Starting phenix.real_space_refine on Tue Jun 17 18:09:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aui_43881/06_2025/9aui_43881_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aui_43881/06_2025/9aui_43881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9aui_43881/06_2025/9aui_43881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aui_43881/06_2025/9aui_43881.map" model { file = "/net/cci-nas-00/data/ceres_data/9aui_43881/06_2025/9aui_43881_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aui_43881/06_2025/9aui_43881_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 12576 2.51 5 N 3333 2.21 5 O 4140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20184 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "C" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.30, per 1000 atoms: 0.66 Number of scatterers: 20184 At special positions: 0 Unit cell: (142.56, 157.68, 156.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4140 8.00 N 3333 7.00 C 12576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " 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 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 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.01 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 N 4 " - " MAN N 5 " " MAN S 4 " - " MAN S 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 362 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 442 " " NAG B 601 " - " ASN B 386 " " NAG B 602 " - " ASN B 392 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 362 " " NAG B 605 " - " ASN B 276 " " NAG B 606 " - " ASN B 88 " " NAG B 607 " - " ASN B 241 " " NAG B 608 " - " ASN B 448 " " NAG B 609 " - " ASN B 442 " " NAG C 601 " - " ASN C 386 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 362 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 442 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 300 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 332 " " NAG T 1 " - " ASN C 300 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN B 262 " " NAG X 1 " - " ASN B 332 " " NAG Y 1 " - " ASN B 300 " " NAG Z 1 " - " ASN B 156 " " NAG a 1 " - " ASN B 197 " Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 2.7 seconds 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4506 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 48 sheets defined 18.6% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 3.819A pdb=" N TYR A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 58 through 61 removed outlier: 3.561A pdb=" N TYR B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.779A pdb=" N CYS B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.204A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.637A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.562A pdb=" N ASN B 408 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 409 " --> pdb=" O SER B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 409' Processing helix chain 'B' and resid 475 through 483 removed outlier: 4.236A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.516A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.260A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 540 through 544 removed outlier: 3.624A pdb=" N ASN D 543 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 544 " --> pdb=" O ALA D 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 540 through 544' Processing helix chain 'D' and resid 573 through 596 removed outlier: 4.337A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 619 through 625 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.639A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 664 removed outlier: 3.741A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.551A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 541 removed outlier: 3.689A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 536 through 541' Processing helix chain 'E' and resid 542 through 545 removed outlier: 3.813A pdb=" N LEU E 545 " --> pdb=" O ARG E 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 542 through 545' Processing helix chain 'E' and resid 570 through 596 removed outlier: 4.151A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.760A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.759A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.924A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 662 " --> pdb=" O GLN E 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.916A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 540 removed outlier: 5.675A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN F 540 " --> pdb=" O LEU F 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 535 through 540' Processing helix chain 'F' and resid 572 through 596 removed outlier: 4.424A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.571A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.660A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 4.037A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.874A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.233A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.749A pdb=" N ASP J 84 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU J 85 " --> pdb=" O ALA J 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 81 through 85' Processing helix chain 'K' and resid 81 through 85 removed outlier: 4.075A pdb=" N GLU K 85 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.579A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.591A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.754A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.539A pdb=" N SER A 56 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.671A pdb=" N GLU A 466 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 413 through 418 removed outlier: 4.478A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 294 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 309 Processing sheet with id=AB1, first strand: chain 'A' and resid 382 through 383 removed outlier: 4.626A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.273A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.568A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB7, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AB8, first strand: chain 'B' and resid 271 through 273 removed outlier: 5.840A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY B 393 " --> pdb=" O TYR B 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 377 removed outlier: 4.157A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 294 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.645A pdb=" N ILE B 424 " --> pdb=" O MET B 434 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.628A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR F 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS F 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.613A pdb=" N LEU C 84 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC9, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AD1, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.358A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.339A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 393 " --> pdb=" O TYR C 361 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 294 through 297 removed outlier: 3.727A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.555A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.499A pdb=" N GLU G 10 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 51 through 52 removed outlier: 3.528A pdb=" N GLY G 57 " --> pdb=" O ASN G 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.980A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.518A pdb=" N GLU I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.695A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AE5, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AE6, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'K' and resid 17 through 23 Processing sheet with id=AE8, first strand: chain 'K' and resid 47 through 50 removed outlier: 6.616A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 47 through 50 removed outlier: 6.616A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.521A pdb=" N GLY L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 105 " --> pdb=" O TYR L 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.521A pdb=" N GLY L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR L 105 " --> pdb=" O TYR L 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 18 through 23 627 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 6.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6327 1.34 - 1.47: 5474 1.47 - 1.60: 8611 1.60 - 1.73: 0 1.73 - 1.86: 183 Bond restraints: 20595 Sorted by residual: bond pdb=" C1 NAG A 606 " pdb=" O5 NAG A 606 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C1 MAN X 8 " pdb=" C2 MAN X 8 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 MAN N 8 " pdb=" O5 MAN N 8 " ideal model delta sigma weight residual 1.399 1.446 -0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" C5 MAN X 5 " pdb=" O5 MAN X 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" C1 MAN X 8 " pdb=" O5 MAN X 8 " ideal model delta sigma weight residual 1.399 1.446 -0.047 2.00e-02 2.50e+03 5.45e+00 ... (remaining 20590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 27590 3.68 - 7.36: 349 7.36 - 11.04: 33 11.04 - 14.73: 11 14.73 - 18.41: 1 Bond angle restraints: 27984 Sorted by residual: angle pdb=" C CYS A 218 " pdb=" N ALA A 219 " pdb=" CA ALA A 219 " ideal model delta sigma weight residual 120.68 139.09 -18.41 1.52e+00 4.33e-01 1.47e+02 angle pdb=" CA CYS C 418 " pdb=" CB CYS C 418 " pdb=" SG CYS C 418 " ideal model delta sigma weight residual 114.40 127.39 -12.99 2.30e+00 1.89e-01 3.19e+01 angle pdb=" CB MET I 34 " pdb=" CG MET I 34 " pdb=" SD MET I 34 " ideal model delta sigma weight residual 112.70 127.18 -14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N GLU F 634 " pdb=" CA GLU F 634 " pdb=" CB GLU F 634 " ideal model delta sigma weight residual 110.47 117.41 -6.94 1.45e+00 4.76e-01 2.29e+01 angle pdb=" CB LYS L 106 " pdb=" CG LYS L 106 " pdb=" CD LYS L 106 " ideal model delta sigma weight residual 111.30 122.02 -10.72 2.30e+00 1.89e-01 2.17e+01 ... (remaining 27979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.66: 12300 23.66 - 47.31: 855 47.31 - 70.97: 114 70.97 - 94.63: 76 94.63 - 118.28: 68 Dihedral angle restraints: 13413 sinusoidal: 6357 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -164.99 78.99 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CB CYS A 201 " pdb=" SG CYS A 201 " pdb=" SG CYS A 433 " pdb=" CB CYS A 433 " ideal model delta sinusoidal sigma weight residual 93.00 17.30 75.70 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual -86.00 -17.52 -68.48 1 1.00e+01 1.00e-02 6.08e+01 ... (remaining 13410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2874 0.083 - 0.166: 446 0.166 - 0.249: 42 0.249 - 0.333: 14 0.333 - 0.416: 2 Chirality restraints: 3378 Sorted by residual: chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 88 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C2 NAG Q 1 " pdb=" C1 NAG Q 1 " pdb=" C3 NAG Q 1 " pdb=" N2 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" C1 NAG C 609 " pdb=" ND2 ASN C 442 " pdb=" C2 NAG C 609 " pdb=" O5 NAG C 609 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3375 not shown) Planarity restraints: 3495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 36 " -0.021 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP G 36 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP G 36 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP G 36 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 36 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP G 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 36 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 36 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP G 36 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 596 " 0.032 2.00e-02 2.50e+03 2.75e-02 1.90e+01 pdb=" CG TRP D 596 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP D 596 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 596 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 596 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 596 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 596 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 596 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 596 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 596 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 571 " 0.023 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP D 571 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 571 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 571 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 571 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 571 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 571 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 571 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 571 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP D 571 " -0.005 2.00e-02 2.50e+03 ... (remaining 3492 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3716 2.77 - 3.31: 17283 3.31 - 3.84: 31839 3.84 - 4.37: 33988 4.37 - 4.90: 61293 Nonbonded interactions: 148119 Sorted by model distance: nonbonded pdb=" OG1 THR D 627 " pdb=" OE1 GLN D 630 " model vdw 2.242 3.040 nonbonded pdb=" OG SER J 65 " pdb=" OG1 THR J 76 " model vdw 2.267 3.040 nonbonded pdb=" OG SER C 185 " pdb=" O THR C 185b" model vdw 2.268 3.040 nonbonded pdb=" OH TYR J 51 " pdb=" O4 MAN N 5 " model vdw 2.296 3.040 nonbonded pdb=" OG SER A 447 " pdb=" O7 NAG M 1 " model vdw 2.299 3.040 ... (remaining 148114 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 49.830 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20720 Z= 0.295 Angle : 1.098 18.407 28321 Z= 0.522 Chirality : 0.062 0.416 3378 Planarity : 0.007 0.071 3453 Dihedral : 18.388 118.282 8793 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.15), residues: 2427 helix: -1.45 (0.23), residues: 408 sheet: -0.59 (0.20), residues: 627 loop : -2.43 (0.14), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP D 596 HIS 0.005 0.001 HIS G 35 PHE 0.033 0.003 PHE K 64 TYR 0.045 0.002 TYR C 395 ARG 0.018 0.001 ARG B 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 42) link_NAG-ASN : angle 4.21395 ( 126) link_ALPHA1-6 : bond 0.00603 ( 9) link_ALPHA1-6 : angle 1.53548 ( 27) link_BETA1-4 : bond 0.00593 ( 24) link_BETA1-4 : angle 2.13852 ( 72) link_ALPHA1-2 : bond 0.00575 ( 3) link_ALPHA1-2 : angle 3.11773 ( 9) link_ALPHA1-3 : bond 0.00337 ( 9) link_ALPHA1-3 : angle 1.92396 ( 27) hydrogen bonds : bond 0.14207 ( 611) hydrogen bonds : angle 6.42890 ( 1674) SS BOND : bond 0.00625 ( 38) SS BOND : angle 1.60668 ( 76) covalent geometry : bond 0.00645 (20595) covalent geometry : angle 1.05511 (27984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 LYS cc_start: 0.8557 (mmpt) cc_final: 0.8095 (mtmt) REVERT: D 652 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8395 (tp-100) REVERT: D 657 GLU cc_start: 0.8644 (tp30) cc_final: 0.8207 (tt0) REVERT: E 534 SER cc_start: 0.8890 (t) cc_final: 0.8565 (t) REVERT: E 543 ASN cc_start: 0.9002 (m110) cc_final: 0.8757 (m110) REVERT: E 652 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8434 (tm-30) REVERT: G 46 GLU cc_start: 0.8566 (tp30) cc_final: 0.8335 (tp30) REVERT: G 63 LYS cc_start: 0.8467 (pptt) cc_final: 0.8017 (pptt) REVERT: H 46 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8170 (mm-30) REVERT: H 50 TRP cc_start: 0.8589 (p-90) cc_final: 0.8221 (p-90) REVERT: H 73 ASP cc_start: 0.7761 (t0) cc_final: 0.7520 (t0) REVERT: H 82 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7191 (mm-30) REVERT: J 48 LEU cc_start: 0.8642 (pt) cc_final: 0.8429 (pt) REVERT: L 22 CYS cc_start: 0.3187 (m) cc_final: 0.2402 (m) REVERT: L 81 GLN cc_start: 0.7914 (mp10) cc_final: 0.7706 (mp10) REVERT: L 87 ASP cc_start: 0.8611 (m-30) cc_final: 0.8274 (m-30) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.3171 time to fit residues: 196.4070 Evaluate side-chains 351 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 190 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 GLN F 618 ASN ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 39 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107033 restraints weight = 35790.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108079 restraints weight = 27563.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109283 restraints weight = 20992.444| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20720 Z= 0.172 Angle : 0.741 11.602 28321 Z= 0.350 Chirality : 0.047 0.391 3378 Planarity : 0.004 0.065 3453 Dihedral : 14.765 103.091 4410 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.61 % Allowed : 10.40 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2427 helix: -0.09 (0.27), residues: 405 sheet: -0.45 (0.20), residues: 654 loop : -2.38 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 596 HIS 0.005 0.001 HIS A 287 PHE 0.011 0.001 PHE C 317 TYR 0.025 0.001 TYR K 51 ARG 0.007 0.000 ARG K 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 42) link_NAG-ASN : angle 3.20184 ( 126) link_ALPHA1-6 : bond 0.00684 ( 9) link_ALPHA1-6 : angle 1.64530 ( 27) link_BETA1-4 : bond 0.00465 ( 24) link_BETA1-4 : angle 2.06222 ( 72) link_ALPHA1-2 : bond 0.00789 ( 3) link_ALPHA1-2 : angle 3.18475 ( 9) link_ALPHA1-3 : bond 0.00920 ( 9) link_ALPHA1-3 : angle 2.18642 ( 27) hydrogen bonds : bond 0.04009 ( 611) hydrogen bonds : angle 5.16931 ( 1674) SS BOND : bond 0.00379 ( 38) SS BOND : angle 0.98737 ( 76) covalent geometry : bond 0.00398 (20595) covalent geometry : angle 0.69703 (27984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 360 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 355 ASN cc_start: 0.7729 (p0) cc_final: 0.7520 (p0) REVERT: C 434 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7953 (ttp) REVERT: D 540 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8373 (tm-30) REVERT: D 657 GLU cc_start: 0.8603 (tp30) cc_final: 0.8343 (tp30) REVERT: E 543 ASN cc_start: 0.8972 (m110) cc_final: 0.8758 (m110) REVERT: E 615 SER cc_start: 0.9185 (p) cc_final: 0.8938 (p) REVERT: H 50 TRP cc_start: 0.8795 (p-90) cc_final: 0.8395 (p-90) REVERT: I 10 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: I 43 GLN cc_start: 0.8999 (mp10) cc_final: 0.8791 (mp10) REVERT: I 73 ASP cc_start: 0.7062 (t0) cc_final: 0.6713 (t0) REVERT: I 81 MET cc_start: 0.8419 (tmm) cc_final: 0.7374 (tmm) REVERT: J 55 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7654 (tmtt) REVERT: K 40 GLN cc_start: 0.8036 (tp40) cc_final: 0.7563 (tp-100) REVERT: L 22 CYS cc_start: 0.3112 (m) cc_final: 0.2775 (m) REVERT: L 38 TYR cc_start: 0.7996 (m-80) cc_final: 0.7627 (m-80) outliers start: 34 outliers final: 26 residues processed: 371 average time/residue: 0.4320 time to fit residues: 253.8582 Evaluate side-chains 360 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 332 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 186 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 630 GLN J 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106138 restraints weight = 35954.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106930 restraints weight = 26252.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108229 restraints weight = 21260.225| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20720 Z= 0.213 Angle : 0.734 9.759 28321 Z= 0.351 Chirality : 0.048 0.374 3378 Planarity : 0.004 0.062 3453 Dihedral : 13.279 109.338 4410 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.79 % Allowed : 13.76 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2427 helix: 0.37 (0.28), residues: 405 sheet: -0.60 (0.19), residues: 699 loop : -2.29 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 37 HIS 0.007 0.001 HIS C 330 PHE 0.011 0.002 PHE C 376 TYR 0.022 0.001 TYR K 51 ARG 0.008 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 42) link_NAG-ASN : angle 3.23853 ( 126) link_ALPHA1-6 : bond 0.00768 ( 9) link_ALPHA1-6 : angle 1.68158 ( 27) link_BETA1-4 : bond 0.00489 ( 24) link_BETA1-4 : angle 1.89837 ( 72) link_ALPHA1-2 : bond 0.00686 ( 3) link_ALPHA1-2 : angle 2.34306 ( 9) link_ALPHA1-3 : bond 0.00868 ( 9) link_ALPHA1-3 : angle 1.97531 ( 27) hydrogen bonds : bond 0.04109 ( 611) hydrogen bonds : angle 4.97048 ( 1674) SS BOND : bond 0.00423 ( 38) SS BOND : angle 1.08707 ( 76) covalent geometry : bond 0.00499 (20595) covalent geometry : angle 0.69129 (27984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 349 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8026 (ttm) REVERT: A 475 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7429 (tpp) REVERT: B 317 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7991 (p90) REVERT: B 482 GLU cc_start: 0.7878 (tp30) cc_final: 0.7612 (mm-30) REVERT: C 122 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8455 (pp) REVERT: C 180 ASP cc_start: 0.8761 (m-30) cc_final: 0.8540 (t0) REVERT: C 369 MET cc_start: 0.8342 (tmm) cc_final: 0.7692 (ptm) REVERT: D 530 MET cc_start: 0.8663 (mmt) cc_final: 0.7672 (mmt) REVERT: D 540 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8405 (tm-30) REVERT: D 571 TRP cc_start: 0.7702 (m-10) cc_final: 0.7463 (m-10) REVERT: D 657 GLU cc_start: 0.8628 (tp30) cc_final: 0.8333 (tp30) REVERT: E 543 ASN cc_start: 0.9026 (m110) cc_final: 0.8825 (m110) REVERT: H 19 LYS cc_start: 0.9139 (tppt) cc_final: 0.8751 (tptp) REVERT: H 48 MET cc_start: 0.8219 (mmm) cc_final: 0.8008 (mmt) REVERT: H 50 TRP cc_start: 0.8994 (p-90) cc_final: 0.8280 (p-90) REVERT: H 70 MET cc_start: 0.8808 (mtt) cc_final: 0.8521 (mtt) REVERT: H 82 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7580 (mm-30) REVERT: H 115 ASP cc_start: 0.9027 (p0) cc_final: 0.8751 (p0) REVERT: I 10 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: I 73 ASP cc_start: 0.7389 (t0) cc_final: 0.6983 (t0) REVERT: I 81 MET cc_start: 0.8513 (tmm) cc_final: 0.7769 (tmm) REVERT: J 55 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7754 (tmtt) REVERT: K 40 GLN cc_start: 0.8199 (tp40) cc_final: 0.7768 (tp40) REVERT: L 38 TYR cc_start: 0.8151 (m-80) cc_final: 0.7764 (m-80) outliers start: 59 outliers final: 43 residues processed: 375 average time/residue: 0.4481 time to fit residues: 268.3997 Evaluate side-chains 381 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 333 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 100 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 134 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109071 restraints weight = 36191.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110565 restraints weight = 25805.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111700 restraints weight = 19814.478| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20720 Z= 0.120 Angle : 0.654 9.712 28321 Z= 0.310 Chirality : 0.046 0.366 3378 Planarity : 0.004 0.047 3453 Dihedral : 12.159 104.688 4410 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.32 % Allowed : 16.41 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2427 helix: 0.70 (0.28), residues: 405 sheet: -0.44 (0.20), residues: 672 loop : -2.16 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 37 HIS 0.003 0.001 HIS A 287 PHE 0.009 0.001 PHE A 317 TYR 0.026 0.001 TYR K 51 ARG 0.009 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 42) link_NAG-ASN : angle 2.97351 ( 126) link_ALPHA1-6 : bond 0.00841 ( 9) link_ALPHA1-6 : angle 1.63597 ( 27) link_BETA1-4 : bond 0.00465 ( 24) link_BETA1-4 : angle 1.67886 ( 72) link_ALPHA1-2 : bond 0.01297 ( 3) link_ALPHA1-2 : angle 2.35087 ( 9) link_ALPHA1-3 : bond 0.01042 ( 9) link_ALPHA1-3 : angle 1.94707 ( 27) hydrogen bonds : bond 0.03318 ( 611) hydrogen bonds : angle 4.65752 ( 1674) SS BOND : bond 0.00353 ( 38) SS BOND : angle 0.86693 ( 76) covalent geometry : bond 0.00270 (20595) covalent geometry : angle 0.61304 (27984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 351 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASP cc_start: 0.8187 (t70) cc_final: 0.7890 (t0) REVERT: B 317 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7815 (p90) REVERT: C 122 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8368 (pp) REVERT: C 369 MET cc_start: 0.8234 (tmm) cc_final: 0.7591 (ptm) REVERT: D 596 TRP cc_start: 0.7375 (p90) cc_final: 0.7069 (p90) REVERT: D 652 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8606 (tp-100) REVERT: D 653 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8491 (tm-30) REVERT: D 657 GLU cc_start: 0.8617 (tp30) cc_final: 0.8310 (tp30) REVERT: E 530 MET cc_start: 0.7579 (mmm) cc_final: 0.7343 (mmm) REVERT: H 19 LYS cc_start: 0.9103 (tppt) cc_final: 0.8761 (tptp) REVERT: H 50 TRP cc_start: 0.9003 (p-90) cc_final: 0.8205 (p-90) REVERT: H 82 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7582 (mm-30) REVERT: H 115 ASP cc_start: 0.8978 (p0) cc_final: 0.8745 (p0) REVERT: I 10 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7937 (mm-30) REVERT: I 73 ASP cc_start: 0.7248 (t0) cc_final: 0.6788 (t0) REVERT: I 81 MET cc_start: 0.8474 (tmm) cc_final: 0.7730 (tmm) REVERT: J 55 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7524 (ttpt) REVERT: K 40 GLN cc_start: 0.8145 (tp40) cc_final: 0.7762 (tp-100) outliers start: 49 outliers final: 35 residues processed: 373 average time/residue: 0.3014 time to fit residues: 175.9215 Evaluate side-chains 376 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 339 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 228 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS B 287 HIS C 287 HIS E 543 ASN G 113 ASN I 3 GLN J 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098020 restraints weight = 36328.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099065 restraints weight = 26382.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100091 restraints weight = 21863.278| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 20720 Z= 0.409 Angle : 0.923 10.165 28321 Z= 0.446 Chirality : 0.053 0.369 3378 Planarity : 0.005 0.061 3453 Dihedral : 12.883 110.984 4410 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 3.69 % Allowed : 17.54 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2427 helix: 0.31 (0.28), residues: 387 sheet: -0.59 (0.20), residues: 630 loop : -2.28 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP G 36 HIS 0.009 0.002 HIS B 330 PHE 0.021 0.003 PHE B 93 TYR 0.027 0.002 TYR C 361 ARG 0.011 0.001 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 42) link_NAG-ASN : angle 3.64145 ( 126) link_ALPHA1-6 : bond 0.00623 ( 9) link_ALPHA1-6 : angle 1.78496 ( 27) link_BETA1-4 : bond 0.00616 ( 24) link_BETA1-4 : angle 1.99510 ( 72) link_ALPHA1-2 : bond 0.00255 ( 3) link_ALPHA1-2 : angle 2.74743 ( 9) link_ALPHA1-3 : bond 0.00570 ( 9) link_ALPHA1-3 : angle 2.12453 ( 27) hydrogen bonds : bond 0.05139 ( 611) hydrogen bonds : angle 5.21302 ( 1674) SS BOND : bond 0.00708 ( 38) SS BOND : angle 1.66468 ( 76) covalent geometry : bond 0.00966 (20595) covalent geometry : angle 0.87995 (27984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 336 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8578 (tpp) cc_final: 0.8113 (ttm) REVERT: C 122 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8653 (pp) REVERT: C 301 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8225 (t0) REVERT: C 369 MET cc_start: 0.8314 (tmm) cc_final: 0.8085 (ttt) REVERT: D 530 MET cc_start: 0.8867 (mmt) cc_final: 0.7944 (mmt) REVERT: D 571 TRP cc_start: 0.7894 (m-10) cc_final: 0.7598 (m-10) REVERT: E 520 LEU cc_start: 0.7235 (mm) cc_final: 0.6483 (tp) REVERT: E 653 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8353 (tm-30) REVERT: H 19 LYS cc_start: 0.9071 (tppt) cc_final: 0.8833 (tptp) REVERT: H 50 TRP cc_start: 0.9249 (p-90) cc_final: 0.8280 (p-90) REVERT: H 82 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7728 (mm-30) REVERT: H 115 ASP cc_start: 0.9107 (p0) cc_final: 0.8869 (p0) REVERT: I 10 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: I 73 ASP cc_start: 0.7627 (t0) cc_final: 0.7335 (t0) REVERT: I 81 MET cc_start: 0.8575 (tmm) cc_final: 0.7816 (tmm) REVERT: J 52 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7902 (mm-30) REVERT: J 68 LYS cc_start: 0.7691 (tttp) cc_final: 0.7190 (tttp) REVERT: L 33 ASN cc_start: 0.8860 (p0) cc_final: 0.8036 (p0) REVERT: L 106 LYS cc_start: 0.8667 (tppt) cc_final: 0.8451 (tppt) outliers start: 78 outliers final: 58 residues processed: 381 average time/residue: 0.3009 time to fit residues: 179.8716 Evaluate side-chains 384 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 100 ILE Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 100 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 75 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106123 restraints weight = 36279.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107087 restraints weight = 27237.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108439 restraints weight = 20960.635| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20720 Z= 0.142 Angle : 0.703 10.275 28321 Z= 0.333 Chirality : 0.047 0.366 3378 Planarity : 0.004 0.056 3453 Dihedral : 11.819 98.250 4410 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.65 % Allowed : 19.95 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2427 helix: 0.67 (0.28), residues: 405 sheet: -0.63 (0.20), residues: 690 loop : -2.06 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 36 HIS 0.003 0.001 HIS I 35 PHE 0.009 0.001 PHE A 317 TYR 0.031 0.001 TYR K 51 ARG 0.011 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 42) link_NAG-ASN : angle 3.18508 ( 126) link_ALPHA1-6 : bond 0.00826 ( 9) link_ALPHA1-6 : angle 1.63007 ( 27) link_BETA1-4 : bond 0.00467 ( 24) link_BETA1-4 : angle 1.62148 ( 72) link_ALPHA1-2 : bond 0.01268 ( 3) link_ALPHA1-2 : angle 2.42452 ( 9) link_ALPHA1-3 : bond 0.00973 ( 9) link_ALPHA1-3 : angle 1.91725 ( 27) hydrogen bonds : bond 0.03663 ( 611) hydrogen bonds : angle 4.72153 ( 1674) SS BOND : bond 0.00481 ( 38) SS BOND : angle 1.18081 ( 76) covalent geometry : bond 0.00325 (20595) covalent geometry : angle 0.66056 (27984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 364 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 ASP cc_start: 0.8218 (t70) cc_final: 0.7912 (t0) REVERT: B 317 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7952 (p90) REVERT: C 122 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8530 (pp) REVERT: C 180 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8372 (t0) REVERT: C 369 MET cc_start: 0.8236 (tmm) cc_final: 0.7662 (ptm) REVERT: D 540 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 652 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8673 (tp-100) REVERT: E 520 LEU cc_start: 0.7107 (mm) cc_final: 0.6337 (tp) REVERT: E 530 MET cc_start: 0.8510 (tpp) cc_final: 0.8277 (tpp) REVERT: E 653 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8326 (tm-30) REVERT: F 654 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8578 (tm-30) REVERT: G 12 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7588 (mmtm) REVERT: H 19 LYS cc_start: 0.9092 (tppt) cc_final: 0.8743 (tptp) REVERT: H 50 TRP cc_start: 0.9194 (p-90) cc_final: 0.8248 (p-90) REVERT: H 82 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7719 (mm-30) REVERT: H 90 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7981 (t0) REVERT: H 115 ASP cc_start: 0.9029 (p0) cc_final: 0.8801 (p0) REVERT: I 10 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7909 (mm-30) REVERT: I 73 ASP cc_start: 0.7478 (t0) cc_final: 0.7128 (t0) REVERT: I 81 MET cc_start: 0.8512 (tmm) cc_final: 0.7411 (tmm) REVERT: J 68 LYS cc_start: 0.7746 (tttp) cc_final: 0.7320 (tttp) REVERT: K 40 GLN cc_start: 0.8233 (tp40) cc_final: 0.7639 (tp40) REVERT: L 33 ASN cc_start: 0.8855 (p0) cc_final: 0.8130 (p0) REVERT: L 106 LYS cc_start: 0.8646 (tppt) cc_final: 0.8374 (tppt) outliers start: 56 outliers final: 42 residues processed: 393 average time/residue: 0.3223 time to fit residues: 200.2120 Evaluate side-chains 392 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 346 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 174 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103893 restraints weight = 36092.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105006 restraints weight = 26555.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106047 restraints weight = 20979.825| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20720 Z= 0.209 Angle : 0.738 9.793 28321 Z= 0.351 Chirality : 0.048 0.361 3378 Planarity : 0.004 0.060 3453 Dihedral : 11.688 100.716 4410 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.36 % Allowed : 20.05 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.17), residues: 2427 helix: 0.94 (0.29), residues: 387 sheet: -0.52 (0.20), residues: 660 loop : -2.07 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 36 HIS 0.006 0.001 HIS C 330 PHE 0.014 0.002 PHE B 376 TYR 0.029 0.001 TYR K 51 ARG 0.013 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00505 ( 42) link_NAG-ASN : angle 3.21620 ( 126) link_ALPHA1-6 : bond 0.00754 ( 9) link_ALPHA1-6 : angle 1.66866 ( 27) link_BETA1-4 : bond 0.00480 ( 24) link_BETA1-4 : angle 1.65461 ( 72) link_ALPHA1-2 : bond 0.01118 ( 3) link_ALPHA1-2 : angle 2.58800 ( 9) link_ALPHA1-3 : bond 0.00840 ( 9) link_ALPHA1-3 : angle 1.95877 ( 27) hydrogen bonds : bond 0.03950 ( 611) hydrogen bonds : angle 4.74409 ( 1674) SS BOND : bond 0.00447 ( 38) SS BOND : angle 1.20204 ( 76) covalent geometry : bond 0.00493 (20595) covalent geometry : angle 0.69638 (27984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 357 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8195 (ttm) REVERT: B 107 ASP cc_start: 0.8228 (t70) cc_final: 0.7927 (t0) REVERT: B 317 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8246 (p90) REVERT: C 122 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8608 (pp) REVERT: C 180 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8409 (t0) REVERT: C 295 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8921 (t) REVERT: C 369 MET cc_start: 0.8270 (tmm) cc_final: 0.8012 (ttt) REVERT: D 530 MET cc_start: 0.8725 (mmt) cc_final: 0.7792 (mmt) REVERT: D 540 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8382 (tm-30) REVERT: D 571 TRP cc_start: 0.7702 (m-10) cc_final: 0.7437 (m-10) REVERT: D 652 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8705 (tp-100) REVERT: E 520 LEU cc_start: 0.7130 (mm) cc_final: 0.6357 (tp) REVERT: E 530 MET cc_start: 0.8352 (tpp) cc_final: 0.8088 (tpp) REVERT: E 653 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8308 (tm-30) REVERT: G 12 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7605 (mmtm) REVERT: G 122 LEU cc_start: 0.8927 (pp) cc_final: 0.8726 (pt) REVERT: H 19 LYS cc_start: 0.9089 (tppt) cc_final: 0.8702 (tptp) REVERT: H 50 TRP cc_start: 0.9200 (p-90) cc_final: 0.8234 (p-90) REVERT: H 82 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7587 (mm-30) REVERT: H 90 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8076 (t0) REVERT: H 115 ASP cc_start: 0.9060 (p0) cc_final: 0.8852 (p0) REVERT: I 10 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7826 (mm-30) REVERT: I 73 ASP cc_start: 0.7520 (t0) cc_final: 0.7142 (t0) REVERT: I 81 MET cc_start: 0.8537 (tmm) cc_final: 0.7794 (tmm) REVERT: J 68 LYS cc_start: 0.7806 (tttp) cc_final: 0.7315 (tttp) REVERT: L 33 ASN cc_start: 0.8887 (p0) cc_final: 0.8138 (p0) REVERT: L 106 LYS cc_start: 0.8643 (tppt) cc_final: 0.8394 (tppt) outliers start: 71 outliers final: 53 residues processed: 399 average time/residue: 0.3119 time to fit residues: 194.8986 Evaluate side-chains 405 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 90 CYS Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 100 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 150 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 chunk 238 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102476 restraints weight = 36335.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104875 restraints weight = 22294.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105814 restraints weight = 15960.656| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20720 Z= 0.177 Angle : 0.726 10.563 28321 Z= 0.344 Chirality : 0.047 0.362 3378 Planarity : 0.004 0.063 3453 Dihedral : 11.346 101.056 4410 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.22 % Allowed : 21.09 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.17), residues: 2427 helix: 1.04 (0.29), residues: 387 sheet: -0.54 (0.20), residues: 675 loop : -2.02 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP L 37 HIS 0.005 0.001 HIS C 330 PHE 0.014 0.001 PHE B 376 TYR 0.030 0.001 TYR K 51 ARG 0.014 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 42) link_NAG-ASN : angle 3.17161 ( 126) link_ALPHA1-6 : bond 0.00799 ( 9) link_ALPHA1-6 : angle 1.61420 ( 27) link_BETA1-4 : bond 0.00471 ( 24) link_BETA1-4 : angle 1.57431 ( 72) link_ALPHA1-2 : bond 0.01381 ( 3) link_ALPHA1-2 : angle 2.36568 ( 9) link_ALPHA1-3 : bond 0.00884 ( 9) link_ALPHA1-3 : angle 1.91558 ( 27) hydrogen bonds : bond 0.03734 ( 611) hydrogen bonds : angle 4.63426 ( 1674) SS BOND : bond 0.00450 ( 38) SS BOND : angle 1.10161 ( 76) covalent geometry : bond 0.00415 (20595) covalent geometry : angle 0.68650 (27984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 354 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: B 107 ASP cc_start: 0.8228 (t70) cc_final: 0.7940 (t0) REVERT: B 317 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8171 (p90) REVERT: C 122 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8573 (pp) REVERT: C 180 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8470 (t0) REVERT: C 295 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8939 (t) REVERT: C 369 MET cc_start: 0.8168 (tmm) cc_final: 0.7863 (ttt) REVERT: D 530 MET cc_start: 0.8693 (mmt) cc_final: 0.7759 (mmt) REVERT: D 540 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8351 (tm-30) REVERT: D 571 TRP cc_start: 0.7678 (m-10) cc_final: 0.7454 (m-10) REVERT: D 596 TRP cc_start: 0.7646 (p90) cc_final: 0.7260 (p90) REVERT: D 652 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8663 (tp-100) REVERT: D 657 GLU cc_start: 0.8519 (tp30) cc_final: 0.8181 (tt0) REVERT: E 520 LEU cc_start: 0.7063 (mm) cc_final: 0.6277 (tp) REVERT: E 653 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8257 (tm-30) REVERT: F 657 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8430 (tm-30) REVERT: G 12 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7652 (mmtm) REVERT: G 122 LEU cc_start: 0.8965 (pp) cc_final: 0.8728 (pt) REVERT: H 19 LYS cc_start: 0.9058 (tppt) cc_final: 0.8586 (tptp) REVERT: H 50 TRP cc_start: 0.9252 (p-90) cc_final: 0.9011 (p-90) REVERT: H 82 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7621 (mm-30) REVERT: H 90 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8182 (t0) REVERT: I 10 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7871 (mm-30) REVERT: I 73 ASP cc_start: 0.7630 (t0) cc_final: 0.7186 (t0) REVERT: I 81 MET cc_start: 0.8511 (tmm) cc_final: 0.7741 (tmm) REVERT: J 68 LYS cc_start: 0.7789 (tttp) cc_final: 0.7299 (tttp) REVERT: L 33 ASN cc_start: 0.8900 (p0) cc_final: 0.8123 (p0) REVERT: L 106 LYS cc_start: 0.8645 (tppt) cc_final: 0.8355 (tppt) outliers start: 68 outliers final: 54 residues processed: 392 average time/residue: 0.3081 time to fit residues: 188.8564 Evaluate side-chains 402 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 342 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 100 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 190 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 67 optimal weight: 0.0030 chunk 73 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN J 40 GLN J 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.139787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103718 restraints weight = 36045.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106153 restraints weight = 23064.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106797 restraints weight = 16319.798| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20720 Z= 0.126 Angle : 0.692 10.512 28321 Z= 0.327 Chirality : 0.046 0.354 3378 Planarity : 0.004 0.062 3453 Dihedral : 10.659 99.564 4410 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.46 % Allowed : 21.61 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.17), residues: 2427 helix: 1.01 (0.29), residues: 405 sheet: -0.48 (0.20), residues: 702 loop : -2.00 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP L 37 HIS 0.004 0.001 HIS I 35 PHE 0.010 0.001 PHE B 376 TYR 0.029 0.001 TYR K 51 ARG 0.016 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 42) link_NAG-ASN : angle 2.95604 ( 126) link_ALPHA1-6 : bond 0.00886 ( 9) link_ALPHA1-6 : angle 1.48995 ( 27) link_BETA1-4 : bond 0.00511 ( 24) link_BETA1-4 : angle 1.46843 ( 72) link_ALPHA1-2 : bond 0.01495 ( 3) link_ALPHA1-2 : angle 2.01212 ( 9) link_ALPHA1-3 : bond 0.00941 ( 9) link_ALPHA1-3 : angle 1.80628 ( 27) hydrogen bonds : bond 0.03239 ( 611) hydrogen bonds : angle 4.45641 ( 1674) SS BOND : bond 0.00376 ( 38) SS BOND : angle 0.93370 ( 76) covalent geometry : bond 0.00288 (20595) covalent geometry : angle 0.65596 (27984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: B 107 ASP cc_start: 0.8203 (t70) cc_final: 0.7968 (t0) REVERT: B 317 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8035 (p90) REVERT: C 122 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8468 (pp) REVERT: C 180 ASP cc_start: 0.8803 (m-30) cc_final: 0.8437 (t0) REVERT: C 257 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8632 (m) REVERT: C 295 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8835 (t) REVERT: C 369 MET cc_start: 0.8265 (tmm) cc_final: 0.7638 (ptm) REVERT: D 540 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8289 (tm-30) REVERT: D 652 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8625 (tp-100) REVERT: D 657 GLU cc_start: 0.8522 (tp30) cc_final: 0.8139 (tt0) REVERT: E 520 LEU cc_start: 0.7113 (mm) cc_final: 0.6433 (tp) REVERT: E 653 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8245 (tm-30) REVERT: G 12 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7621 (mmtm) REVERT: G 122 LEU cc_start: 0.8926 (pp) cc_final: 0.8718 (pt) REVERT: H 19 LYS cc_start: 0.9042 (tppt) cc_final: 0.8643 (tptp) REVERT: H 50 TRP cc_start: 0.9195 (p-90) cc_final: 0.8930 (p-90) REVERT: H 82 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7572 (mm-30) REVERT: I 10 GLU cc_start: 0.8627 (mm-30) cc_final: 0.7912 (mm-30) REVERT: I 23 LYS cc_start: 0.8598 (tttt) cc_final: 0.8317 (tttm) REVERT: I 73 ASP cc_start: 0.7511 (t0) cc_final: 0.7053 (t0) REVERT: I 81 MET cc_start: 0.8454 (tmm) cc_final: 0.7277 (tmm) REVERT: J 68 LYS cc_start: 0.7700 (tttp) cc_final: 0.7272 (tttp) REVERT: L 33 ASN cc_start: 0.8895 (p0) cc_final: 0.8117 (p0) REVERT: L 106 LYS cc_start: 0.8655 (tppt) cc_final: 0.8335 (tppt) outliers start: 52 outliers final: 40 residues processed: 391 average time/residue: 0.3191 time to fit residues: 194.3931 Evaluate side-chains 389 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 344 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 64 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102706 restraints weight = 36177.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103853 restraints weight = 23856.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104756 restraints weight = 17609.792| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20720 Z= 0.154 Angle : 0.710 10.390 28321 Z= 0.335 Chirality : 0.047 0.354 3378 Planarity : 0.004 0.068 3453 Dihedral : 10.496 102.188 4410 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.41 % Allowed : 22.13 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2427 helix: 1.31 (0.29), residues: 387 sheet: -0.45 (0.20), residues: 708 loop : -2.00 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP L 37 HIS 0.004 0.001 HIS C 330 PHE 0.012 0.001 PHE B 376 TYR 0.026 0.001 TYR K 51 ARG 0.016 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 42) link_NAG-ASN : angle 2.96868 ( 126) link_ALPHA1-6 : bond 0.00871 ( 9) link_ALPHA1-6 : angle 1.50841 ( 27) link_BETA1-4 : bond 0.00494 ( 24) link_BETA1-4 : angle 1.47357 ( 72) link_ALPHA1-2 : bond 0.01241 ( 3) link_ALPHA1-2 : angle 2.02909 ( 9) link_ALPHA1-3 : bond 0.00907 ( 9) link_ALPHA1-3 : angle 1.83303 ( 27) hydrogen bonds : bond 0.03410 ( 611) hydrogen bonds : angle 4.45828 ( 1674) SS BOND : bond 0.00375 ( 38) SS BOND : angle 1.04683 ( 76) covalent geometry : bond 0.00361 (20595) covalent geometry : angle 0.67422 (27984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8034 (ttm) REVERT: B 107 ASP cc_start: 0.8213 (t70) cc_final: 0.7961 (t0) REVERT: B 317 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8204 (p90) REVERT: C 122 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8517 (pp) REVERT: C 180 ASP cc_start: 0.8862 (m-30) cc_final: 0.8438 (t0) REVERT: C 257 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8571 (m) REVERT: C 295 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8846 (t) REVERT: C 369 MET cc_start: 0.8163 (tmm) cc_final: 0.7590 (ptm) REVERT: D 540 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8310 (tm-30) REVERT: D 652 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8620 (tp-100) REVERT: D 657 GLU cc_start: 0.8532 (tp30) cc_final: 0.8121 (tt0) REVERT: E 520 LEU cc_start: 0.7082 (mm) cc_final: 0.6337 (tp) REVERT: E 653 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8256 (tm-30) REVERT: G 12 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7658 (mmtm) REVERT: H 19 LYS cc_start: 0.9023 (tppt) cc_final: 0.8619 (tptp) REVERT: H 50 TRP cc_start: 0.9238 (p-90) cc_final: 0.8233 (p-90) REVERT: H 82 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7611 (mm-30) REVERT: H 90 ASP cc_start: 0.8303 (t0) cc_final: 0.7650 (t70) REVERT: I 10 GLU cc_start: 0.8644 (mm-30) cc_final: 0.7896 (mm-30) REVERT: I 73 ASP cc_start: 0.7601 (t0) cc_final: 0.6939 (t0) REVERT: I 81 MET cc_start: 0.8482 (tmm) cc_final: 0.7673 (tmm) REVERT: J 68 LYS cc_start: 0.7712 (tttp) cc_final: 0.7232 (tttp) REVERT: L 33 ASN cc_start: 0.8886 (p0) cc_final: 0.8008 (p0) REVERT: L 106 LYS cc_start: 0.8626 (tppt) cc_final: 0.8290 (tppt) outliers start: 51 outliers final: 41 residues processed: 384 average time/residue: 0.3118 time to fit residues: 186.0773 Evaluate side-chains 393 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 347 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 623 TRP Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain L residue 41 HIS Chi-restraints excluded: chain L residue 55 LYS Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 22 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 236 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 231 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105509 restraints weight = 36267.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107052 restraints weight = 23434.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108124 restraints weight = 17942.918| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20720 Z= 0.118 Angle : 0.688 10.636 28321 Z= 0.324 Chirality : 0.046 0.351 3378 Planarity : 0.004 0.066 3453 Dihedral : 10.052 99.149 4410 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.94 % Allowed : 22.51 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2427 helix: 1.16 (0.29), residues: 405 sheet: -0.38 (0.20), residues: 708 loop : -1.96 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP L 37 HIS 0.003 0.001 HIS A 287 PHE 0.009 0.001 PHE A 317 TYR 0.024 0.001 TYR K 51 ARG 0.016 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 42) link_NAG-ASN : angle 2.85366 ( 126) link_ALPHA1-6 : bond 0.00937 ( 9) link_ALPHA1-6 : angle 1.45378 ( 27) link_BETA1-4 : bond 0.00516 ( 24) link_BETA1-4 : angle 1.38267 ( 72) link_ALPHA1-2 : bond 0.01301 ( 3) link_ALPHA1-2 : angle 1.93518 ( 9) link_ALPHA1-3 : bond 0.00974 ( 9) link_ALPHA1-3 : angle 1.73770 ( 27) hydrogen bonds : bond 0.03064 ( 611) hydrogen bonds : angle 4.36608 ( 1674) SS BOND : bond 0.00324 ( 38) SS BOND : angle 0.92512 ( 76) covalent geometry : bond 0.00268 (20595) covalent geometry : angle 0.65514 (27984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6797.35 seconds wall clock time: 121 minutes 11.16 seconds (7271.16 seconds total)