : angle 1.56884 / 0.81 ( 9) link_ALPHA1-3 : bond 0.00877 / 0.44 ( 7) link_ALPHA1-3 : angle 2.68621 / 1.54 ( 21) link_ALPHA1-6 : bond 0.00456 / 0.25 ( 6) link_ALPHA1-6 : angle 1.43097 / 0.86 ( 18) link_BETA1-4 : bond 0.00393 / 0.21 ( 29) link_BETA1-4 : angle 1.10396 / 0.76 ( 87) link_NAG-ASN : bond 0.00670 / 0.37 ( 63) link_NAG-ASN : angle 3.01503 / 2.25 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7728 (p0) cc_final: 0.7382 (p0) REVERT: B 615 SER cc_start: 0.8735 (t) cc_final: 0.8460 (m) REVERT: C 337 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8332 (m) REVERT: F 590 GLN cc_start: 0.9132 (tp40) cc_final: 0.8874 (tp40) REVERT: G 97 LYS cc_start: 0.8184 (mttp) cc_final: 0.7783 (mttp) REVERT: I 39 TYR cc_start: 0.8963 (m-80) cc_final: 0.8763 (m-80) REVERT: I 121 LYS cc_start: 0.8274 (mttp) cc_final: 0.8043 (tttm) REVERT: H 32 GLN cc_start: 0.6912 (mt0) cc_final: 0.6711 (mt0) REVERT: H 52 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8053 (mtmt) REVERT: H 56 GLU cc_start: 0.8121 (pm20) cc_final: 0.7894 (pp20) outliers start: 44 outliers final: 34 residues processed: 257 average time/residue: 0.1143 time to fit residues: 45.3042 Evaluate side-chains 229 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN F 658 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN H 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.129191 restraints weight = 26082.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132169 restraints weight = 22353.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133022 restraints weight = 17432.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133204 restraints weight = 14023.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133391 restraints weight = 13988.805| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17415 Z= 0.233 Angle : 0.789 31.643 23837 Z= 0.360 Chirality : 0.048 0.463 2941 Planarity : 0.004 0.089 2846 Dihedral : 4.364 31.026 2107 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.04 % Allowed : 14.66 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 1934 helix: 0.57 (0.27), residues: 376 sheet: 0.15 (0.23), residues: 488 loop : -0.41 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 166 TYR 0.022 0.002 TYR B 638 PHE 0.018 0.002 PHE C 382 TRP 0.027 0.002 TRP L 35 HIS 0.007 0.001 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (17269) covalent geometry : angle 0.69056 / 0.34 (23437) SS BOND : bond 0.00515 / 0.30 ( 38) SS BOND : angle 1.97552 / 1.24 ( 76) hydrogen bonds : bond 0.05516 / 3.66 ( 408) hydrogen bonds : angle 5.17540 / 3.77 ( 1149) link_ALPHA1-2 : bond 0.00650 / 0.30 ( 3) link_ALPHA1-2 : angle 1.73318 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00775 / 0.39 ( 7) link_ALPHA1-3 : angle 2.66589 / 1.51 ( 21) link_ALPHA1-6 : bond 0.00354 / 0.18 ( 6) link_ALPHA1-6 : angle 1.55138 / 0.90 ( 18) link_BETA1-4 : bond 0.00414 / 0.23 ( 29) link_BETA1-4 : angle 1.18732 / 0.82 ( 87) link_NAG-ASN : bond 0.00543 / 0.30 ( 63) link_NAG-ASN : angle 3.99282 / 2.83 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 206 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 615 SER cc_start: 0.8927 (t) cc_final: 0.8675 (m) REVERT: C 190 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: C 337 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8589 (m) REVERT: G 97 LYS cc_start: 0.8351 (mttp) cc_final: 0.7860 (mttp) REVERT: H 52 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8252 (mtpp) REVERT: L 94 ARG cc_start: 0.8483 (ttp-110) cc_final: 0.8200 (ttp-110) outliers start: 70 outliers final: 49 residues processed: 257 average time/residue: 0.1103 time to fit residues: 43.9289 Evaluate side-chains 233 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LYS Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 9 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.158265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126439 restraints weight = 25007.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130205 restraints weight = 19423.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131528 restraints weight = 15437.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131683 restraints weight = 13118.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131873 restraints weight = 12716.677| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17415 Z= 0.130 Angle : 0.689 23.553 23837 Z= 0.316 Chirality : 0.046 0.474 2941 Planarity : 0.003 0.041 2846 Dihedral : 4.139 29.055 2107 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.46 % Allowed : 16.21 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1934 helix: 0.74 (0.27), residues: 376 sheet: 0.31 (0.23), residues: 487 loop : -0.41 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 503 TYR 0.029 0.002 TYR H 58 PHE 0.019 0.001 PHE C 382 TRP 0.029 0.001 TRP L 35 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17269) covalent geometry : angle 0.60110 / 0.30 (23437) SS BOND : bond 0.00333 / 0.23 ( 38) SS BOND : angle 1.65122 / 1.05 ( 76) hydrogen bonds : bond 0.04729 / 3.12 ( 408) hydrogen bonds : angle 4.91642 / 3.59 ( 1149) link_ALPHA1-2 : bond 0.00594 / 0.27 ( 3) link_ALPHA1-2 : angle 1.64688 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00741 / 0.38 ( 7) link_ALPHA1-3 : angle 2.62664 / 1.50 ( 21) link_ALPHA1-6 : bond 0.00440 / 0.24 ( 6) link_ALPHA1-6 : angle 1.40144 / 0.83 ( 18) link_BETA1-4 : bond 0.00377 / 0.21 ( 29) link_BETA1-4 : angle 1.07507 / 0.74 ( 87) link_NAG-ASN : bond 0.00492 / 0.26 ( 63) link_NAG-ASN : angle 3.51777 / 2.55 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7738 (p0) cc_final: 0.7531 (p0) REVERT: B 615 SER cc_start: 0.8921 (t) cc_final: 0.8638 (m) REVERT: C 190 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: C 337 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8417 (m) REVERT: C 434 MET cc_start: 0.7373 (tmm) cc_final: 0.7169 (tmm) REVERT: G 97 LYS cc_start: 0.8215 (mttp) cc_final: 0.7804 (mttp) REVERT: H 52 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8082 (mtpt) REVERT: L 94 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8343 (ttp-110) outliers start: 60 outliers final: 43 residues processed: 245 average time/residue: 0.1066 time to fit residues: 40.7492 Evaluate side-chains 231 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.156840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122006 restraints weight = 25762.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.124049 restraints weight = 20758.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125886 restraints weight = 16796.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126519 restraints weight = 14377.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126938 restraints weight = 13681.191| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 17415 Z= 0.279 Angle : 0.801 18.615 23837 Z= 0.375 Chirality : 0.049 0.438 2941 Planarity : 0.004 0.042 2846 Dihedral : 4.599 29.842 2107 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.21 % Allowed : 16.96 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1934 helix: 0.42 (0.27), residues: 377 sheet: -0.09 (0.23), residues: 503 loop : -0.54 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 617 TYR 0.020 0.002 TYR C 191 PHE 0.021 0.002 PHE C 382 TRP 0.025 0.002 TRP L 35 HIS 0.009 0.002 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.28 (17269) covalent geometry : angle 0.73587 / 0.36 (23437) SS BOND : bond 0.00474 / 0.31 ( 38) SS BOND : angle 2.00444 / 1.29 ( 76) hydrogen bonds : bond 0.05509 / 3.69 ( 408) hydrogen bonds : angle 5.19616 / 3.78 ( 1149) link_ALPHA1-2 : bond 0.00484 / 0.22 ( 3) link_ALPHA1-2 : angle 1.86037 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00681 / 0.35 ( 7) link_ALPHA1-3 : angle 2.62775 / 1.50 ( 21) link_ALPHA1-6 : bond 0.00335 / 0.16 ( 6) link_ALPHA1-6 : angle 1.60073 / 0.96 ( 18) link_BETA1-4 : bond 0.00418 / 0.23 ( 29) link_BETA1-4 : angle 1.28594 / 0.87 ( 87) link_NAG-ASN : bond 0.00594 / 0.34 ( 63) link_NAG-ASN : angle 3.20867 / 2.32 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 194 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 612 SER cc_start: 0.8639 (m) cc_final: 0.8313 (p) REVERT: B 615 SER cc_start: 0.9012 (t) cc_final: 0.8663 (m) REVERT: C 104 MET cc_start: 0.8663 (ttm) cc_final: 0.8374 (ttt) REVERT: C 190 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: C 426 MET cc_start: 0.8346 (tpt) cc_final: 0.8080 (tpt) REVERT: C 434 MET cc_start: 0.7647 (tmm) cc_final: 0.7291 (tmm) REVERT: F 542 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7658 (ttm110) REVERT: G 97 LYS cc_start: 0.8352 (mttp) cc_final: 0.7857 (mttp) REVERT: G 102 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: G 164 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7719 (mt-10) outliers start: 73 outliers final: 54 residues processed: 251 average time/residue: 0.1096 time to fit residues: 42.4414 Evaluate side-chains 233 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 217 TYR Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128108 restraints weight = 25752.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.129868 restraints weight = 23243.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131647 restraints weight = 18678.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133419 restraints weight = 14282.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133771 restraints weight = 13706.364| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17415 Z= 0.129 Angle : 0.712 17.919 23837 Z= 0.326 Chirality : 0.047 0.464 2941 Planarity : 0.003 0.041 2846 Dihedral : 4.256 27.681 2107 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.52 % Allowed : 18.18 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.19), residues: 1934 helix: 0.66 (0.27), residues: 381 sheet: 0.04 (0.23), residues: 504 loop : -0.45 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 503 TYR 0.016 0.001 TYR H 58 PHE 0.017 0.001 PHE C 382 TRP 0.029 0.001 TRP L 35 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17269) covalent geometry : angle 0.63183 / 0.31 (23437) SS BOND : bond 0.00405 / 0.27 ( 38) SS BOND : angle 1.68870 / 1.07 ( 76) hydrogen bonds : bond 0.04480 / 2.94 ( 408) hydrogen bonds : angle 4.89435 / 3.59 ( 1149) link_ALPHA1-2 : bond 0.00503 / 0.23 ( 3) link_ALPHA1-2 : angle 1.72424 / 0.88 ( 9) link_ALPHA1-3 : bond 0.00683 / 0.36 ( 7) link_ALPHA1-3 : angle 2.54945 / 1.46 ( 21) link_ALPHA1-6 : bond 0.00487 / 0.27 ( 6) link_ALPHA1-6 : angle 1.38363 / 0.81 ( 18) link_BETA1-4 : bond 0.00369 / 0.20 ( 29) link_BETA1-4 : angle 1.09738 / 0.74 ( 87) link_NAG-ASN : bond 0.00506 / 0.28 ( 63) link_NAG-ASN : angle 3.42514 / 2.38 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 190 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8144 (mtp) cc_final: 0.7853 (mtp) REVERT: B 607 ASN cc_start: 0.7719 (p0) cc_final: 0.7515 (p0) REVERT: B 612 SER cc_start: 0.8518 (m) cc_final: 0.8169 (p) REVERT: B 615 SER cc_start: 0.8941 (t) cc_final: 0.8667 (m) REVERT: C 104 MET cc_start: 0.8578 (ttm) cc_final: 0.8218 (ttt) REVERT: C 190 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: F 542 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7642 (ttm110) REVERT: G 97 LYS cc_start: 0.8297 (mttp) cc_final: 0.7877 (mttp) REVERT: G 102 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: G 215 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8078 (tp) outliers start: 61 outliers final: 46 residues processed: 234 average time/residue: 0.1101 time to fit residues: 40.2157 Evaluate side-chains 226 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 165 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN I 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127778 restraints weight = 26246.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130665 restraints weight = 22573.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131757 restraints weight = 17414.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131948 restraints weight = 13911.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132127 restraints weight = 13788.218| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17415 Z= 0.170 Angle : 0.724 15.362 23837 Z= 0.333 Chirality : 0.047 0.431 2941 Planarity : 0.004 0.088 2846 Dihedral : 4.295 27.480 2107 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.58 % Allowed : 18.52 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1934 helix: 0.66 (0.28), residues: 383 sheet: -0.01 (0.23), residues: 517 loop : -0.46 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 617 TYR 0.021 0.001 TYR H 58 PHE 0.015 0.001 PHE C 382 TRP 0.034 0.001 TRP L 35 HIS 0.004 0.001 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (17269) covalent geometry : angle 0.64934 / 0.31 (23437) SS BOND : bond 0.00421 / 0.28 ( 38) SS BOND : angle 1.73284 / 1.10 ( 76) hydrogen bonds : bond 0.04550 / 3.00 ( 408) hydrogen bonds : angle 4.86875 / 3.57 ( 1149) link_ALPHA1-2 : bond 0.00452 / 0.21 ( 3) link_ALPHA1-2 : angle 1.73867 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00713 / 0.37 ( 7) link_ALPHA1-3 : angle 2.49282 / 1.43 ( 21) link_ALPHA1-6 : bond 0.00391 / 0.22 ( 6) link_ALPHA1-6 : angle 1.47454 / 0.87 ( 18) link_BETA1-4 : bond 0.00398 / 0.21 ( 29) link_BETA1-4 : angle 1.13477 / 0.77 ( 87) link_NAG-ASN : bond 0.00502 / 0.28 ( 63) link_NAG-ASN : angle 3.30641 / 2.29 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7322 (t0) REVERT: B 607 ASN cc_start: 0.7849 (p0) cc_final: 0.7568 (p0) REVERT: B 612 SER cc_start: 0.8548 (m) cc_final: 0.8195 (p) REVERT: B 615 SER cc_start: 0.8944 (t) cc_final: 0.8669 (m) REVERT: C 104 MET cc_start: 0.8644 (ttm) cc_final: 0.8307 (ttt) REVERT: C 190 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: C 434 MET cc_start: 0.7450 (tmm) cc_final: 0.7114 (tmm) REVERT: F 542 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7736 (ttm110) REVERT: G 97 LYS cc_start: 0.8402 (mttp) cc_final: 0.7926 (mttp) REVERT: G 102 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: G 215 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8073 (tp) REVERT: H 100 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: L 89 LYS cc_start: 0.7390 (tmtt) cc_final: 0.7102 (tmtt) outliers start: 62 outliers final: 51 residues processed: 238 average time/residue: 0.1078 time to fit residues: 39.4463 Evaluate side-chains 239 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 GLN G 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128076 restraints weight = 26035.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129996 restraints weight = 23427.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131789 restraints weight = 18704.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132370 restraints weight = 14293.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133089 restraints weight = 14530.857| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17415 Z= 0.137 Angle : 0.693 13.666 23837 Z= 0.320 Chirality : 0.046 0.445 2941 Planarity : 0.004 0.101 2846 Dihedral : 4.218 26.848 2107 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.64 % Allowed : 18.75 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1934 helix: 0.79 (0.28), residues: 383 sheet: 0.05 (0.23), residues: 496 loop : -0.51 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 304 TYR 0.046 0.001 TYR A 638 PHE 0.016 0.001 PHE C 382 TRP 0.034 0.001 TRP L 35 HIS 0.003 0.001 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17269) covalent geometry : angle 0.62560 / 0.30 (23437) SS BOND : bond 0.00409 / 0.27 ( 38) SS BOND : angle 1.68098 / 1.07 ( 76) hydrogen bonds : bond 0.04249 / 2.79 ( 408) hydrogen bonds : angle 4.75678 / 3.49 ( 1149) link_ALPHA1-2 : bond 0.00444 / 0.20 ( 3) link_ALPHA1-2 : angle 1.69061 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00747 / 0.38 ( 7) link_ALPHA1-3 : angle 2.45182 / 1.41 ( 21) link_ALPHA1-6 : bond 0.00449 / 0.26 ( 6) link_ALPHA1-6 : angle 1.40290 / 0.82 ( 18) link_BETA1-4 : bond 0.00385 / 0.20 ( 29) link_BETA1-4 : angle 1.10342 / 0.75 ( 87) link_NAG-ASN : bond 0.00504 / 0.28 ( 63) link_NAG-ASN : angle 3.05620 / 2.15 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7331 (t0) REVERT: B 607 ASN cc_start: 0.7785 (p0) cc_final: 0.7521 (p0) REVERT: B 612 SER cc_start: 0.8580 (m) cc_final: 0.8221 (p) REVERT: B 615 SER cc_start: 0.8956 (t) cc_final: 0.8679 (m) REVERT: B 625 ASN cc_start: 0.7722 (p0) cc_final: 0.7512 (p0) REVERT: C 104 MET cc_start: 0.8586 (ttm) cc_final: 0.8218 (ttt) REVERT: C 190 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: F 542 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7731 (ttm110) REVERT: G 97 LYS cc_start: 0.8347 (mttp) cc_final: 0.7883 (mttp) REVERT: G 102 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: G 215 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7996 (tp) REVERT: H 100 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8084 (mtp) REVERT: L 89 LYS cc_start: 0.7349 (tmtt) cc_final: 0.7040 (tmtt) outliers start: 63 outliers final: 56 residues processed: 232 average time/residue: 0.1071 time to fit residues: 38.6906 Evaluate side-chains 245 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain G residue 302 ASN Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN C 398 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 GLN G 302 ASN H 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.156327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127187 restraints weight = 25969.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130018 restraints weight = 22397.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131161 restraints weight = 17419.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131283 restraints weight = 13867.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131518 restraints weight = 13666.200| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17415 Z= 0.189 Angle : 0.738 18.035 23837 Z= 0.341 Chirality : 0.047 0.437 2941 Planarity : 0.004 0.106 2846 Dihedral : 4.348 32.693 2107 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.40 % Allowed : 19.22 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1934 helix: 0.74 (0.27), residues: 383 sheet: -0.11 (0.23), residues: 525 loop : -0.51 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 617 TYR 0.036 0.002 TYR A 638 PHE 0.027 0.002 PHE G 288 TRP 0.032 0.002 TRP L 35 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (17269) covalent geometry : angle 0.66375 / 0.32 (23437) SS BOND : bond 0.00413 / 0.28 ( 38) SS BOND : angle 1.74286 / 1.12 ( 76) hydrogen bonds : bond 0.04501 / 2.96 ( 408) hydrogen bonds : angle 4.84993 / 3.55 ( 1149) link_ALPHA1-2 : bond 0.00414 / 0.19 ( 3) link_ALPHA1-2 : angle 1.74565 / 0.90 ( 9) link_ALPHA1-3 : bond 0.00701 / 0.36 ( 7) link_ALPHA1-3 : angle 2.42554 / 1.39 ( 21) link_ALPHA1-6 : bond 0.00392 / 0.23 ( 6) link_ALPHA1-6 : angle 1.50885 / 0.91 ( 18) link_BETA1-4 : bond 0.00401 / 0.22 ( 29) link_BETA1-4 : angle 1.15671 / 0.79 ( 87) link_NAG-ASN : bond 0.00498 / 0.29 ( 63) link_NAG-ASN : angle 3.35155 / 2.29 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3868 Ramachandran restraints generated. 1934 Oldfield, 0 Emsley, 1934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 607 ASN cc_start: 0.7884 (p0) cc_final: 0.7651 (p0) REVERT: B 612 SER cc_start: 0.8593 (m) cc_final: 0.8206 (p) REVERT: B 615 SER cc_start: 0.8958 (t) cc_final: 0.8705 (m) REVERT: C 104 MET cc_start: 0.8614 (ttm) cc_final: 0.8272 (ttt) REVERT: C 190 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: F 542 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7843 (ttm110) REVERT: G 97 LYS cc_start: 0.8401 (mttp) cc_final: 0.7925 (mttp) REVERT: G 102 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: G 215 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8005 (tp) REVERT: H 100 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8105 (mtp) REVERT: L 89 LYS cc_start: 0.7374 (tmtt) cc_final: 0.7084 (tmtt) outliers start: 59 outliers final: 51 residues processed: 232 average time/residue: 0.1079 time to fit residues: 38.5419 Evaluate side-chains 239 residues out of total 1736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 272 ILE Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 481 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 653 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128604 restraints weight = 25900.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130643 restraints weight = 22902.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.132091 restraints weight = 18649.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133605 restraints weight = 14318.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133962 restraints weight = 13522.816| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17415 Z= 0.136 Angle : 0.708 17.120 23837 Z= 0.326 Chirality : 0.047 0.437 2941 Planarity : 0.004 0.093 2846 Dihedral : 4.289 33.374 2107 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.00 % Allowed : 19.68 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1934 helix: 0.91 (0.28), residues: 382 sheet: -0.02 (0.24), residues: 480 loop : -0.48 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 617 TYR 0.031 0.001 TYR A 638 PHE 0.035 0.001 PHE G 288 TRP 0.049 0.001 TRP L 35 HIS 0.003 0.001 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (17269) covalent geometry : angle 0.63312 / 0.31 (23437) SS BOND : bond 0.00401 / 0.27 ( 38) SS BOND : angle 1.62550 / 1.04 ( 76) hydrogen bonds : bond 0.04173 / 2.75 ( 408) hydrogen bonds : angle 4.72238 / 3.47 ( 1149) link_ALPHA1-2 : bond 0.00417 / 0.19 ( 3) link_ALPHA1-2 : angle 1.69557 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00683 / 0.35 ( 7) link_ALPHA1-3 : angle 2.38463 / 1.37 ( 21) link_ALPHA1-6 : bond 0.00480 / 0.29 ( 6) link_ALPHA1-6 : angle 1.40039 / 0.83 ( 18) link_BETA1-4 : bond 0.00389 / 0.21 ( 29) link_BETA1-4 : angle 1.11076 / 0.76 ( 87) link_NAG-ASN : bond 0.00470 / 0.26 ( 63) link_NAG-ASN : angle 3.29454 / 2.25 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.93 seconds wall clock time: 39 minutes 23.91 seconds (2363.91 seconds total)