Starting phenix.real_space_refine on Thu Mar 5 03:20:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qfa_4542/03_2026/6qfa_4542.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qfa_4542/03_2026/6qfa_4542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qfa_4542/03_2026/6qfa_4542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qfa_4542/03_2026/6qfa_4542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qfa_4542/03_2026/6qfa_4542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qfa_4542/03_2026/6qfa_4542.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 100 5.16 5 C 12130 2.51 5 N 3060 2.21 5 O 3465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18755 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "D" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "E" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "A" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "F" 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: "G" 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: "H" 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: "I" 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.20 Number of scatterers: 18755 At special positions: 0 Unit cell: (143.38, 138.03, 126.26, 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 100 16.00 O 3465 8.00 N 3060 7.00 C 12130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 80 " " NAG B 501 " - " ASN B 80 " " NAG C 501 " - " ASN C 80 " " NAG D 501 " - " ASN D 80 " " NAG E 501 " - " ASN E 80 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN C 149 " " NAG H 1 " - " ASN D 149 " " NAG I 1 " - " ASN E 149 " " NAG J 1 " - " ASN A 149 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 703.0 milliseconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 30 sheets defined 31.7% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 removed outlier: 3.620A pdb=" N ALA B 73 " --> pdb=" O LYS B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.581A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.687A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.841A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 447 removed outlier: 4.108A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.541A pdb=" N VAL B 447 " --> pdb=" O TRP B 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 497 No H-bonds generated for 'chain 'K' and resid 495 through 497' Processing helix chain 'O' and resid 495 through 497 No H-bonds generated for 'chain 'O' and resid 495 through 497' Processing helix chain 'N' and resid 495 through 497 No H-bonds generated for 'chain 'N' and resid 495 through 497' Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing helix chain 'L' and resid 495 through 497 No H-bonds generated for 'chain 'L' and resid 495 through 497' Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.620A pdb=" N ALA C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.790A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 246 through 271 removed outlier: 3.853A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 447 removed outlier: 4.108A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix removed outlier: 3.541A pdb=" N VAL C 447 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 21 Processing helix chain 'D' and resid 70 through 73 removed outlier: 3.620A pdb=" N ALA D 73 " --> pdb=" O LYS D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.687A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 246 through 271 removed outlier: 3.582A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 447 removed outlier: 4.108A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix removed outlier: 3.541A pdb=" N VAL D 447 " --> pdb=" O TRP D 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.621A pdb=" N ALA E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.687A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 246 through 271 removed outlier: 3.576A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR E 271 " --> pdb=" O HIS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 447 removed outlier: 4.109A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.542A pdb=" N VAL E 447 " --> pdb=" O TRP E 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.621A pdb=" N ALA A 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.688A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 246 through 271 removed outlier: 3.587A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 447 removed outlier: 4.109A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.541A pdb=" N VAL A 447 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.873A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AA5, first strand: chain 'K' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR K 506 " --> pdb=" O TYR K 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'O' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 480 " --> pdb=" O GLN O 426 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR O 501 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 480 " --> pdb=" O GLN O 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR O 506 " --> pdb=" O TYR O 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 2 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 480 " --> pdb=" O GLN N 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 480 " --> pdb=" O GLN N 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR N 506 " --> pdb=" O TYR N 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AB5, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR M 506 " --> pdb=" O TYR M 481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR L 506 " --> pdb=" O TYR L 481 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.259A pdb=" N ASP C 101 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA C 135 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.890A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.868A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.852A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2983 1.32 - 1.45: 5751 1.45 - 1.57: 10336 1.57 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 19240 Sorted by residual: bond pdb=" C PRO C 34 " pdb=" O PRO C 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.40e+01 bond pdb=" C PRO A 34 " pdb=" O PRO A 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.40e+01 bond pdb=" C PRO B 34 " pdb=" O PRO B 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.38e+01 bond pdb=" C PRO E 34 " pdb=" O PRO E 34 " ideal model delta sigma weight residual 1.243 1.202 0.041 8.50e-03 1.38e+04 2.33e+01 bond pdb=" C PRO D 34 " pdb=" O PRO D 34 " ideal model delta sigma weight residual 1.243 1.202 0.041 8.50e-03 1.38e+04 2.31e+01 ... (remaining 19235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 23842 1.31 - 2.63: 1878 2.63 - 3.94: 315 3.94 - 5.25: 89 5.25 - 6.57: 31 Bond angle restraints: 26155 Sorted by residual: angle pdb=" C ARG C 269 " pdb=" N GLU C 270 " pdb=" CA GLU C 270 " ideal model delta sigma weight residual 120.28 125.64 -5.36 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C ARG B 269 " pdb=" N GLU B 270 " pdb=" CA GLU B 270 " ideal model delta sigma weight residual 120.28 125.63 -5.35 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C LEU D 223 " pdb=" N GLN D 224 " pdb=" CA GLN D 224 " ideal model delta sigma weight residual 120.29 125.01 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" C LEU E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta sigma weight residual 120.29 124.99 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" N GLN B 224 " pdb=" CA GLN B 224 " pdb=" C GLN B 224 " ideal model delta sigma weight residual 111.36 114.96 -3.60 1.09e+00 8.42e-01 1.09e+01 ... (remaining 26150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 11100 20.58 - 41.16: 379 41.16 - 61.74: 51 61.74 - 82.32: 35 82.32 - 102.89: 25 Dihedral angle restraints: 11590 sinusoidal: 4945 harmonic: 6645 Sorted by residual: dihedral pdb=" CA SER E 46 " pdb=" C SER E 46 " pdb=" N ILE E 47 " pdb=" CA ILE E 47 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 11587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2317 0.059 - 0.119: 467 0.119 - 0.178: 153 0.178 - 0.237: 21 0.237 - 0.296: 7 Chirality restraints: 2965 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.18e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.14e+02 ... (remaining 2962 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 227 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 228 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 227 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO C 228 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 227 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 228 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.031 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 136 2.56 - 3.14: 13284 3.14 - 3.73: 29256 3.73 - 4.31: 45115 4.31 - 4.90: 71694 Nonbonded interactions: 159485 Sorted by model distance: nonbonded pdb=" OD1 ASP E 101 " pdb=" OG SER E 104 " model vdw 1.973 3.040 nonbonded pdb=" OD1 ASP C 101 " pdb=" OG SER C 104 " model vdw 1.976 3.040 nonbonded pdb=" NH1 ARG E 269 " pdb=" OD1 ASP E 282 " model vdw 2.140 3.120 nonbonded pdb=" NH1 ARG D 269 " pdb=" OD1 ASP D 282 " model vdw 2.145 3.120 nonbonded pdb=" NH1 ARG A 269 " pdb=" OD1 ASP A 282 " model vdw 2.150 3.120 ... (remaining 159480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'A' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'N' selection = chain 'M' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:9.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 0.061 19280 Z= 0.375 Angle : 0.822 7.421 26265 Z= 0.500 Chirality : 0.058 0.296 2965 Planarity : 0.005 0.056 3235 Dihedral : 12.652 102.894 7330 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.16), residues: 2240 helix: -3.79 (0.11), residues: 615 sheet: 0.39 (0.19), residues: 670 loop : -0.92 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.020 0.002 TYR D 299 PHE 0.011 0.002 PHE D 105 TRP 0.011 0.001 TRP C 426 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00531 (19240) covalent geometry : angle 0.79981 (26155) SS BOND : bond 0.00039 ( 10) SS BOND : angle 0.65645 ( 20) hydrogen bonds : bond 0.27035 ( 885) hydrogen bonds : angle 8.92379 ( 2970) link_ALPHA1-3 : bond 0.05915 ( 5) link_ALPHA1-3 : angle 1.98031 ( 15) link_ALPHA1-6 : bond 0.05998 ( 5) link_ALPHA1-6 : angle 1.92579 ( 15) link_BETA1-4 : bond 0.05984 ( 10) link_BETA1-4 : angle 3.28600 ( 30) link_NAG-ASN : bond 0.01554 ( 10) link_NAG-ASN : angle 4.37911 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.505 Fit side-chains REVERT: B 18 LYS cc_start: 0.7636 (tttt) cc_final: 0.7200 (tmmt) REVERT: B 137 MET cc_start: 0.8335 (mmp) cc_final: 0.8078 (mmp) REVERT: B 179 GLU cc_start: 0.8062 (pm20) cc_final: 0.7826 (pm20) REVERT: B 261 MET cc_start: 0.8936 (mmt) cc_final: 0.8675 (tpp) REVERT: K 425 ARG cc_start: 0.7749 (ptt180) cc_final: 0.7547 (ptt180) REVERT: N 447 TYR cc_start: 0.8366 (m-80) cc_final: 0.7743 (m-80) REVERT: C 18 LYS cc_start: 0.7631 (tttt) cc_final: 0.7125 (tmmt) REVERT: C 52 GLU cc_start: 0.8573 (mp0) cc_final: 0.8340 (mp0) REVERT: C 90 GLN cc_start: 0.8795 (mt0) cc_final: 0.8582 (mp10) REVERT: C 261 MET cc_start: 0.9027 (mmt) cc_final: 0.8640 (mmm) REVERT: C 298 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8626 (tm-30) REVERT: C 440 LEU cc_start: 0.8282 (tp) cc_final: 0.8033 (tt) REVERT: D 18 LYS cc_start: 0.7585 (tttt) cc_final: 0.7025 (tmmt) REVERT: D 48 ASP cc_start: 0.7187 (m-30) cc_final: 0.6931 (m-30) REVERT: D 52 GLU cc_start: 0.8570 (mp0) cc_final: 0.8326 (mp0) REVERT: D 115 MET cc_start: 0.8581 (ttm) cc_final: 0.8375 (tmm) REVERT: D 243 ASN cc_start: 0.7858 (t0) cc_final: 0.7219 (t0) REVERT: D 244 TYR cc_start: 0.7784 (p90) cc_final: 0.7551 (p90) REVERT: D 304 TYR cc_start: 0.8847 (t80) cc_final: 0.8469 (t80) REVERT: E 14 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6858 (mt-10) REVERT: E 56 ASP cc_start: 0.8763 (p0) cc_final: 0.8499 (p0) REVERT: E 90 GLN cc_start: 0.8782 (mt0) cc_final: 0.8466 (mp10) REVERT: E 115 MET cc_start: 0.8481 (ttm) cc_final: 0.7973 (tmm) REVERT: E 137 MET cc_start: 0.8428 (mmp) cc_final: 0.8017 (mmp) REVERT: E 215 LYS cc_start: 0.8619 (tttt) cc_final: 0.8390 (tptp) REVERT: E 243 ASN cc_start: 0.7594 (t0) cc_final: 0.7074 (t0) REVERT: E 244 TYR cc_start: 0.7806 (p90) cc_final: 0.7578 (p90) REVERT: E 245 ASP cc_start: 0.7627 (m-30) cc_final: 0.7320 (p0) REVERT: E 261 MET cc_start: 0.9010 (mmt) cc_final: 0.8764 (tpp) REVERT: E 283 MET cc_start: 0.8345 (mmm) cc_final: 0.8111 (mmm) REVERT: A 90 GLN cc_start: 0.8706 (mt0) cc_final: 0.8377 (mp10) REVERT: A 261 MET cc_start: 0.9017 (mmt) cc_final: 0.8742 (tpp) REVERT: A 283 MET cc_start: 0.8371 (mmm) cc_final: 0.8131 (mmm) REVERT: A 440 LEU cc_start: 0.8463 (tp) cc_final: 0.8190 (tt) outliers start: 0 outliers final: 2 residues processed: 353 average time/residue: 0.5969 time to fit residues: 235.5773 Evaluate side-chains 321 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 90 GLN B 185 GLN C 243 ASN D 185 GLN D 265 ASN E 185 GLN A 41 ASN A 185 GLN A 243 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.145597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.102212 restraints weight = 17713.606| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.55 r_work: 0.2806 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19280 Z= 0.203 Angle : 0.642 5.466 26265 Z= 0.341 Chirality : 0.047 0.154 2965 Planarity : 0.005 0.043 3235 Dihedral : 9.832 77.142 3174 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.77 % Allowed : 7.54 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2240 helix: -0.38 (0.18), residues: 615 sheet: 0.78 (0.20), residues: 645 loop : -0.38 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 207 TYR 0.029 0.002 TYR D 299 PHE 0.016 0.002 PHE C 221 TRP 0.008 0.002 TRP B 426 HIS 0.004 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00449 (19240) covalent geometry : angle 0.62304 (26155) SS BOND : bond 0.00326 ( 10) SS BOND : angle 1.48558 ( 20) hydrogen bonds : bond 0.05831 ( 885) hydrogen bonds : angle 5.04281 ( 2970) link_ALPHA1-3 : bond 0.00261 ( 5) link_ALPHA1-3 : angle 2.05453 ( 15) link_ALPHA1-6 : bond 0.00094 ( 5) link_ALPHA1-6 : angle 1.85231 ( 15) link_BETA1-4 : bond 0.00781 ( 10) link_BETA1-4 : angle 2.83036 ( 30) link_NAG-ASN : bond 0.00259 ( 10) link_NAG-ASN : angle 2.94479 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 354 time to evaluate : 0.696 Fit side-chains REVERT: B 18 LYS cc_start: 0.7963 (tttt) cc_final: 0.7106 (tmmt) REVERT: B 70 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8637 (mmtt) REVERT: B 137 MET cc_start: 0.8996 (mmp) cc_final: 0.8674 (mmp) REVERT: B 261 MET cc_start: 0.9136 (mmt) cc_final: 0.8895 (tpp) REVERT: K 415 THR cc_start: 0.8495 (m) cc_final: 0.8088 (t) REVERT: K 425 ARG cc_start: 0.8082 (ptt180) cc_final: 0.7867 (ptt180) REVERT: K 447 TYR cc_start: 0.8547 (m-80) cc_final: 0.8282 (m-80) REVERT: N 433 GLU cc_start: 0.7845 (tt0) cc_final: 0.6797 (tm-30) REVERT: N 447 TYR cc_start: 0.8548 (m-80) cc_final: 0.8165 (m-80) REVERT: L 425 ARG cc_start: 0.8196 (ptt180) cc_final: 0.7892 (ptt180) REVERT: C 18 LYS cc_start: 0.7757 (tttt) cc_final: 0.7084 (tmmt) REVERT: C 52 GLU cc_start: 0.8856 (mp0) cc_final: 0.8586 (mp0) REVERT: C 90 GLN cc_start: 0.9009 (mt0) cc_final: 0.8709 (mp10) REVERT: C 115 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8696 (tmm) REVERT: C 261 MET cc_start: 0.9223 (mmt) cc_final: 0.8738 (mmm) REVERT: C 429 ILE cc_start: 0.8577 (pt) cc_final: 0.8349 (pp) REVERT: C 440 LEU cc_start: 0.8546 (tp) cc_final: 0.8224 (tt) REVERT: D 18 LYS cc_start: 0.7714 (tttt) cc_final: 0.7019 (tmmt) REVERT: D 52 GLU cc_start: 0.8798 (mp0) cc_final: 0.8588 (mp0) REVERT: D 165 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8359 (mm-30) REVERT: D 243 ASN cc_start: 0.8230 (t0) cc_final: 0.7733 (t0) REVERT: D 244 TYR cc_start: 0.8445 (p90) cc_final: 0.8095 (p90) REVERT: D 267 HIS cc_start: 0.7909 (t70) cc_final: 0.7439 (m90) REVERT: D 440 LEU cc_start: 0.8735 (tp) cc_final: 0.8406 (tt) REVERT: E 14 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6973 (mt-10) REVERT: E 18 LYS cc_start: 0.7799 (tttt) cc_final: 0.6892 (tmmt) REVERT: E 56 ASP cc_start: 0.9177 (p0) cc_final: 0.8969 (p0) REVERT: E 90 GLN cc_start: 0.9004 (mt0) cc_final: 0.8655 (mp10) REVERT: E 115 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8711 (tmm) REVERT: E 137 MET cc_start: 0.8951 (mmp) cc_final: 0.8649 (mmp) REVERT: E 165 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8384 (mm-30) REVERT: E 215 LYS cc_start: 0.9127 (tttt) cc_final: 0.8587 (tptp) REVERT: E 243 ASN cc_start: 0.8230 (t0) cc_final: 0.7778 (t0) REVERT: E 244 TYR cc_start: 0.8401 (p90) cc_final: 0.8126 (p90) REVERT: E 245 ASP cc_start: 0.8360 (m-30) cc_final: 0.7651 (p0) REVERT: E 267 HIS cc_start: 0.7978 (t70) cc_final: 0.7540 (m170) REVERT: A 68 ARG cc_start: 0.8947 (tpp80) cc_final: 0.8707 (tpp80) REVERT: A 90 GLN cc_start: 0.8990 (mt0) cc_final: 0.8668 (mp10) REVERT: A 165 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8510 (mm-30) REVERT: A 429 ILE cc_start: 0.8607 (pt) cc_final: 0.8343 (pp) REVERT: A 440 LEU cc_start: 0.8650 (tp) cc_final: 0.8358 (tt) outliers start: 35 outliers final: 19 residues processed: 359 average time/residue: 0.6011 time to fit residues: 240.8095 Evaluate side-chains 350 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain O residue 445 THR Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 204 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 185 GLN C 243 ASN C 265 ASN D 185 GLN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.144079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.100760 restraints weight = 17823.009| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.46 r_work: 0.2788 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19280 Z= 0.226 Angle : 0.639 6.028 26265 Z= 0.338 Chirality : 0.048 0.157 2965 Planarity : 0.005 0.048 3235 Dihedral : 9.455 73.145 3172 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.23 % Allowed : 8.41 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2240 helix: 1.04 (0.20), residues: 615 sheet: 0.74 (0.20), residues: 655 loop : -0.04 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 28 TYR 0.031 0.002 TYR D 299 PHE 0.018 0.002 PHE A 98 TRP 0.009 0.002 TRP B 426 HIS 0.006 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00503 (19240) covalent geometry : angle 0.61990 (26155) SS BOND : bond 0.00329 ( 10) SS BOND : angle 1.17806 ( 20) hydrogen bonds : bond 0.05398 ( 885) hydrogen bonds : angle 4.82302 ( 2970) link_ALPHA1-3 : bond 0.00251 ( 5) link_ALPHA1-3 : angle 1.80818 ( 15) link_ALPHA1-6 : bond 0.00187 ( 5) link_ALPHA1-6 : angle 1.63310 ( 15) link_BETA1-4 : bond 0.00789 ( 10) link_BETA1-4 : angle 2.99931 ( 30) link_NAG-ASN : bond 0.00301 ( 10) link_NAG-ASN : angle 3.11822 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.697 Fit side-chains REVERT: B 18 LYS cc_start: 0.7855 (tttt) cc_final: 0.7014 (tmmt) REVERT: B 40 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8833 (mtm) REVERT: B 137 MET cc_start: 0.8992 (mmp) cc_final: 0.8770 (mmp) REVERT: B 165 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: B 261 MET cc_start: 0.9179 (mmt) cc_final: 0.8933 (tpp) REVERT: B 267 HIS cc_start: 0.7922 (t70) cc_final: 0.7591 (m170) REVERT: K 415 THR cc_start: 0.8367 (m) cc_final: 0.8001 (t) REVERT: K 447 TYR cc_start: 0.8564 (m-80) cc_final: 0.8287 (m-80) REVERT: N 415 THR cc_start: 0.8456 (m) cc_final: 0.8027 (t) REVERT: N 433 GLU cc_start: 0.7904 (tt0) cc_final: 0.6836 (tm-30) REVERT: L 425 ARG cc_start: 0.8217 (ptt180) cc_final: 0.7862 (ptt180) REVERT: C 18 LYS cc_start: 0.7807 (tttt) cc_final: 0.7108 (tmmt) REVERT: C 52 GLU cc_start: 0.8842 (mp0) cc_final: 0.8634 (mp0) REVERT: C 90 GLN cc_start: 0.8981 (mt0) cc_final: 0.8703 (mp10) REVERT: C 115 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8811 (tmm) REVERT: C 182 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8512 (mt-10) REVERT: C 261 MET cc_start: 0.9229 (mmt) cc_final: 0.8899 (mmp) REVERT: C 429 ILE cc_start: 0.8541 (pt) cc_final: 0.8330 (pp) REVERT: C 440 LEU cc_start: 0.8593 (tp) cc_final: 0.8324 (tt) REVERT: D 18 LYS cc_start: 0.7703 (tttt) cc_final: 0.7026 (tmmt) REVERT: D 165 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8354 (mm-30) REVERT: D 243 ASN cc_start: 0.8275 (t0) cc_final: 0.7904 (t0) REVERT: D 244 TYR cc_start: 0.8440 (p90) cc_final: 0.8143 (p90) REVERT: D 267 HIS cc_start: 0.7911 (t70) cc_final: 0.7619 (t70) REVERT: D 440 LEU cc_start: 0.8748 (tp) cc_final: 0.8482 (tt) REVERT: E 14 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7055 (mt-10) REVERT: E 18 LYS cc_start: 0.7850 (tttt) cc_final: 0.6938 (tmmt) REVERT: E 56 ASP cc_start: 0.9157 (p0) cc_final: 0.8945 (p0) REVERT: E 115 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8709 (tmm) REVERT: E 137 MET cc_start: 0.8968 (mmp) cc_final: 0.8693 (mmp) REVERT: E 165 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: E 215 LYS cc_start: 0.9134 (tttt) cc_final: 0.8576 (tptp) REVERT: E 243 ASN cc_start: 0.8341 (t0) cc_final: 0.7937 (t0) REVERT: E 244 TYR cc_start: 0.8377 (p90) cc_final: 0.8164 (p90) REVERT: E 245 ASP cc_start: 0.8431 (m-30) cc_final: 0.7715 (p0) REVERT: E 267 HIS cc_start: 0.7994 (t70) cc_final: 0.7590 (t70) REVERT: A 90 GLN cc_start: 0.8985 (mt0) cc_final: 0.8607 (mp10) REVERT: A 165 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8488 (mm-30) REVERT: A 429 ILE cc_start: 0.8664 (pt) cc_final: 0.8392 (pp) REVERT: A 440 LEU cc_start: 0.8617 (tp) cc_final: 0.8362 (tt) outliers start: 44 outliers final: 23 residues processed: 357 average time/residue: 0.6034 time to fit residues: 240.5443 Evaluate side-chains 361 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 331 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 93 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 92 optimal weight: 0.0870 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 113 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.147033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.111018 restraints weight = 17799.049| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.12 r_work: 0.2845 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19280 Z= 0.132 Angle : 0.545 5.652 26265 Z= 0.289 Chirality : 0.045 0.158 2965 Planarity : 0.004 0.037 3235 Dihedral : 8.504 66.215 3170 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.08 % Allowed : 9.22 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2240 helix: 1.59 (0.21), residues: 615 sheet: 0.69 (0.19), residues: 665 loop : 0.09 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 28 TYR 0.028 0.002 TYR E 299 PHE 0.014 0.001 PHE A 98 TRP 0.008 0.001 TRP B 426 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00281 (19240) covalent geometry : angle 0.52999 (26155) SS BOND : bond 0.00304 ( 10) SS BOND : angle 0.88587 ( 20) hydrogen bonds : bond 0.04282 ( 885) hydrogen bonds : angle 4.51173 ( 2970) link_ALPHA1-3 : bond 0.00719 ( 5) link_ALPHA1-3 : angle 1.61620 ( 15) link_ALPHA1-6 : bond 0.00544 ( 5) link_ALPHA1-6 : angle 1.35213 ( 15) link_BETA1-4 : bond 0.00397 ( 10) link_BETA1-4 : angle 2.31311 ( 30) link_NAG-ASN : bond 0.00091 ( 10) link_NAG-ASN : angle 2.57384 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 355 time to evaluate : 0.708 Fit side-chains REVERT: B 18 LYS cc_start: 0.7837 (tttt) cc_final: 0.6993 (tmmt) REVERT: B 137 MET cc_start: 0.8902 (mmp) cc_final: 0.8675 (mmp) REVERT: B 165 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8358 (mm-30) REVERT: B 261 MET cc_start: 0.9148 (mmt) cc_final: 0.8932 (tpp) REVERT: B 267 HIS cc_start: 0.7758 (t70) cc_final: 0.7524 (m170) REVERT: B 268 LEU cc_start: 0.8529 (tp) cc_final: 0.8307 (tm) REVERT: K 415 THR cc_start: 0.8224 (m) cc_final: 0.7907 (t) REVERT: K 433 GLU cc_start: 0.7779 (tt0) cc_final: 0.6730 (tm-30) REVERT: N 415 THR cc_start: 0.8219 (m) cc_final: 0.7809 (t) REVERT: N 433 GLU cc_start: 0.7888 (tt0) cc_final: 0.6866 (tm-30) REVERT: L 425 ARG cc_start: 0.8232 (ptt180) cc_final: 0.8025 (ptt180) REVERT: C 18 LYS cc_start: 0.7793 (tttt) cc_final: 0.7109 (tmmt) REVERT: C 90 GLN cc_start: 0.8957 (mt0) cc_final: 0.8688 (mp10) REVERT: C 115 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8703 (tmm) REVERT: C 261 MET cc_start: 0.9208 (mmt) cc_final: 0.8767 (mmm) REVERT: C 429 ILE cc_start: 0.8534 (pt) cc_final: 0.8331 (pp) REVERT: C 440 LEU cc_start: 0.8622 (tp) cc_final: 0.8320 (tt) REVERT: D 18 LYS cc_start: 0.7603 (tttt) cc_final: 0.6913 (tmmt) REVERT: D 243 ASN cc_start: 0.8074 (t0) cc_final: 0.7735 (t0) REVERT: D 244 TYR cc_start: 0.8379 (p90) cc_final: 0.8050 (p90) REVERT: D 267 HIS cc_start: 0.7931 (t70) cc_final: 0.7636 (t70) REVERT: D 282 ASP cc_start: 0.8541 (m-30) cc_final: 0.8314 (m-30) REVERT: D 440 LEU cc_start: 0.8737 (tp) cc_final: 0.8497 (tt) REVERT: E 14 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7053 (mt-10) REVERT: E 18 LYS cc_start: 0.7741 (tttt) cc_final: 0.6788 (tmmt) REVERT: E 56 ASP cc_start: 0.9160 (p0) cc_final: 0.8924 (p0) REVERT: E 115 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8646 (tmm) REVERT: E 137 MET cc_start: 0.8930 (mmp) cc_final: 0.8704 (mmp) REVERT: E 165 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: E 215 LYS cc_start: 0.9092 (tttt) cc_final: 0.8572 (tptp) REVERT: E 243 ASN cc_start: 0.8251 (t0) cc_final: 0.7836 (t0) REVERT: E 245 ASP cc_start: 0.8355 (m-30) cc_final: 0.7678 (p0) REVERT: E 267 HIS cc_start: 0.7961 (t70) cc_final: 0.7714 (t70) REVERT: E 269 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8185 (tpp80) REVERT: A 90 GLN cc_start: 0.8983 (mt0) cc_final: 0.8596 (mp10) REVERT: A 429 ILE cc_start: 0.8633 (pt) cc_final: 0.8399 (pp) REVERT: A 440 LEU cc_start: 0.8528 (tp) cc_final: 0.8295 (tt) outliers start: 41 outliers final: 22 residues processed: 365 average time/residue: 0.5858 time to fit residues: 239.3086 Evaluate side-chains 364 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 338 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 244 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 113 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 185 GLN A 243 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.107124 restraints weight = 17531.764| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.22 r_work: 0.2818 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19280 Z= 0.182 Angle : 0.585 5.820 26265 Z= 0.308 Chirality : 0.047 0.151 2965 Planarity : 0.004 0.044 3235 Dihedral : 8.626 66.445 3170 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.28 % Allowed : 9.82 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.18), residues: 2240 helix: 1.69 (0.21), residues: 615 sheet: 0.72 (0.19), residues: 660 loop : 0.14 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 28 TYR 0.029 0.002 TYR C 299 PHE 0.017 0.002 PHE A 98 TRP 0.009 0.001 TRP B 426 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00402 (19240) covalent geometry : angle 0.56796 (26155) SS BOND : bond 0.00243 ( 10) SS BOND : angle 1.18977 ( 20) hydrogen bonds : bond 0.04609 ( 885) hydrogen bonds : angle 4.55345 ( 2970) link_ALPHA1-3 : bond 0.00464 ( 5) link_ALPHA1-3 : angle 1.71642 ( 15) link_ALPHA1-6 : bond 0.00489 ( 5) link_ALPHA1-6 : angle 1.41773 ( 15) link_BETA1-4 : bond 0.00585 ( 10) link_BETA1-4 : angle 2.66249 ( 30) link_NAG-ASN : bond 0.00165 ( 10) link_NAG-ASN : angle 2.78341 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 342 time to evaluate : 0.662 Fit side-chains REVERT: B 18 LYS cc_start: 0.7839 (tttt) cc_final: 0.7012 (tmmt) REVERT: B 165 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: B 267 HIS cc_start: 0.7868 (t70) cc_final: 0.7501 (m170) REVERT: K 415 THR cc_start: 0.8249 (m) cc_final: 0.7948 (t) REVERT: O 468 LEU cc_start: 0.6569 (tp) cc_final: 0.6169 (tp) REVERT: N 415 THR cc_start: 0.8201 (m) cc_final: 0.7785 (t) REVERT: N 433 GLU cc_start: 0.7927 (tt0) cc_final: 0.6986 (tm-30) REVERT: C 18 LYS cc_start: 0.7780 (tttt) cc_final: 0.7081 (tmmt) REVERT: C 48 ASP cc_start: 0.7739 (m-30) cc_final: 0.7206 (m-30) REVERT: C 90 GLN cc_start: 0.9011 (mt0) cc_final: 0.8742 (mp10) REVERT: C 115 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8662 (tmm) REVERT: C 261 MET cc_start: 0.9237 (mmt) cc_final: 0.8792 (mmm) REVERT: C 440 LEU cc_start: 0.8622 (tp) cc_final: 0.8317 (tt) REVERT: D 18 LYS cc_start: 0.7665 (tttt) cc_final: 0.7008 (tmmt) REVERT: D 165 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8326 (mm-30) REVERT: D 243 ASN cc_start: 0.8081 (t0) cc_final: 0.7728 (t0) REVERT: D 244 TYR cc_start: 0.8404 (p90) cc_final: 0.8093 (p90) REVERT: D 267 HIS cc_start: 0.7897 (t70) cc_final: 0.7483 (t70) REVERT: D 440 LEU cc_start: 0.8743 (tp) cc_final: 0.8507 (tt) REVERT: E 14 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7068 (mt-10) REVERT: E 18 LYS cc_start: 0.7851 (tttt) cc_final: 0.6940 (tmmt) REVERT: E 56 ASP cc_start: 0.9193 (p0) cc_final: 0.8970 (p0) REVERT: E 115 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8724 (tmm) REVERT: E 165 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8394 (mm-30) REVERT: E 215 LYS cc_start: 0.9134 (tttt) cc_final: 0.8599 (tptp) REVERT: E 243 ASN cc_start: 0.8357 (t0) cc_final: 0.7956 (t0) REVERT: E 245 ASP cc_start: 0.8411 (m-30) cc_final: 0.7731 (p0) REVERT: E 267 HIS cc_start: 0.8060 (t70) cc_final: 0.7799 (t70) REVERT: A 90 GLN cc_start: 0.9002 (mt0) cc_final: 0.8612 (mp10) REVERT: A 165 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8433 (mm-30) REVERT: A 429 ILE cc_start: 0.8657 (pt) cc_final: 0.8425 (pp) REVERT: A 440 LEU cc_start: 0.8595 (tp) cc_final: 0.8323 (tt) outliers start: 45 outliers final: 26 residues processed: 354 average time/residue: 0.5938 time to fit residues: 235.1686 Evaluate side-chains 364 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 88 optimal weight: 0.0070 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 243 ASN C 265 ASN D 185 GLN D 265 ASN E 185 GLN A 185 GLN A 243 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.109552 restraints weight = 17569.916| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.09 r_work: 0.2809 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19280 Z= 0.117 Angle : 0.522 6.073 26265 Z= 0.275 Chirality : 0.044 0.186 2965 Planarity : 0.003 0.036 3235 Dihedral : 7.873 60.572 3170 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.82 % Allowed : 10.63 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2240 helix: 1.92 (0.22), residues: 610 sheet: 0.75 (0.19), residues: 660 loop : 0.13 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 269 TYR 0.026 0.002 TYR E 299 PHE 0.013 0.001 PHE A 98 TRP 0.008 0.001 TRP M 440 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00246 (19240) covalent geometry : angle 0.50880 (26155) SS BOND : bond 0.00232 ( 10) SS BOND : angle 0.66762 ( 20) hydrogen bonds : bond 0.03920 ( 885) hydrogen bonds : angle 4.34889 ( 2970) link_ALPHA1-3 : bond 0.00783 ( 5) link_ALPHA1-3 : angle 1.55339 ( 15) link_ALPHA1-6 : bond 0.00754 ( 5) link_ALPHA1-6 : angle 1.29212 ( 15) link_BETA1-4 : bond 0.00329 ( 10) link_BETA1-4 : angle 2.09080 ( 30) link_NAG-ASN : bond 0.00093 ( 10) link_NAG-ASN : angle 2.38791 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 350 time to evaluate : 0.506 Fit side-chains REVERT: B 18 LYS cc_start: 0.7715 (tttt) cc_final: 0.6880 (tmmt) REVERT: B 165 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8486 (mm-30) REVERT: B 267 HIS cc_start: 0.7987 (t70) cc_final: 0.7575 (m170) REVERT: B 268 LEU cc_start: 0.8491 (tp) cc_final: 0.8242 (tm) REVERT: K 415 THR cc_start: 0.8142 (m) cc_final: 0.7837 (t) REVERT: K 433 GLU cc_start: 0.7741 (tt0) cc_final: 0.6826 (tm-30) REVERT: O 468 LEU cc_start: 0.6483 (tp) cc_final: 0.5886 (tp) REVERT: N 415 THR cc_start: 0.7962 (m) cc_final: 0.7607 (t) REVERT: N 433 GLU cc_start: 0.7961 (tt0) cc_final: 0.6998 (tm-30) REVERT: C 18 LYS cc_start: 0.7799 (tttt) cc_final: 0.7045 (tmmt) REVERT: C 48 ASP cc_start: 0.7894 (m-30) cc_final: 0.7348 (m-30) REVERT: C 90 GLN cc_start: 0.9025 (mt0) cc_final: 0.8761 (mp10) REVERT: C 115 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8802 (tmm) REVERT: C 261 MET cc_start: 0.9223 (mmt) cc_final: 0.8820 (mmm) REVERT: C 440 LEU cc_start: 0.8612 (tp) cc_final: 0.8323 (tt) REVERT: D 18 LYS cc_start: 0.7577 (tttt) cc_final: 0.6870 (tmmt) REVERT: D 49 MET cc_start: 0.8195 (tmm) cc_final: 0.7824 (pp-130) REVERT: D 115 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.9038 (ppp) REVERT: D 165 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8390 (mm-30) REVERT: D 243 ASN cc_start: 0.8090 (t0) cc_final: 0.7760 (t0) REVERT: D 244 TYR cc_start: 0.8415 (p90) cc_final: 0.8084 (p90) REVERT: D 267 HIS cc_start: 0.8006 (t70) cc_final: 0.7594 (t70) REVERT: D 440 LEU cc_start: 0.8738 (tp) cc_final: 0.8520 (tt) REVERT: E 14 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6974 (mt-10) REVERT: E 18 LYS cc_start: 0.7878 (tttt) cc_final: 0.6912 (tmmt) REVERT: E 56 ASP cc_start: 0.9224 (p0) cc_final: 0.9014 (p0) REVERT: E 115 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8851 (tmm) REVERT: E 215 LYS cc_start: 0.9150 (tttt) cc_final: 0.8624 (tptp) REVERT: E 243 ASN cc_start: 0.8445 (t0) cc_final: 0.8046 (t0) REVERT: E 245 ASP cc_start: 0.8380 (m-30) cc_final: 0.7643 (p0) REVERT: E 267 HIS cc_start: 0.8218 (t70) cc_final: 0.7912 (t70) REVERT: A 90 GLN cc_start: 0.9032 (mt0) cc_final: 0.8644 (mp10) REVERT: A 165 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: A 429 ILE cc_start: 0.8648 (pt) cc_final: 0.8418 (pp) REVERT: A 440 LEU cc_start: 0.8600 (tp) cc_final: 0.8342 (tt) outliers start: 36 outliers final: 24 residues processed: 360 average time/residue: 0.5863 time to fit residues: 235.9270 Evaluate side-chains 368 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 338 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain L residue 438 ILE Chi-restraints excluded: chain L residue 468 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 198 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.144903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107565 restraints weight = 17618.470| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.09 r_work: 0.2804 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19280 Z= 0.205 Angle : 0.609 6.958 26265 Z= 0.319 Chirality : 0.048 0.158 2965 Planarity : 0.004 0.045 3235 Dihedral : 8.435 63.000 3170 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.94 % Allowed : 9.82 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 2240 helix: 1.79 (0.22), residues: 615 sheet: 0.73 (0.19), residues: 660 loop : 0.17 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 28 TYR 0.030 0.002 TYR D 299 PHE 0.018 0.002 PHE C 221 TRP 0.010 0.002 TRP B 426 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00457 (19240) covalent geometry : angle 0.59152 (26155) SS BOND : bond 0.00303 ( 10) SS BOND : angle 1.01680 ( 20) hydrogen bonds : bond 0.04698 ( 885) hydrogen bonds : angle 4.57106 ( 2970) link_ALPHA1-3 : bond 0.00399 ( 5) link_ALPHA1-3 : angle 1.81451 ( 15) link_ALPHA1-6 : bond 0.00519 ( 5) link_ALPHA1-6 : angle 1.42088 ( 15) link_BETA1-4 : bond 0.00696 ( 10) link_BETA1-4 : angle 2.76822 ( 30) link_NAG-ASN : bond 0.00208 ( 10) link_NAG-ASN : angle 2.91829 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 337 time to evaluate : 0.700 Fit side-chains REVERT: B 18 LYS cc_start: 0.7771 (tttt) cc_final: 0.6950 (tmmt) REVERT: B 165 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8448 (mm-30) REVERT: B 267 HIS cc_start: 0.7934 (t70) cc_final: 0.7478 (m170) REVERT: K 415 THR cc_start: 0.8205 (m) cc_final: 0.7894 (t) REVERT: O 468 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.5881 (tp) REVERT: N 415 THR cc_start: 0.8112 (m) cc_final: 0.7766 (t) REVERT: N 433 GLU cc_start: 0.7934 (tt0) cc_final: 0.6966 (tm-30) REVERT: C 18 LYS cc_start: 0.7790 (tttt) cc_final: 0.7074 (tmmt) REVERT: C 48 ASP cc_start: 0.7824 (m-30) cc_final: 0.7228 (m-30) REVERT: C 90 GLN cc_start: 0.9027 (mt0) cc_final: 0.8713 (mp10) REVERT: C 115 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8839 (tmm) REVERT: C 261 MET cc_start: 0.9240 (mmt) cc_final: 0.8803 (mmm) REVERT: C 440 LEU cc_start: 0.8627 (tp) cc_final: 0.8331 (tt) REVERT: D 9 MET cc_start: 0.8002 (mtp) cc_final: 0.7643 (mtm) REVERT: D 18 LYS cc_start: 0.7722 (tttt) cc_final: 0.7030 (tmmt) REVERT: D 165 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: D 243 ASN cc_start: 0.8123 (t0) cc_final: 0.7747 (t0) REVERT: D 244 TYR cc_start: 0.8400 (p90) cc_final: 0.8083 (p90) REVERT: D 267 HIS cc_start: 0.7930 (t70) cc_final: 0.7527 (t70) REVERT: D 440 LEU cc_start: 0.8745 (tp) cc_final: 0.8511 (tt) REVERT: E 18 LYS cc_start: 0.7913 (tttt) cc_final: 0.6997 (tmmt) REVERT: E 48 ASP cc_start: 0.7813 (m-30) cc_final: 0.7111 (m-30) REVERT: E 56 ASP cc_start: 0.9198 (p0) cc_final: 0.8979 (p0) REVERT: E 115 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8745 (tmm) REVERT: E 165 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: E 215 LYS cc_start: 0.9146 (tttt) cc_final: 0.8581 (tptp) REVERT: E 243 ASN cc_start: 0.8403 (t0) cc_final: 0.7996 (t0) REVERT: E 245 ASP cc_start: 0.8399 (m-30) cc_final: 0.7726 (p0) REVERT: E 267 HIS cc_start: 0.8165 (t70) cc_final: 0.7888 (t70) REVERT: A 90 GLN cc_start: 0.9002 (mt0) cc_final: 0.8606 (mp10) REVERT: A 165 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8513 (mm-30) REVERT: A 429 ILE cc_start: 0.8645 (pt) cc_final: 0.8395 (pp) REVERT: A 440 LEU cc_start: 0.8611 (tp) cc_final: 0.8349 (tt) outliers start: 58 outliers final: 35 residues processed: 355 average time/residue: 0.6018 time to fit residues: 239.0136 Evaluate side-chains 376 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain L residue 468 LEU Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 7 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 243 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110784 restraints weight = 17572.433| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.00 r_work: 0.2858 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19280 Z= 0.124 Angle : 0.538 7.546 26265 Z= 0.282 Chirality : 0.045 0.185 2965 Planarity : 0.003 0.048 3235 Dihedral : 7.838 58.536 3170 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.97 % Allowed : 10.73 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2240 helix: 1.91 (0.22), residues: 615 sheet: 0.72 (0.19), residues: 660 loop : 0.18 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.027 0.002 TYR C 299 PHE 0.014 0.001 PHE A 98 TRP 0.007 0.001 TRP A 168 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00265 (19240) covalent geometry : angle 0.52429 (26155) SS BOND : bond 0.00202 ( 10) SS BOND : angle 0.74152 ( 20) hydrogen bonds : bond 0.03980 ( 885) hydrogen bonds : angle 4.39371 ( 2970) link_ALPHA1-3 : bond 0.00724 ( 5) link_ALPHA1-3 : angle 1.54016 ( 15) link_ALPHA1-6 : bond 0.00735 ( 5) link_ALPHA1-6 : angle 1.28445 ( 15) link_BETA1-4 : bond 0.00347 ( 10) link_BETA1-4 : angle 2.16948 ( 30) link_NAG-ASN : bond 0.00078 ( 10) link_NAG-ASN : angle 2.51600 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 339 time to evaluate : 0.567 Fit side-chains REVERT: B 18 LYS cc_start: 0.7723 (tttt) cc_final: 0.6916 (tmmt) REVERT: B 165 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8376 (mm-30) REVERT: B 267 HIS cc_start: 0.7865 (t70) cc_final: 0.7462 (m170) REVERT: B 268 LEU cc_start: 0.8529 (tp) cc_final: 0.8301 (tm) REVERT: K 415 THR cc_start: 0.8118 (m) cc_final: 0.7808 (t) REVERT: K 433 GLU cc_start: 0.7754 (tt0) cc_final: 0.6817 (tm-30) REVERT: O 468 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.5762 (tp) REVERT: N 415 THR cc_start: 0.7971 (m) cc_final: 0.7613 (t) REVERT: N 433 GLU cc_start: 0.7907 (tt0) cc_final: 0.6949 (tm-30) REVERT: C 18 LYS cc_start: 0.7806 (tttt) cc_final: 0.7079 (tmmt) REVERT: C 48 ASP cc_start: 0.7740 (m-30) cc_final: 0.7174 (m-30) REVERT: C 90 GLN cc_start: 0.8997 (mt0) cc_final: 0.8711 (mp10) REVERT: C 115 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8759 (tmm) REVERT: C 261 MET cc_start: 0.9203 (mmt) cc_final: 0.8793 (mmm) REVERT: C 440 LEU cc_start: 0.8610 (tp) cc_final: 0.8327 (tt) REVERT: D 9 MET cc_start: 0.7974 (mtp) cc_final: 0.7659 (mtm) REVERT: D 18 LYS cc_start: 0.7628 (tttt) cc_final: 0.6924 (tmmt) REVERT: D 165 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: D 243 ASN cc_start: 0.8031 (t0) cc_final: 0.7690 (t0) REVERT: D 244 TYR cc_start: 0.8363 (p90) cc_final: 0.8033 (p90) REVERT: D 267 HIS cc_start: 0.7887 (t70) cc_final: 0.7496 (t70) REVERT: D 440 LEU cc_start: 0.8722 (tp) cc_final: 0.8503 (tt) REVERT: E 18 LYS cc_start: 0.7868 (tttt) cc_final: 0.6919 (tmmt) REVERT: E 48 ASP cc_start: 0.7745 (m-30) cc_final: 0.7034 (m-30) REVERT: E 56 ASP cc_start: 0.9182 (p0) cc_final: 0.8943 (p0) REVERT: E 115 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8677 (tmm) REVERT: E 215 LYS cc_start: 0.9113 (tttt) cc_final: 0.8582 (tptp) REVERT: E 243 ASN cc_start: 0.8426 (t0) cc_final: 0.8023 (t0) REVERT: E 245 ASP cc_start: 0.8311 (m-30) cc_final: 0.7664 (p0) REVERT: E 267 HIS cc_start: 0.8144 (t70) cc_final: 0.7863 (t70) REVERT: A 165 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8396 (mm-30) REVERT: A 429 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 440 LEU cc_start: 0.8590 (tp) cc_final: 0.8338 (tt) outliers start: 39 outliers final: 27 residues processed: 353 average time/residue: 0.6059 time to fit residues: 238.6658 Evaluate side-chains 364 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 429 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 168 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN C 243 ASN D 185 GLN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.144917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.111536 restraints weight = 17515.694| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.70 r_work: 0.2803 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19280 Z= 0.197 Angle : 0.611 8.239 26265 Z= 0.319 Chirality : 0.047 0.167 2965 Planarity : 0.004 0.069 3235 Dihedral : 8.296 60.950 3170 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.43 % Allowed : 10.68 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2240 helix: 1.76 (0.21), residues: 615 sheet: 0.72 (0.19), residues: 660 loop : 0.24 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 269 TYR 0.030 0.002 TYR D 299 PHE 0.017 0.002 PHE A 98 TRP 0.010 0.001 TRP B 426 HIS 0.004 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00441 (19240) covalent geometry : angle 0.59413 (26155) SS BOND : bond 0.00281 ( 10) SS BOND : angle 1.09548 ( 20) hydrogen bonds : bond 0.04636 ( 885) hydrogen bonds : angle 4.56429 ( 2970) link_ALPHA1-3 : bond 0.00374 ( 5) link_ALPHA1-3 : angle 1.75382 ( 15) link_ALPHA1-6 : bond 0.00545 ( 5) link_ALPHA1-6 : angle 1.40943 ( 15) link_BETA1-4 : bond 0.00656 ( 10) link_BETA1-4 : angle 2.73162 ( 30) link_NAG-ASN : bond 0.00180 ( 10) link_NAG-ASN : angle 2.88543 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 333 time to evaluate : 0.664 Fit side-chains REVERT: B 18 LYS cc_start: 0.7790 (tttt) cc_final: 0.6976 (tmmt) REVERT: B 165 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8430 (mm-30) REVERT: B 267 HIS cc_start: 0.7956 (t70) cc_final: 0.7476 (m170) REVERT: K 415 THR cc_start: 0.8246 (m) cc_final: 0.7946 (t) REVERT: O 468 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.5939 (tp) REVERT: N 415 THR cc_start: 0.8096 (m) cc_final: 0.7741 (t) REVERT: N 433 GLU cc_start: 0.7959 (tt0) cc_final: 0.7075 (tm-30) REVERT: L 433 GLU cc_start: 0.7880 (tt0) cc_final: 0.7360 (tt0) REVERT: C 18 LYS cc_start: 0.7787 (tttt) cc_final: 0.7065 (tmmt) REVERT: C 48 ASP cc_start: 0.7813 (m-30) cc_final: 0.7232 (m-30) REVERT: C 90 GLN cc_start: 0.9019 (mt0) cc_final: 0.8704 (mp10) REVERT: C 115 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8837 (tmm) REVERT: C 261 MET cc_start: 0.9238 (mmt) cc_final: 0.8807 (mmm) REVERT: C 440 LEU cc_start: 0.8637 (tp) cc_final: 0.8355 (tt) REVERT: D 9 MET cc_start: 0.8112 (mtp) cc_final: 0.7641 (mtm) REVERT: D 18 LYS cc_start: 0.7721 (tttt) cc_final: 0.7048 (tmmt) REVERT: D 165 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8387 (mm-30) REVERT: D 243 ASN cc_start: 0.8144 (t0) cc_final: 0.7776 (t0) REVERT: D 244 TYR cc_start: 0.8396 (p90) cc_final: 0.8060 (p90) REVERT: D 267 HIS cc_start: 0.7892 (t70) cc_final: 0.7462 (t70) REVERT: D 440 LEU cc_start: 0.8747 (tp) cc_final: 0.8521 (tt) REVERT: E 18 LYS cc_start: 0.7987 (tttt) cc_final: 0.7056 (tmmt) REVERT: E 48 ASP cc_start: 0.7722 (m-30) cc_final: 0.7000 (m-30) REVERT: E 56 ASP cc_start: 0.9189 (p0) cc_final: 0.8973 (p0) REVERT: E 115 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8739 (tmm) REVERT: E 165 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8404 (mm-30) REVERT: E 215 LYS cc_start: 0.9134 (tttt) cc_final: 0.8579 (tptp) REVERT: E 243 ASN cc_start: 0.8412 (t0) cc_final: 0.8001 (t0) REVERT: E 245 ASP cc_start: 0.8394 (m-30) cc_final: 0.7749 (p0) REVERT: E 267 HIS cc_start: 0.8177 (t70) cc_final: 0.7891 (t70) REVERT: A 90 GLN cc_start: 0.8994 (mt0) cc_final: 0.8605 (mp10) REVERT: A 165 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8489 (mm-30) REVERT: A 429 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 440 LEU cc_start: 0.8618 (tp) cc_final: 0.8372 (tt) outliers start: 48 outliers final: 32 residues processed: 351 average time/residue: 0.6101 time to fit residues: 239.0088 Evaluate side-chains 364 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 324 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain L residue 468 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 243 ASN D 185 GLN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.144429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.105772 restraints weight = 17414.911| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.11 r_work: 0.2752 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19280 Z= 0.226 Angle : 0.645 8.618 26265 Z= 0.337 Chirality : 0.049 0.165 2965 Planarity : 0.005 0.064 3235 Dihedral : 8.803 64.947 3170 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.23 % Allowed : 10.94 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2240 helix: 1.67 (0.21), residues: 615 sheet: 0.64 (0.19), residues: 685 loop : 0.32 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 269 TYR 0.031 0.002 TYR D 299 PHE 0.018 0.002 PHE C 221 TRP 0.010 0.002 TRP B 426 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00511 (19240) covalent geometry : angle 0.62761 (26155) SS BOND : bond 0.00304 ( 10) SS BOND : angle 1.20496 ( 20) hydrogen bonds : bond 0.04851 ( 885) hydrogen bonds : angle 4.67689 ( 2970) link_ALPHA1-3 : bond 0.00297 ( 5) link_ALPHA1-3 : angle 1.67511 ( 15) link_ALPHA1-6 : bond 0.00386 ( 5) link_ALPHA1-6 : angle 1.49381 ( 15) link_BETA1-4 : bond 0.00761 ( 10) link_BETA1-4 : angle 2.94546 ( 30) link_NAG-ASN : bond 0.00237 ( 10) link_NAG-ASN : angle 3.01110 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 331 time to evaluate : 0.571 Fit side-chains REVERT: B 18 LYS cc_start: 0.7737 (tttt) cc_final: 0.6965 (tmmt) REVERT: B 165 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8523 (mm-30) REVERT: B 267 HIS cc_start: 0.8085 (t70) cc_final: 0.7465 (m170) REVERT: B 268 LEU cc_start: 0.8522 (tp) cc_final: 0.8276 (tm) REVERT: K 415 THR cc_start: 0.8300 (m) cc_final: 0.7998 (t) REVERT: K 447 TYR cc_start: 0.8603 (m-80) cc_final: 0.8384 (m-80) REVERT: O 468 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.5999 (tp) REVERT: N 415 THR cc_start: 0.8175 (m) cc_final: 0.7768 (t) REVERT: N 433 GLU cc_start: 0.8040 (tt0) cc_final: 0.7136 (tm-30) REVERT: L 433 GLU cc_start: 0.7983 (tt0) cc_final: 0.7428 (tt0) REVERT: C 18 LYS cc_start: 0.7789 (tttt) cc_final: 0.7065 (tmmt) REVERT: C 48 ASP cc_start: 0.7969 (m-30) cc_final: 0.7386 (m-30) REVERT: C 90 GLN cc_start: 0.9071 (mt0) cc_final: 0.8748 (mp10) REVERT: C 115 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8898 (tmm) REVERT: C 243 ASN cc_start: 0.8369 (t0) cc_final: 0.8126 (t0) REVERT: C 261 MET cc_start: 0.9267 (mmt) cc_final: 0.8866 (mmm) REVERT: C 440 LEU cc_start: 0.8641 (tp) cc_final: 0.8356 (tt) REVERT: D 18 LYS cc_start: 0.7731 (tttt) cc_final: 0.7052 (tmmt) REVERT: D 165 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8493 (mm-30) REVERT: D 243 ASN cc_start: 0.8235 (t0) cc_final: 0.7871 (t0) REVERT: D 244 TYR cc_start: 0.8448 (p90) cc_final: 0.8138 (p90) REVERT: D 267 HIS cc_start: 0.7965 (t70) cc_final: 0.7690 (t70) REVERT: D 440 LEU cc_start: 0.8759 (tp) cc_final: 0.8532 (tt) REVERT: E 18 LYS cc_start: 0.8001 (tttt) cc_final: 0.7056 (tmmt) REVERT: E 48 ASP cc_start: 0.7853 (m-30) cc_final: 0.7156 (m-30) REVERT: E 56 ASP cc_start: 0.9226 (p0) cc_final: 0.9020 (p0) REVERT: E 115 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8803 (tmm) REVERT: E 165 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: E 215 LYS cc_start: 0.9188 (tttt) cc_final: 0.8619 (tptp) REVERT: E 243 ASN cc_start: 0.8492 (t0) cc_final: 0.8084 (t0) REVERT: E 245 ASP cc_start: 0.8476 (m-30) cc_final: 0.7765 (p0) REVERT: E 267 HIS cc_start: 0.8235 (t70) cc_final: 0.7945 (t70) REVERT: A 90 GLN cc_start: 0.9038 (mt0) cc_final: 0.8648 (mp10) REVERT: A 165 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8605 (mm-30) REVERT: A 429 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8347 (pp) REVERT: A 440 LEU cc_start: 0.8627 (tp) cc_final: 0.8374 (tt) outliers start: 44 outliers final: 32 residues processed: 347 average time/residue: 0.5850 time to fit residues: 226.8692 Evaluate side-chains 370 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 330 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 105 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.145648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.107175 restraints weight = 17566.961| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.13 r_work: 0.2774 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19280 Z= 0.168 Angle : 0.592 8.409 26265 Z= 0.309 Chirality : 0.046 0.165 2965 Planarity : 0.004 0.061 3235 Dihedral : 8.379 62.885 3170 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.23 % Allowed : 10.99 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2240 helix: 1.75 (0.21), residues: 615 sheet: 0.72 (0.19), residues: 660 loop : 0.28 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 269 TYR 0.029 0.002 TYR E 299 PHE 0.017 0.002 PHE A 98 TRP 0.007 0.001 TRP B 426 HIS 0.003 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00373 (19240) covalent geometry : angle 0.57638 (26155) SS BOND : bond 0.00249 ( 10) SS BOND : angle 0.97988 ( 20) hydrogen bonds : bond 0.04385 ( 885) hydrogen bonds : angle 4.53710 ( 2970) link_ALPHA1-3 : bond 0.00528 ( 5) link_ALPHA1-3 : angle 1.55876 ( 15) link_ALPHA1-6 : bond 0.00552 ( 5) link_ALPHA1-6 : angle 1.39326 ( 15) link_BETA1-4 : bond 0.00504 ( 10) link_BETA1-4 : angle 2.56305 ( 30) link_NAG-ASN : bond 0.00106 ( 10) link_NAG-ASN : angle 2.73667 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8125.63 seconds wall clock time: 139 minutes 27.30 seconds (8367.30 seconds total)