Starting phenix.real_space_refine on Thu Sep 18 21:07:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aui_43881/09_2025/9aui_43881_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aui_43881/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9aui_43881/09_2025/9aui_43881_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aui_43881/09_2025/9aui_43881_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9aui_43881/09_2025/9aui_43881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aui_43881/09_2025/9aui_43881.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.38, per 1000 atoms: 0.27 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: 2.15 Conformation dependent library (CDL) restraints added in 816.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.80 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: 4.03 Time building geometry restraints manager: 2.77 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: 0.02 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.810 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.018 0.001 ARG B 500 TYR 0.045 0.002 TYR C 395 PHE 0.033 0.003 PHE K 64 TRP 0.073 0.003 TRP D 596 HIS 0.005 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00645 (20595) covalent geometry : angle 1.05511 (27984) SS BOND : bond 0.00625 ( 38) SS BOND : angle 1.60668 ( 76) hydrogen bonds : bond 0.14207 ( 611) hydrogen bonds : angle 6.42890 ( 1674) 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) 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_NAG-ASN : bond 0.00715 ( 42) link_NAG-ASN : angle 4.21395 ( 126) *********************** 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 : 0.686 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: 0.8564 (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: 0.7705 (mp10) REVERT: L 87 ASP cc_start: 0.8611 (m-30) cc_final: 0.8275 (m-30) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1446 time to fit residues: 89.8681 Evaluate side-chains 352 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 287 HIS E 656 ASN F 618 ASN J 41 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN K 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102065 restraints weight = 35968.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102569 restraints weight = 26817.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103819 restraints weight = 22100.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104880 restraints weight = 17183.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105064 restraints weight = 15591.030| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 20720 Z= 0.310 Angle : 0.857 11.711 28321 Z= 0.410 Chirality : 0.051 0.389 3378 Planarity : 0.005 0.096 3453 Dihedral : 14.881 108.993 4410 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.32 % Allowed : 11.54 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.16), residues: 2427 helix: -0.15 (0.27), residues: 405 sheet: -0.63 (0.20), residues: 687 loop : -2.41 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 63 TYR 0.022 0.002 TYR C 361 PHE 0.016 0.002 PHE C 317 TRP 0.036 0.002 TRP D 596 HIS 0.008 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00730 (20595) covalent geometry : angle 0.81188 (27984) SS BOND : bond 0.00540 ( 38) SS BOND : angle 1.26119 ( 76) hydrogen bonds : bond 0.04740 ( 611) hydrogen bonds : angle 5.33885 ( 1674) link_ALPHA1-2 : bond 0.00304 ( 3) link_ALPHA1-2 : angle 3.39252 ( 9) link_ALPHA1-3 : bond 0.00751 ( 9) link_ALPHA1-3 : angle 2.36938 ( 27) link_ALPHA1-6 : bond 0.00701 ( 9) link_ALPHA1-6 : angle 1.67640 ( 27) link_BETA1-4 : bond 0.00409 ( 24) link_BETA1-4 : angle 2.33225 ( 72) link_NAG-ASN : bond 0.00565 ( 42) link_NAG-ASN : angle 3.46480 ( 126) *********************** 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 405 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 317 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8122 (p90) REVERT: C 355 ASN cc_start: 0.7731 (p0) cc_final: 0.7524 (p0) REVERT: C 426 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6629 (mtt) REVERT: D 657 GLU cc_start: 0.8647 (tp30) cc_final: 0.8357 (tp30) REVERT: E 520 LEU cc_start: 0.7268 (mm) cc_final: 0.6270 (tp) REVERT: E 543 ASN cc_start: 0.9082 (m110) cc_final: 0.8861 (m110) REVERT: E 615 SER cc_start: 0.9134 (p) cc_final: 0.8875 (p) REVERT: G 43 GLN cc_start: 0.8841 (pm20) cc_final: 0.8590 (pm20) REVERT: H 19 LYS cc_start: 0.9115 (tppt) cc_final: 0.8769 (tptp) REVERT: H 48 MET cc_start: 0.8119 (mmt) cc_final: 0.7713 (mmm) REVERT: H 50 TRP cc_start: 0.9007 (p-90) cc_final: 0.8365 (p-90) REVERT: H 115 ASP cc_start: 0.9039 (p0) cc_final: 0.8733 (p0) REVERT: I 10 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: I 43 GLN cc_start: 0.8948 (mp10) cc_final: 0.8698 (mp10) REVERT: I 73 ASP cc_start: 0.7210 (t0) cc_final: 0.6894 (t0) REVERT: I 81 MET cc_start: 0.8480 (tmm) cc_final: 0.7378 (tmm) REVERT: J 55 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8128 (ttmm) REVERT: J 68 LYS cc_start: 0.7866 (tttm) cc_final: 0.7441 (tttp) REVERT: K 40 GLN cc_start: 0.8032 (tp40) cc_final: 0.7529 (tp-100) REVERT: L 22 CYS cc_start: 0.3251 (m) cc_final: 0.2917 (m) outliers start: 49 outliers final: 37 residues processed: 378 average time/residue: 0.1432 time to fit residues: 84.6919 Evaluate side-chains 368 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 328 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 B residue 199 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 534 SER 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 595 ILE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 58 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 18 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 41 HIS Chi-restraints excluded: chain J residue 100 ILE 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 155 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 GLN F 630 GLN J 41 HIS J 62 ASN J 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.141344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107314 restraints weight = 35996.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108334 restraints weight = 26835.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109631 restraints weight = 20569.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110666 restraints weight = 15983.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110888 restraints weight = 14530.871| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 20720 Z= 0.146 Angle : 0.694 9.740 28321 Z= 0.329 Chirality : 0.046 0.380 3378 Planarity : 0.004 0.052 3453 Dihedral : 13.056 105.413 4410 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.32 % Allowed : 15.51 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.17), residues: 2427 helix: 0.44 (0.28), residues: 405 sheet: -0.60 (0.20), residues: 699 loop : -2.28 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 500 TYR 0.027 0.001 TYR K 51 PHE 0.026 0.001 PHE C 317 TRP 0.035 0.002 TRP L 37 HIS 0.006 0.001 HIS J 41 Details of bonding type rmsd covalent geometry : bond 0.00342 (20595) covalent geometry : angle 0.64902 (27984) SS BOND : bond 0.00417 ( 38) SS BOND : angle 1.05016 ( 76) hydrogen bonds : bond 0.03725 ( 611) hydrogen bonds : angle 4.87163 ( 1674) link_ALPHA1-2 : bond 0.01041 ( 3) link_ALPHA1-2 : angle 2.37506 ( 9) link_ALPHA1-3 : bond 0.00973 ( 9) link_ALPHA1-3 : angle 1.92810 ( 27) link_ALPHA1-6 : bond 0.00785 ( 9) link_ALPHA1-6 : angle 1.67106 ( 27) link_BETA1-4 : bond 0.00481 ( 24) link_BETA1-4 : angle 1.88474 ( 72) link_NAG-ASN : bond 0.00459 ( 42) link_NAG-ASN : angle 3.17248 ( 126) *********************** 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 402 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8044 (ttm) REVERT: A 475 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7262 (tpp) REVERT: C 122 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 369 MET cc_start: 0.8189 (tmm) cc_final: 0.7517 (ptm) REVERT: C 426 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6432 (mtt) REVERT: D 540 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8404 (tm-30) REVERT: D 652 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8649 (tp-100) REVERT: D 653 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8513 (tm-30) REVERT: D 657 GLU cc_start: 0.8608 (tp30) cc_final: 0.8314 (tp30) REVERT: E 530 MET cc_start: 0.7641 (mmm) cc_final: 0.7440 (mmm) REVERT: F 630 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: G 43 GLN cc_start: 0.8807 (pm20) cc_final: 0.8532 (pm20) REVERT: H 19 LYS cc_start: 0.9155 (tppt) cc_final: 0.8866 (tptp) REVERT: H 48 MET cc_start: 0.8083 (mmt) cc_final: 0.7511 (mmm) REVERT: H 50 TRP cc_start: 0.9023 (p-90) cc_final: 0.8210 (p-90) REVERT: H 82 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7555 (mm-30) REVERT: H 115 ASP cc_start: 0.8972 (p0) cc_final: 0.8752 (p0) REVERT: I 10 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7913 (mm-30) REVERT: I 73 ASP cc_start: 0.7285 (t0) cc_final: 0.6892 (t0) REVERT: I 81 MET cc_start: 0.8452 (tmm) cc_final: 0.7702 (tmm) REVERT: J 55 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7602 (tmtt) REVERT: J 68 LYS cc_start: 0.7820 (tttm) cc_final: 0.7392 (tttp) REVERT: K 40 GLN cc_start: 0.8136 (tp40) cc_final: 0.7736 (tp40) outliers start: 49 outliers final: 34 residues processed: 378 average time/residue: 0.1380 time to fit residues: 81.7284 Evaluate side-chains 372 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 333 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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 110 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 THR 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 595 ILE Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 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 90 ASP Chi-restraints excluded: chain I residue 62 GLN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 168 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 12 optimal weight: 0.0040 chunk 158 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS C 287 HIS E 543 ASN I 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104446 restraints weight = 36241.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105213 restraints weight = 26263.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106515 restraints weight = 21365.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107373 restraints weight = 16457.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107686 restraints weight = 15027.183| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20720 Z= 0.232 Angle : 0.746 10.122 28321 Z= 0.356 Chirality : 0.048 0.371 3378 Planarity : 0.004 0.052 3453 Dihedral : 12.671 109.826 4410 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.50 % Allowed : 16.83 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.17), residues: 2427 helix: 0.52 (0.28), residues: 405 sheet: -0.57 (0.20), residues: 690 loop : -2.27 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 87 TYR 0.023 0.001 TYR K 51 PHE 0.024 0.002 PHE C 317 TRP 0.033 0.002 TRP L 37 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00545 (20595) covalent geometry : angle 0.70335 (27984) SS BOND : bond 0.00464 ( 38) SS BOND : angle 1.11261 ( 76) hydrogen bonds : bond 0.04056 ( 611) hydrogen bonds : angle 4.85740 ( 1674) link_ALPHA1-2 : bond 0.00781 ( 3) link_ALPHA1-2 : angle 2.49169 ( 9) link_ALPHA1-3 : bond 0.00866 ( 9) link_ALPHA1-3 : angle 2.04133 ( 27) link_ALPHA1-6 : bond 0.00730 ( 9) link_ALPHA1-6 : angle 1.71488 ( 27) link_BETA1-4 : bond 0.00481 ( 24) link_BETA1-4 : angle 1.83088 ( 72) link_NAG-ASN : bond 0.00507 ( 42) link_NAG-ASN : angle 3.24533 ( 126) *********************** 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 412 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 338 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8088 (ttm) REVERT: A 475 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7452 (tpp) REVERT: B 317 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8228 (p90) REVERT: C 122 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8480 (pp) REVERT: C 154 MET cc_start: 0.8488 (mtt) cc_final: 0.8197 (mtt) REVERT: C 295 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8944 (t) REVERT: C 369 MET cc_start: 0.8337 (tmm) cc_final: 0.7621 (ptm) REVERT: C 426 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6636 (mtt) REVERT: D 530 MET cc_start: 0.8705 (mmt) cc_final: 0.7698 (mmt) REVERT: D 540 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 571 TRP cc_start: 0.7720 (m-10) cc_final: 0.7489 (m-10) REVERT: D 596 TRP cc_start: 0.7509 (p90) cc_final: 0.7169 (p90) REVERT: D 657 GLU cc_start: 0.8616 (tp30) cc_final: 0.8353 (tp30) REVERT: E 520 LEU cc_start: 0.7177 (mm) cc_final: 0.6318 (tp) REVERT: E 632 ASP cc_start: 0.8975 (t70) cc_final: 0.8405 (t0) REVERT: H 19 LYS cc_start: 0.9089 (tppt) cc_final: 0.8773 (tptp) REVERT: H 48 MET cc_start: 0.8255 (mmt) cc_final: 0.7950 (mmm) REVERT: H 50 TRP cc_start: 0.9135 (p-90) cc_final: 0.8303 (p-90) REVERT: H 63 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8061 (ptpp) REVERT: H 82 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7638 (mm-30) REVERT: H 115 ASP cc_start: 0.9040 (p0) cc_final: 0.8795 (p0) REVERT: I 10 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7815 (mm-30) REVERT: I 73 ASP cc_start: 0.7389 (t0) cc_final: 0.6939 (t0) REVERT: I 81 MET cc_start: 0.8519 (tmm) cc_final: 0.7738 (tmm) REVERT: J 55 LYS cc_start: 0.8427 (ttmt) cc_final: 0.7718 (tmtt) REVERT: J 68 LYS cc_start: 0.7845 (tttm) cc_final: 0.7380 (tttp) outliers start: 74 outliers final: 54 residues processed: 381 average time/residue: 0.1232 time to fit residues: 74.1100 Evaluate side-chains 388 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 443 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 THR 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 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 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 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 H residue 63 LYS Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain J residue 100 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 139 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.137697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104361 restraints weight = 35860.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104990 restraints weight = 26013.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106257 restraints weight = 21450.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107175 restraints weight = 16584.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107421 restraints weight = 15104.579| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20720 Z= 0.195 Angle : 0.723 9.758 28321 Z= 0.344 Chirality : 0.047 0.365 3378 Planarity : 0.004 0.048 3453 Dihedral : 12.129 101.928 4410 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.36 % Allowed : 18.39 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.17), residues: 2427 helix: 0.61 (0.28), residues: 405 sheet: -0.57 (0.20), residues: 675 loop : -2.20 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 87 TYR 0.026 0.001 TYR K 51 PHE 0.022 0.001 PHE C 317 TRP 0.026 0.002 TRP L 37 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00456 (20595) covalent geometry : angle 0.68034 (27984) SS BOND : bond 0.00454 ( 38) SS BOND : angle 1.12839 ( 76) hydrogen bonds : bond 0.03875 ( 611) hydrogen bonds : angle 4.76676 ( 1674) link_ALPHA1-2 : bond 0.01090 ( 3) link_ALPHA1-2 : angle 2.54846 ( 9) link_ALPHA1-3 : bond 0.00894 ( 9) link_ALPHA1-3 : angle 1.98734 ( 27) link_ALPHA1-6 : bond 0.00772 ( 9) link_ALPHA1-6 : angle 1.67885 ( 27) link_BETA1-4 : bond 0.00473 ( 24) link_BETA1-4 : angle 1.68063 ( 72) link_NAG-ASN : bond 0.00478 ( 42) link_NAG-ASN : angle 3.21522 ( 126) *********************** 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 420 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 349 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8020 (ttm) REVERT: B 107 ASP cc_start: 0.8234 (t70) cc_final: 0.7914 (t0) REVERT: B 317 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8171 (p90) REVERT: C 122 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8504 (pp) REVERT: C 154 MET cc_start: 0.8582 (mtt) cc_final: 0.8354 (mtt) REVERT: C 295 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8960 (t) REVERT: C 369 MET cc_start: 0.8250 (tmm) cc_final: 0.7567 (ptm) REVERT: D 530 MET cc_start: 0.8680 (mmt) cc_final: 0.7680 (mmt) REVERT: D 540 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 596 TRP cc_start: 0.7483 (p90) cc_final: 0.7033 (p90) REVERT: D 657 GLU cc_start: 0.8625 (tp30) cc_final: 0.8350 (tp30) REVERT: E 520 LEU cc_start: 0.7227 (mm) cc_final: 0.6336 (tp) REVERT: E 632 ASP cc_start: 0.8974 (t70) cc_final: 0.8396 (t0) REVERT: H 19 LYS cc_start: 0.9076 (tppt) cc_final: 0.8832 (tptp) REVERT: H 48 MET cc_start: 0.8280 (mmt) cc_final: 0.7955 (mmm) REVERT: H 50 TRP cc_start: 0.9171 (p-90) cc_final: 0.8239 (p-90) REVERT: H 63 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7960 (ptpp) REVERT: H 70 MET cc_start: 0.8865 (mtt) cc_final: 0.8625 (mtt) REVERT: H 82 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7692 (mm-30) REVERT: H 115 ASP cc_start: 0.9042 (p0) cc_final: 0.8832 (p0) REVERT: I 10 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: I 73 ASP cc_start: 0.7494 (t0) cc_final: 0.7157 (t0) REVERT: I 81 MET cc_start: 0.8548 (tmm) cc_final: 0.7740 (tmm) REVERT: J 37 TRP cc_start: 0.8173 (m100) cc_final: 0.7835 (m100) REVERT: J 68 LYS cc_start: 0.7849 (tttm) cc_final: 0.7400 (tttp) REVERT: L 33 ASN cc_start: 0.8866 (p0) cc_final: 0.8153 (p0) outliers start: 71 outliers final: 53 residues processed: 390 average time/residue: 0.1249 time to fit residues: 77.2720 Evaluate side-chains 395 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 336 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 199 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 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 164 GLU 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 417 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 450 THR 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 622 ILE Chi-restraints excluded: chain F residue 660 LEU 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 86 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 63 LYS 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 J residue 98 THR 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 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 160 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 150 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 656 ASN L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104439 restraints weight = 35975.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105818 restraints weight = 26324.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106908 restraints weight = 20425.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107629 restraints weight = 16025.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108006 restraints weight = 14757.654| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20720 Z= 0.200 Angle : 0.730 10.185 28321 Z= 0.346 Chirality : 0.047 0.362 3378 Planarity : 0.004 0.053 3453 Dihedral : 11.823 100.495 4410 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.78 % Allowed : 19.24 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2427 helix: 0.89 (0.29), residues: 387 sheet: -0.58 (0.20), residues: 660 loop : -2.11 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 87 TYR 0.025 0.001 TYR K 51 PHE 0.023 0.001 PHE C 317 TRP 0.037 0.002 TRP L 37 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00469 (20595) covalent geometry : angle 0.68894 (27984) SS BOND : bond 0.00431 ( 38) SS BOND : angle 1.16009 ( 76) hydrogen bonds : bond 0.03873 ( 611) hydrogen bonds : angle 4.72132 ( 1674) link_ALPHA1-2 : bond 0.01060 ( 3) link_ALPHA1-2 : angle 2.63678 ( 9) link_ALPHA1-3 : bond 0.00921 ( 9) link_ALPHA1-3 : angle 2.01517 ( 27) link_ALPHA1-6 : bond 0.00766 ( 9) link_ALPHA1-6 : angle 1.66781 ( 27) link_BETA1-4 : bond 0.00473 ( 24) link_BETA1-4 : angle 1.65001 ( 72) link_NAG-ASN : bond 0.00488 ( 42) link_NAG-ASN : angle 3.18011 ( 126) *********************** 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 429 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 349 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8035 (ttm) REVERT: A 475 MET cc_start: 0.8499 (tpp) cc_final: 0.8251 (tpt) REVERT: B 107 ASP cc_start: 0.8230 (t70) cc_final: 0.7935 (t0) REVERT: B 317 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8189 (p90) REVERT: C 122 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8581 (pp) REVERT: C 295 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8939 (t) REVERT: C 369 MET cc_start: 0.8241 (tmm) cc_final: 0.7985 (ttt) REVERT: D 530 MET cc_start: 0.8690 (mmt) cc_final: 0.7709 (mmt) REVERT: D 540 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8412 (tm-30) REVERT: D 571 TRP cc_start: 0.7701 (m-10) cc_final: 0.7458 (m-10) REVERT: D 596 TRP cc_start: 0.7510 (p90) cc_final: 0.6953 (p90) REVERT: D 657 GLU cc_start: 0.8627 (tp30) cc_final: 0.8354 (tp30) REVERT: E 520 LEU cc_start: 0.7139 (mm) cc_final: 0.6329 (tp) REVERT: E 632 ASP cc_start: 0.8948 (t70) cc_final: 0.8360 (t0) REVERT: G 122 LEU cc_start: 0.8877 (pp) cc_final: 0.8647 (pt) REVERT: H 19 LYS cc_start: 0.9053 (tppt) cc_final: 0.8666 (tptp) REVERT: H 48 MET cc_start: 0.8300 (mmt) cc_final: 0.7957 (mmm) REVERT: H 50 TRP cc_start: 0.9209 (p-90) cc_final: 0.8199 (p-90) REVERT: H 63 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7943 (ptpp) REVERT: H 70 MET cc_start: 0.8874 (mtt) cc_final: 0.8614 (mtt) REVERT: H 82 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7656 (mm-30) REVERT: H 115 ASP cc_start: 0.9047 (p0) cc_final: 0.8821 (p0) REVERT: I 10 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: I 73 ASP cc_start: 0.7471 (t0) cc_final: 0.7106 (t0) REVERT: I 81 MET cc_start: 0.8568 (tmm) cc_final: 0.7331 (tmm) REVERT: J 52 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7760 (mm-30) REVERT: J 55 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8028 (tmtt) REVERT: J 68 LYS cc_start: 0.7902 (tttm) cc_final: 0.7501 (tttp) REVERT: L 33 ASN cc_start: 0.8873 (p0) cc_final: 0.8227 (p0) outliers start: 80 outliers final: 58 residues processed: 400 average time/residue: 0.1319 time to fit residues: 83.6228 Evaluate side-chains 397 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 A residue 443 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 199 SER 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 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 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 417 GLN 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 534 SER Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 538 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 608 VAL 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 63 LYS Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain J residue 98 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 VAL 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 100 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 0.0060 chunk 111 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 150 optimal weight: 0.0370 chunk 200 optimal weight: 8.9990 overall best weight: 0.3432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 40 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 = 0.3805 r_free = 0.3805 target = 0.141908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108746 restraints weight = 35831.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109750 restraints weight = 26418.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111038 restraints weight = 20735.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112049 restraints weight = 16045.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112276 restraints weight = 14637.147| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20720 Z= 0.112 Angle : 0.676 9.707 28321 Z= 0.319 Chirality : 0.046 0.359 3378 Planarity : 0.004 0.053 3453 Dihedral : 10.987 96.548 4410 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.60 % Allowed : 20.76 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.17), residues: 2427 helix: 0.95 (0.29), residues: 405 sheet: -0.47 (0.20), residues: 687 loop : -2.02 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 87 TYR 0.031 0.001 TYR K 51 PHE 0.018 0.001 PHE C 317 TRP 0.044 0.001 TRP L 37 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00246 (20595) covalent geometry : angle 0.63949 (27984) SS BOND : bond 0.00334 ( 38) SS BOND : angle 0.97943 ( 76) hydrogen bonds : bond 0.03056 ( 611) hydrogen bonds : angle 4.49759 ( 1674) link_ALPHA1-2 : bond 0.01675 ( 3) link_ALPHA1-2 : angle 2.29197 ( 9) link_ALPHA1-3 : bond 0.00990 ( 9) link_ALPHA1-3 : angle 1.85580 ( 27) link_ALPHA1-6 : bond 0.00900 ( 9) link_ALPHA1-6 : angle 1.57567 ( 27) link_BETA1-4 : bond 0.00511 ( 24) link_BETA1-4 : angle 1.48551 ( 72) link_NAG-ASN : bond 0.00468 ( 42) link_NAG-ASN : angle 2.92474 ( 126) *********************** 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 422 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 367 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8311 (tpp) cc_final: 0.7940 (tpt) REVERT: B 104 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.7195 (tpt) REVERT: B 107 ASP cc_start: 0.8187 (t70) cc_final: 0.7981 (t0) REVERT: B 217 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: B 317 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7891 (p90) REVERT: C 122 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8425 (pp) REVERT: C 369 MET cc_start: 0.8239 (tmm) cc_final: 0.7647 (ptm) REVERT: C 387 THR cc_start: 0.9099 (p) cc_final: 0.8882 (t) REVERT: D 596 TRP cc_start: 0.7197 (p90) cc_final: 0.6943 (p90) REVERT: D 652 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8625 (tp-100) REVERT: D 653 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8507 (tm-30) REVERT: D 657 GLU cc_start: 0.8626 (tp30) cc_final: 0.8327 (tp30) REVERT: F 657 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8381 (tm-30) REVERT: H 19 LYS cc_start: 0.9051 (tppt) cc_final: 0.8686 (tptp) REVERT: H 48 MET cc_start: 0.8325 (mmt) cc_final: 0.7908 (mmm) REVERT: H 50 TRP cc_start: 0.9129 (p-90) cc_final: 0.8144 (p-90) REVERT: H 82 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7607 (mm-30) REVERT: H 113 ASN cc_start: 0.9255 (m-40) cc_final: 0.9051 (m110) REVERT: I 10 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7876 (mm-30) REVERT: I 73 ASP cc_start: 0.7440 (t0) cc_final: 0.7006 (t0) REVERT: I 81 MET cc_start: 0.8499 (tmm) cc_final: 0.7667 (tmm) REVERT: J 55 LYS cc_start: 0.8583 (ttmt) cc_final: 0.7925 (tmtt) REVERT: J 68 LYS cc_start: 0.7876 (tttm) cc_final: 0.7479 (tttp) REVERT: L 33 ASN cc_start: 0.8871 (p0) cc_final: 0.8411 (p0) outliers start: 55 outliers final: 39 residues processed: 402 average time/residue: 0.1329 time to fit residues: 83.9964 Evaluate side-chains 397 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 354 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 378 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 284 ILE 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 358 ILE Chi-restraints excluded: chain B residue 387 THR 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 C residue 317 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE 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 F residue 538 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 622 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 86 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 235 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105199 restraints weight = 36182.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106080 restraints weight = 27915.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107375 restraints weight = 21625.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108191 restraints weight = 16672.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108504 restraints weight = 15302.573| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20720 Z= 0.230 Angle : 0.756 9.793 28321 Z= 0.359 Chirality : 0.048 0.355 3378 Planarity : 0.004 0.060 3453 Dihedral : 11.200 106.455 4410 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.74 % Allowed : 21.28 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.17), residues: 2427 helix: 1.08 (0.29), residues: 387 sheet: -0.53 (0.20), residues: 681 loop : -2.06 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 87 TYR 0.026 0.001 TYR K 51 PHE 0.024 0.002 PHE C 317 TRP 0.046 0.002 TRP G 36 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00541 (20595) covalent geometry : angle 0.71808 (27984) SS BOND : bond 0.00470 ( 38) SS BOND : angle 1.19239 ( 76) hydrogen bonds : bond 0.03902 ( 611) hydrogen bonds : angle 4.64296 ( 1674) link_ALPHA1-2 : bond 0.01111 ( 3) link_ALPHA1-2 : angle 2.48003 ( 9) link_ALPHA1-3 : bond 0.00839 ( 9) link_ALPHA1-3 : angle 1.98539 ( 27) link_ALPHA1-6 : bond 0.00768 ( 9) link_ALPHA1-6 : angle 1.60560 ( 27) link_BETA1-4 : bond 0.00508 ( 24) link_BETA1-4 : angle 1.62343 ( 72) link_NAG-ASN : bond 0.00519 ( 42) link_NAG-ASN : angle 3.11833 ( 126) *********************** 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 405 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 347 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 THR cc_start: 0.9021 (t) cc_final: 0.8808 (p) REVERT: A 475 MET cc_start: 0.8285 (tpp) cc_final: 0.8075 (tpt) REVERT: B 104 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.7180 (tpt) REVERT: B 107 ASP cc_start: 0.8247 (t70) cc_final: 0.8009 (t0) REVERT: B 217 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.7041 (m-10) REVERT: C 122 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8603 (pp) REVERT: C 369 MET cc_start: 0.8183 (tmm) cc_final: 0.7933 (ttt) REVERT: D 530 MET cc_start: 0.8635 (mmt) cc_final: 0.7697 (mmt) REVERT: D 540 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8433 (tm-30) REVERT: D 596 TRP cc_start: 0.7418 (p90) cc_final: 0.7164 (p90) REVERT: D 652 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8706 (tp-100) REVERT: D 657 GLU cc_start: 0.8624 (tp30) cc_final: 0.8358 (tp30) REVERT: E 520 LEU cc_start: 0.7073 (mm) cc_final: 0.6244 (tp) REVERT: H 19 LYS cc_start: 0.9060 (tppt) cc_final: 0.8684 (tptp) REVERT: H 48 MET cc_start: 0.8320 (mmt) cc_final: 0.7993 (mmm) REVERT: H 50 TRP cc_start: 0.9244 (p-90) cc_final: 0.8229 (p-90) REVERT: H 82 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7601 (mm-30) REVERT: I 10 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7814 (mm-30) REVERT: I 73 ASP cc_start: 0.7451 (t0) cc_final: 0.7062 (t0) REVERT: I 81 MET cc_start: 0.8556 (tmm) cc_final: 0.7277 (tmm) REVERT: J 55 LYS cc_start: 0.8583 (ttmt) cc_final: 0.7813 (ttpt) REVERT: J 68 LYS cc_start: 0.7913 (tttm) cc_final: 0.7493 (tttp) REVERT: L 33 ASN cc_start: 0.8847 (p0) cc_final: 0.8483 (p0) REVERT: L 87 ASP cc_start: 0.8273 (m-30) cc_final: 0.8063 (m-30) REVERT: L 106 LYS cc_start: 0.8725 (tppt) cc_final: 0.8500 (tppt) outliers start: 58 outliers final: 46 residues processed: 384 average time/residue: 0.1441 time to fit residues: 86.8977 Evaluate side-chains 386 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 337 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 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 378 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 323 ILE 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 123 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE 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 F residue 538 THR Chi-restraints excluded: chain F residue 635 ILE 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 86 LEU Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 10 VAL 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 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 242 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.141662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.107463 restraints weight = 35895.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108259 restraints weight = 27283.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109657 restraints weight = 20774.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111052 restraints weight = 16074.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111195 restraints weight = 14437.038| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2231 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= 0.132 Angle : 0.697 9.702 28321 Z= 0.329 Chirality : 0.047 0.358 3378 Planarity : 0.004 0.063 3453 Dihedral : 10.627 100.987 4410 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.36 % Allowed : 21.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.17), residues: 2427 helix: 1.25 (0.29), residues: 387 sheet: -0.48 (0.20), residues: 708 loop : -2.04 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 87 TYR 0.028 0.001 TYR K 51 PHE 0.019 0.001 PHE C 317 TRP 0.051 0.002 TRP G 36 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00303 (20595) covalent geometry : angle 0.66071 (27984) SS BOND : bond 0.00351 ( 38) SS BOND : angle 0.97020 ( 76) hydrogen bonds : bond 0.03311 ( 611) hydrogen bonds : angle 4.52720 ( 1674) link_ALPHA1-2 : bond 0.01384 ( 3) link_ALPHA1-2 : angle 2.11393 ( 9) link_ALPHA1-3 : bond 0.00934 ( 9) link_ALPHA1-3 : angle 1.83241 ( 27) link_ALPHA1-6 : bond 0.00903 ( 9) link_ALPHA1-6 : angle 1.47267 ( 27) link_BETA1-4 : bond 0.00482 ( 24) link_BETA1-4 : angle 1.47931 ( 72) link_NAG-ASN : bond 0.00452 ( 42) link_NAG-ASN : angle 2.99791 ( 126) *********************** 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 409 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 359 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.7155 (tpt) REVERT: B 107 ASP cc_start: 0.8200 (t70) cc_final: 0.7992 (t0) REVERT: B 217 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7283 (m-10) REVERT: B 317 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8214 (p90) REVERT: C 122 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8552 (pp) REVERT: C 295 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8834 (t) REVERT: C 369 MET cc_start: 0.8167 (tmm) cc_final: 0.7564 (ptm) REVERT: C 400 TYR cc_start: 0.8658 (t80) cc_final: 0.8398 (t80) REVERT: D 540 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8364 (tm-30) REVERT: D 652 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8654 (tp-100) REVERT: D 653 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 657 GLU cc_start: 0.8621 (tp30) cc_final: 0.8334 (tp30) REVERT: E 520 LEU cc_start: 0.7198 (mm) cc_final: 0.6408 (tp) REVERT: G 6 GLN cc_start: 0.7788 (mt0) cc_final: 0.7483 (pt0) REVERT: H 19 LYS cc_start: 0.9056 (tppt) cc_final: 0.8659 (tptp) REVERT: H 48 MET cc_start: 0.8424 (mmt) cc_final: 0.8032 (mmm) REVERT: H 50 TRP cc_start: 0.9202 (p-90) cc_final: 0.8228 (p-90) REVERT: H 82 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7543 (mm-30) REVERT: H 90 ASP cc_start: 0.8243 (t0) cc_final: 0.7727 (t70) REVERT: I 10 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7792 (mm-30) REVERT: I 73 ASP cc_start: 0.7481 (t0) cc_final: 0.7070 (t0) REVERT: I 81 MET cc_start: 0.8515 (tmm) cc_final: 0.7291 (tmm) REVERT: J 55 LYS cc_start: 0.8523 (ttmt) cc_final: 0.7779 (tmtt) REVERT: J 68 LYS cc_start: 0.7919 (tttm) cc_final: 0.7508 (tttp) REVERT: J 81 GLN cc_start: 0.7808 (pm20) cc_final: 0.7553 (mp10) REVERT: L 33 ASN cc_start: 0.8869 (p0) cc_final: 0.8015 (p0) REVERT: L 52 GLU cc_start: 0.7683 (tp30) cc_final: 0.7106 (tp30) REVERT: L 106 LYS cc_start: 0.8773 (tppt) cc_final: 0.8545 (tppt) outliers start: 50 outliers final: 42 residues processed: 391 average time/residue: 0.1438 time to fit residues: 88.2915 Evaluate side-chains 398 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 351 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 378 CYS Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 284 ILE 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 358 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 THR 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 317 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE 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 F residue 538 THR Chi-restraints excluded: chain F residue 635 ILE 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 86 LEU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain J residue 107 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 134 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102455 restraints weight = 36331.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104145 restraints weight = 24290.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104965 restraints weight = 18186.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105638 restraints weight = 15953.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105828 restraints weight = 14762.575| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20720 Z= 0.161 Angle : 0.719 10.705 28321 Z= 0.339 Chirality : 0.047 0.350 3378 Planarity : 0.004 0.067 3453 Dihedral : 10.490 104.136 4410 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.51 % Allowed : 22.13 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.17), residues: 2427 helix: 1.30 (0.29), residues: 387 sheet: -0.47 (0.20), residues: 708 loop : -2.05 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 87 TYR 0.026 0.001 TYR K 51 PHE 0.022 0.001 PHE C 317 TRP 0.052 0.002 TRP D 571 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00377 (20595) covalent geometry : angle 0.68452 (27984) SS BOND : bond 0.00365 ( 38) SS BOND : angle 0.99994 ( 76) hydrogen bonds : bond 0.03450 ( 611) hydrogen bonds : angle 4.50495 ( 1674) link_ALPHA1-2 : bond 0.01178 ( 3) link_ALPHA1-2 : angle 2.12582 ( 9) link_ALPHA1-3 : bond 0.00887 ( 9) link_ALPHA1-3 : angle 1.82029 ( 27) link_ALPHA1-6 : bond 0.00872 ( 9) link_ALPHA1-6 : angle 1.49697 ( 27) link_BETA1-4 : bond 0.00514 ( 24) link_BETA1-4 : angle 1.46727 ( 72) link_NAG-ASN : bond 0.00455 ( 42) link_NAG-ASN : angle 2.98524 ( 126) ********************** 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: 53 poor density : 350 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6257 (tpp) REVERT: B 104 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.7193 (tpt) REVERT: B 107 ASP cc_start: 0.8205 (t70) cc_final: 0.7999 (t0) REVERT: B 217 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.7204 (m-10) REVERT: B 317 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8200 (p90) REVERT: C 122 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8576 (pp) REVERT: C 295 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8856 (t) REVERT: D 540 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 652 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8648 (tp-100) REVERT: D 657 GLU cc_start: 0.8674 (tp30) cc_final: 0.8339 (tp30) REVERT: E 520 LEU cc_start: 0.7070 (mm) cc_final: 0.6290 (tp) REVERT: G 6 GLN cc_start: 0.7955 (mt0) cc_final: 0.7572 (pt0) REVERT: G 10 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8104 (mm-30) REVERT: H 19 LYS cc_start: 0.8995 (tppt) cc_final: 0.8631 (tptp) REVERT: H 48 MET cc_start: 0.8404 (mmt) cc_final: 0.8013 (mmm) REVERT: H 50 TRP cc_start: 0.9275 (p-90) cc_final: 0.8242 (p-90) REVERT: H 90 ASP cc_start: 0.8342 (t0) cc_final: 0.7928 (t70) REVERT: I 10 GLU cc_start: 0.8657 (mm-30) cc_final: 0.7894 (mm-30) REVERT: I 73 ASP cc_start: 0.7498 (t0) cc_final: 0.7045 (t0) REVERT: I 81 MET cc_start: 0.8515 (tmm) cc_final: 0.7635 (tmm) REVERT: J 68 LYS cc_start: 0.7911 (tttm) cc_final: 0.7510 (tttp) REVERT: L 33 ASN cc_start: 0.8849 (p0) cc_final: 0.8289 (p0) REVERT: L 106 LYS cc_start: 0.8825 (tppt) cc_final: 0.8588 (tppt) outliers start: 53 outliers final: 47 residues processed: 381 average time/residue: 0.1493 time to fit residues: 89.4371 Evaluate side-chains 401 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 378 CYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 217 TYR 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 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 123 THR 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 317 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE 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 538 THR 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 28 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain J residue 107 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 185 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 ASN J 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.138594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102047 restraints weight = 36201.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103938 restraints weight = 23577.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104639 restraints weight = 16977.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105356 restraints weight = 15952.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105565 restraints weight = 14817.674| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20720 Z= 0.166 Angle : 0.723 10.818 28321 Z= 0.342 Chirality : 0.047 0.353 3378 Planarity : 0.004 0.067 3453 Dihedral : 10.356 103.626 4410 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.88 % Allowed : 22.03 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.17), residues: 2427 helix: 1.29 (0.29), residues: 387 sheet: -0.46 (0.20), residues: 723 loop : -2.09 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 87 TYR 0.026 0.001 TYR K 51 PHE 0.021 0.001 PHE C 317 TRP 0.055 0.002 TRP L 37 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00390 (20595) covalent geometry : angle 0.68775 (27984) SS BOND : bond 0.00411 ( 38) SS BOND : angle 1.06546 ( 76) hydrogen bonds : bond 0.03484 ( 611) hydrogen bonds : angle 4.50617 ( 1674) link_ALPHA1-2 : bond 0.01177 ( 3) link_ALPHA1-2 : angle 2.17570 ( 9) link_ALPHA1-3 : bond 0.00889 ( 9) link_ALPHA1-3 : angle 1.84479 ( 27) link_ALPHA1-6 : bond 0.00880 ( 9) link_ALPHA1-6 : angle 1.47555 ( 27) link_BETA1-4 : bond 0.00498 ( 24) link_BETA1-4 : angle 1.45974 ( 72) link_NAG-ASN : bond 0.00450 ( 42) link_NAG-ASN : angle 3.02378 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3173.43 seconds wall clock time: 56 minutes 3.51 seconds (3363.51 seconds total)