Starting phenix.real_space_refine on Mon Jun 16 15:05:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qfa_4542/06_2025/6qfa_4542.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qfa_4542/06_2025/6qfa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6qfa_4542/06_2025/6qfa_4542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qfa_4542/06_2025/6qfa_4542.map" model { file = "/net/cci-nas-00/data/ceres_data/6qfa_4542/06_2025/6qfa_4542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qfa_4542/06_2025/6qfa_4542.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.67, per 1000 atoms: 0.57 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: 4.93 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.75 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: 6.59 Time building geometry restraints manager: 5.71 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: 0.13 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.460 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.070 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (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 TRP 0.011 0.001 TRP C 426 HIS 0.003 0.001 HIS A 119 PHE 0.011 0.002 PHE D 105 TYR 0.020 0.002 TYR D 299 ARG 0.004 0.000 ARG C 129 Details of bonding type rmsd link_NAG-ASN : bond 0.01554 ( 10) link_NAG-ASN : angle 4.37911 ( 30) 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_ALPHA1-3 : bond 0.05915 ( 5) link_ALPHA1-3 : angle 1.98031 ( 15) hydrogen bonds : bond 0.27035 ( 885) hydrogen bonds : angle 8.92379 ( 2970) SS BOND : bond 0.00039 ( 10) SS BOND : angle 0.65645 ( 20) covalent geometry : bond 0.00531 (19240) covalent geometry : angle 0.79981 (26155) *********************** 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 : 2.182 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: 0.8641 (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: 0.8783 (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: 1.4094 time to fit residues: 558.1792 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 : 1.838 ------------------------------------------------------------------------------- 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 189 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.0040 chunk 176 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.147934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112211 restraints weight = 17725.171| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.28 r_work: 0.2890 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19280 Z= 0.146 Angle : 0.590 5.157 26265 Z= 0.313 Chirality : 0.045 0.145 2965 Planarity : 0.005 0.041 3235 Dihedral : 9.398 74.406 3174 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.47 % Allowed : 7.49 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2240 helix: -0.15 (0.18), residues: 610 sheet: 0.76 (0.20), residues: 645 loop : -0.47 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 426 HIS 0.003 0.001 HIS E 119 PHE 0.014 0.002 PHE K 424 TYR 0.026 0.002 TYR E 299 ARG 0.006 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 10) link_NAG-ASN : angle 2.60906 ( 30) link_ALPHA1-6 : bond 0.00114 ( 5) link_ALPHA1-6 : angle 1.71447 ( 15) link_BETA1-4 : bond 0.00470 ( 10) link_BETA1-4 : angle 2.50481 ( 30) link_ALPHA1-3 : bond 0.00440 ( 5) link_ALPHA1-3 : angle 2.23088 ( 15) hydrogen bonds : bond 0.05158 ( 885) hydrogen bonds : angle 4.88508 ( 2970) SS BOND : bond 0.00269 ( 10) SS BOND : angle 1.27252 ( 20) covalent geometry : bond 0.00311 (19240) covalent geometry : angle 0.57380 (26155) *********************** 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 394 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 365 time to evaluate : 2.082 Fit side-chains REVERT: B 18 LYS cc_start: 0.7962 (tttt) cc_final: 0.7102 (tmmt) REVERT: B 137 MET cc_start: 0.8989 (mmp) cc_final: 0.8624 (mmp) REVERT: B 261 MET cc_start: 0.9074 (mmt) cc_final: 0.8816 (tpp) REVERT: K 415 THR cc_start: 0.8340 (m) cc_final: 0.7980 (t) REVERT: K 425 ARG cc_start: 0.8072 (ptt180) cc_final: 0.7552 (ptt180) REVERT: K 433 GLU cc_start: 0.7754 (tt0) cc_final: 0.6587 (tm-30) REVERT: N 421 MET cc_start: 0.9133 (mmt) cc_final: 0.8873 (tpp) REVERT: N 433 GLU cc_start: 0.7812 (tt0) cc_final: 0.6776 (tm-30) REVERT: N 447 TYR cc_start: 0.8515 (m-80) cc_final: 0.7997 (m-80) REVERT: L 425 ARG cc_start: 0.8243 (ptt180) cc_final: 0.7963 (ptt180) REVERT: C 18 LYS cc_start: 0.7753 (tttt) cc_final: 0.7079 (tmmt) REVERT: C 52 GLU cc_start: 0.8820 (mp0) cc_final: 0.8593 (mp0) REVERT: C 90 GLN cc_start: 0.8978 (mt0) cc_final: 0.8698 (mp10) REVERT: C 115 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8653 (tmm) REVERT: C 261 MET cc_start: 0.9199 (mmt) cc_final: 0.8814 (mmp) REVERT: C 285 LEU cc_start: 0.9270 (mt) cc_final: 0.9063 (mm) REVERT: C 429 ILE cc_start: 0.8520 (pt) cc_final: 0.8308 (pp) REVERT: C 440 LEU cc_start: 0.8582 (tp) cc_final: 0.8271 (tt) REVERT: D 18 LYS cc_start: 0.7646 (tttt) cc_final: 0.6929 (tmmt) REVERT: D 49 MET cc_start: 0.8103 (tmm) cc_final: 0.7894 (tmm) REVERT: D 52 GLU cc_start: 0.8721 (mp0) cc_final: 0.8481 (mp0) REVERT: D 165 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: D 243 ASN cc_start: 0.8057 (t0) cc_final: 0.7743 (t0) REVERT: D 244 TYR cc_start: 0.8359 (p90) cc_final: 0.8006 (p90) REVERT: D 245 ASP cc_start: 0.7709 (p0) cc_final: 0.7429 (m-30) REVERT: D 267 HIS cc_start: 0.7887 (t70) cc_final: 0.7450 (m90) REVERT: D 304 TYR cc_start: 0.8899 (t80) cc_final: 0.8561 (t80) REVERT: D 440 LEU cc_start: 0.8672 (tp) cc_final: 0.8411 (tt) REVERT: E 14 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6978 (mt-10) REVERT: E 18 LYS cc_start: 0.7711 (tttt) cc_final: 0.6769 (tmmt) REVERT: E 56 ASP cc_start: 0.9137 (p0) cc_final: 0.8918 (p0) REVERT: E 90 GLN cc_start: 0.9013 (mt0) cc_final: 0.8713 (mp10) REVERT: E 115 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8655 (tmm) REVERT: E 137 MET cc_start: 0.8961 (mmp) cc_final: 0.8627 (mmp) REVERT: E 165 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: E 215 LYS cc_start: 0.9092 (tttt) cc_final: 0.8554 (tptp) REVERT: E 243 ASN cc_start: 0.8159 (t0) cc_final: 0.7730 (t0) REVERT: E 244 TYR cc_start: 0.8376 (p90) cc_final: 0.8155 (p90) REVERT: E 245 ASP cc_start: 0.8333 (m-30) cc_final: 0.7628 (p0) REVERT: E 267 HIS cc_start: 0.7957 (t70) cc_final: 0.7614 (m170) REVERT: A 68 ARG cc_start: 0.8870 (tpp80) cc_final: 0.8642 (tpp80) REVERT: A 90 GLN cc_start: 0.8960 (mt0) cc_final: 0.8619 (mp10) REVERT: A 165 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: A 267 HIS cc_start: 0.7863 (t70) cc_final: 0.7604 (m170) REVERT: A 429 ILE cc_start: 0.8556 (pt) cc_final: 0.8314 (pp) REVERT: A 440 LEU cc_start: 0.8630 (tp) cc_final: 0.8338 (tt) outliers start: 29 outliers final: 18 residues processed: 370 average time/residue: 1.3313 time to fit residues: 550.2617 Evaluate side-chains 355 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 332 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 115 MET 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 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 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 126 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 176 optimal weight: 0.0770 chunk 149 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.143522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.100313 restraints weight = 17633.369| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.38 r_work: 0.2783 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19280 Z= 0.244 Angle : 0.660 6.153 26265 Z= 0.348 Chirality : 0.049 0.157 2965 Planarity : 0.005 0.050 3235 Dihedral : 9.531 73.622 3172 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.23 % Allowed : 8.91 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2240 helix: 1.04 (0.20), residues: 615 sheet: 0.67 (0.19), residues: 665 loop : -0.11 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 426 HIS 0.006 0.001 HIS D 107 PHE 0.019 0.002 PHE C 221 TYR 0.034 0.003 TYR D 299 ARG 0.008 0.001 ARG C 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 10) link_NAG-ASN : angle 3.30433 ( 30) link_ALPHA1-6 : bond 0.00155 ( 5) link_ALPHA1-6 : angle 1.66509 ( 15) link_BETA1-4 : bond 0.00860 ( 10) link_BETA1-4 : angle 3.10467 ( 30) link_ALPHA1-3 : bond 0.00143 ( 5) link_ALPHA1-3 : angle 1.88061 ( 15) hydrogen bonds : bond 0.05562 ( 885) hydrogen bonds : angle 4.85232 ( 2970) SS BOND : bond 0.00369 ( 10) SS BOND : angle 1.24840 ( 20) covalent geometry : bond 0.00546 (19240) covalent geometry : angle 0.63943 (26155) *********************** 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 385 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 2.181 Fit side-chains REVERT: B 18 LYS cc_start: 0.7860 (tttt) cc_final: 0.7015 (tmmt) REVERT: B 137 MET cc_start: 0.8984 (mmp) cc_final: 0.8739 (mmp) REVERT: B 165 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8398 (mm-30) REVERT: B 267 HIS cc_start: 0.7842 (t70) cc_final: 0.7570 (m170) REVERT: K 415 THR cc_start: 0.8437 (m) cc_final: 0.8093 (t) REVERT: K 447 TYR cc_start: 0.8541 (m-80) cc_final: 0.8314 (m-80) REVERT: N 415 THR cc_start: 0.8489 (m) cc_final: 0.8052 (t) REVERT: N 421 MET cc_start: 0.9162 (mmt) cc_final: 0.8887 (tpp) REVERT: N 433 GLU cc_start: 0.7872 (tt0) cc_final: 0.6803 (tm-30) REVERT: L 425 ARG cc_start: 0.8199 (ptt180) cc_final: 0.7836 (ptt180) REVERT: C 18 LYS cc_start: 0.7816 (tttt) cc_final: 0.7116 (tmmt) REVERT: C 52 GLU cc_start: 0.8839 (mp0) cc_final: 0.8630 (mp0) REVERT: C 90 GLN cc_start: 0.8980 (mt0) cc_final: 0.8693 (mp10) REVERT: C 115 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8798 (tmm) REVERT: C 261 MET cc_start: 0.9235 (mmt) cc_final: 0.8920 (mmp) REVERT: C 429 ILE cc_start: 0.8542 (pt) cc_final: 0.8334 (pp) REVERT: C 440 LEU cc_start: 0.8602 (tp) cc_final: 0.8314 (tt) REVERT: D 18 LYS cc_start: 0.7725 (tttt) cc_final: 0.7031 (tmmt) REVERT: D 165 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8330 (mm-30) REVERT: D 243 ASN cc_start: 0.8315 (t0) cc_final: 0.8055 (t0) REVERT: D 244 TYR cc_start: 0.8450 (p90) cc_final: 0.8143 (p90) REVERT: D 245 ASP cc_start: 0.7837 (p0) cc_final: 0.7589 (m-30) REVERT: D 267 HIS cc_start: 0.7890 (t70) cc_final: 0.7363 (m90) REVERT: D 440 LEU cc_start: 0.8777 (tp) cc_final: 0.8511 (tt) REVERT: E 18 LYS cc_start: 0.7853 (tttt) cc_final: 0.6942 (tmmt) REVERT: E 56 ASP cc_start: 0.9159 (p0) cc_final: 0.8933 (p0) REVERT: E 115 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8702 (tmm) REVERT: E 137 MET cc_start: 0.8973 (mmp) cc_final: 0.8737 (mmp) REVERT: E 165 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8395 (mm-30) REVERT: E 215 LYS cc_start: 0.9129 (tttt) cc_final: 0.8573 (tptp) REVERT: E 243 ASN cc_start: 0.8307 (t0) cc_final: 0.7887 (t0) REVERT: E 245 ASP cc_start: 0.8423 (m-30) cc_final: 0.7701 (p0) REVERT: E 267 HIS cc_start: 0.7975 (t70) cc_final: 0.7573 (t70) REVERT: A 90 GLN cc_start: 0.8982 (mt0) cc_final: 0.8603 (mp10) REVERT: A 165 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8493 (mm-30) REVERT: A 429 ILE cc_start: 0.8641 (pt) cc_final: 0.8333 (pp) REVERT: A 440 LEU cc_start: 0.8617 (tp) cc_final: 0.8369 (tt) outliers start: 44 outliers final: 27 residues processed: 355 average time/residue: 1.3557 time to fit residues: 539.0303 Evaluate side-chains 364 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 331 time to evaluate : 1.889 ------------------------------------------------------------------------------- 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 268 LEU Chi-restraints excluded: chain B residue 429 ILE 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 59 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 105 optimal weight: 4.9990 chunk 209 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 224 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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 113 ASN C 243 ASN C 265 ASN 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 = 0.3582 r_free = 0.3582 target = 0.147345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.110830 restraints weight = 17655.066| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.12 r_work: 0.2879 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19280 Z= 0.118 Angle : 0.525 5.489 26265 Z= 0.279 Chirality : 0.044 0.173 2965 Planarity : 0.003 0.037 3235 Dihedral : 8.271 64.550 3170 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.82 % Allowed : 9.72 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2240 helix: 1.70 (0.21), residues: 610 sheet: 0.82 (0.19), residues: 655 loop : 0.01 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 426 HIS 0.002 0.001 HIS E 119 PHE 0.012 0.001 PHE A 98 TYR 0.026 0.001 TYR C 299 ARG 0.005 0.000 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 10) link_NAG-ASN : angle 2.42632 ( 30) link_ALPHA1-6 : bond 0.00663 ( 5) link_ALPHA1-6 : angle 1.32017 ( 15) link_BETA1-4 : bond 0.00315 ( 10) link_BETA1-4 : angle 2.13660 ( 30) link_ALPHA1-3 : bond 0.00789 ( 5) link_ALPHA1-3 : angle 1.49778 ( 15) hydrogen bonds : bond 0.04075 ( 885) hydrogen bonds : angle 4.44351 ( 2970) SS BOND : bond 0.00436 ( 10) SS BOND : angle 0.80864 ( 20) covalent geometry : bond 0.00249 (19240) covalent geometry : angle 0.51187 (26155) *********************** 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 394 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 358 time to evaluate : 2.005 Fit side-chains REVERT: B 18 LYS cc_start: 0.7772 (tttt) cc_final: 0.6964 (tmmt) REVERT: B 137 MET cc_start: 0.8892 (mmp) cc_final: 0.8657 (mmp) REVERT: B 165 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8359 (mm-30) REVERT: B 267 HIS cc_start: 0.7747 (t70) cc_final: 0.7528 (m170) REVERT: B 268 LEU cc_start: 0.8557 (tp) cc_final: 0.8351 (tm) REVERT: K 415 THR cc_start: 0.8212 (m) cc_final: 0.7896 (t) REVERT: K 433 GLU cc_start: 0.7786 (tt0) cc_final: 0.6751 (tm-30) REVERT: O 468 LEU cc_start: 0.6438 (tp) cc_final: 0.6025 (tp) REVERT: N 415 THR cc_start: 0.8090 (m) cc_final: 0.7672 (t) REVERT: N 421 MET cc_start: 0.9172 (mmt) cc_final: 0.8893 (tpp) REVERT: N 433 GLU cc_start: 0.7847 (tt0) cc_final: 0.6801 (tm-30) REVERT: C 18 LYS cc_start: 0.7849 (tttt) cc_final: 0.7151 (tmmt) REVERT: C 90 GLN cc_start: 0.8936 (mt0) cc_final: 0.8664 (mp10) REVERT: C 115 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8667 (tmm) REVERT: C 165 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8290 (mm-30) REVERT: C 261 MET cc_start: 0.9191 (mmt) cc_final: 0.8752 (mmm) REVERT: C 286 MET cc_start: 0.9028 (mtp) cc_final: 0.8807 (mtp) REVERT: C 440 LEU cc_start: 0.8613 (tp) cc_final: 0.8317 (tt) REVERT: D 18 LYS cc_start: 0.7601 (tttt) cc_final: 0.6915 (tmmt) REVERT: D 59 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8895 (tt) REVERT: D 243 ASN cc_start: 0.8208 (t0) cc_final: 0.7913 (t0) REVERT: D 244 TYR cc_start: 0.8373 (p90) cc_final: 0.8095 (p90) REVERT: D 245 ASP cc_start: 0.7757 (p0) cc_final: 0.7492 (m-30) REVERT: D 267 HIS cc_start: 0.7923 (t70) cc_final: 0.7636 (t70) REVERT: D 440 LEU cc_start: 0.8731 (tp) cc_final: 0.8489 (tt) REVERT: E 18 LYS cc_start: 0.7740 (tttt) cc_final: 0.6809 (tmmt) REVERT: E 56 ASP cc_start: 0.9151 (p0) cc_final: 0.8925 (p0) REVERT: E 115 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8612 (tmm) REVERT: E 137 MET cc_start: 0.8947 (mmp) cc_final: 0.8670 (mmp) REVERT: E 215 LYS cc_start: 0.9083 (tttt) cc_final: 0.8574 (tptp) REVERT: E 243 ASN cc_start: 0.8286 (t0) cc_final: 0.7876 (t0) REVERT: E 245 ASP cc_start: 0.8275 (m-30) cc_final: 0.7632 (p0) REVERT: E 267 HIS cc_start: 0.7972 (t70) cc_final: 0.7712 (t70) REVERT: A 90 GLN cc_start: 0.8966 (mt0) cc_final: 0.8598 (mp10) REVERT: A 429 ILE cc_start: 0.8592 (pt) cc_final: 0.8369 (pp) REVERT: A 440 LEU cc_start: 0.8519 (tp) cc_final: 0.8290 (tt) outliers start: 36 outliers final: 16 residues processed: 365 average time/residue: 1.3831 time to fit residues: 567.3452 Evaluate side-chains 361 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 340 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 165 GLU Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain M residue 408 SER 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 165 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 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 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 244 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 151 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.144443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106639 restraints weight = 17678.473| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.27 r_work: 0.2812 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19280 Z= 0.240 Angle : 0.644 6.068 26265 Z= 0.338 Chirality : 0.049 0.155 2965 Planarity : 0.005 0.052 3235 Dihedral : 8.980 68.310 3170 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.68 % Allowed : 9.57 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2240 helix: 1.62 (0.21), residues: 615 sheet: 0.75 (0.19), residues: 660 loop : 0.18 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 426 HIS 0.006 0.001 HIS D 107 PHE 0.019 0.002 PHE C 221 TYR 0.032 0.003 TYR D 299 ARG 0.010 0.001 ARG B 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 3.06321 ( 30) link_ALPHA1-6 : bond 0.00366 ( 5) link_ALPHA1-6 : angle 1.51235 ( 15) link_BETA1-4 : bond 0.00838 ( 10) link_BETA1-4 : angle 3.04618 ( 30) link_ALPHA1-3 : bond 0.00236 ( 5) link_ALPHA1-3 : angle 1.81074 ( 15) hydrogen bonds : bond 0.05059 ( 885) hydrogen bonds : angle 4.69165 ( 2970) SS BOND : bond 0.00313 ( 10) SS BOND : angle 1.43237 ( 20) covalent geometry : bond 0.00541 (19240) covalent geometry : angle 0.62513 (26155) *********************** 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 395 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 342 time to evaluate : 2.278 Fit side-chains REVERT: B 18 LYS cc_start: 0.7715 (tttt) cc_final: 0.6962 (tmmt) REVERT: B 165 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8461 (mm-30) REVERT: B 267 HIS cc_start: 0.7860 (t70) cc_final: 0.7463 (m170) REVERT: K 415 THR cc_start: 0.8289 (m) cc_final: 0.7990 (t) REVERT: K 447 TYR cc_start: 0.8551 (m-80) cc_final: 0.8336 (m-80) REVERT: O 468 LEU cc_start: 0.6468 (tp) cc_final: 0.5962 (tp) REVERT: N 415 THR cc_start: 0.8238 (m) cc_final: 0.7831 (t) REVERT: N 433 GLU cc_start: 0.7910 (tt0) cc_final: 0.6908 (tm-30) REVERT: L 433 GLU cc_start: 0.7834 (tt0) cc_final: 0.7250 (tt0) REVERT: C 18 LYS cc_start: 0.7781 (tttt) cc_final: 0.7070 (tmmt) REVERT: C 90 GLN cc_start: 0.9009 (mt0) cc_final: 0.8716 (mp10) REVERT: C 261 MET cc_start: 0.9245 (mmt) cc_final: 0.8782 (mmm) REVERT: C 440 LEU cc_start: 0.8631 (tp) cc_final: 0.8327 (tt) REVERT: D 18 LYS cc_start: 0.7659 (tttt) cc_final: 0.6988 (tmmt) REVERT: D 165 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8375 (mm-30) REVERT: D 243 ASN cc_start: 0.8340 (t0) cc_final: 0.8071 (t0) REVERT: D 244 TYR cc_start: 0.8470 (p90) cc_final: 0.8206 (p90) REVERT: D 245 ASP cc_start: 0.7826 (p0) cc_final: 0.7555 (m-30) REVERT: D 267 HIS cc_start: 0.7896 (t70) cc_final: 0.7640 (t70) REVERT: D 440 LEU cc_start: 0.8752 (tp) cc_final: 0.8505 (tt) REVERT: E 18 LYS cc_start: 0.7812 (tttt) cc_final: 0.6921 (tmmt) REVERT: E 48 ASP cc_start: 0.7711 (m-30) cc_final: 0.7063 (m-30) REVERT: E 56 ASP cc_start: 0.9188 (p0) cc_final: 0.8968 (p0) REVERT: E 115 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8731 (tmm) REVERT: E 165 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8421 (mm-30) REVERT: E 215 LYS cc_start: 0.9128 (tttt) cc_final: 0.8571 (tptp) REVERT: E 243 ASN cc_start: 0.8395 (t0) cc_final: 0.8007 (t0) REVERT: E 245 ASP cc_start: 0.8425 (m-30) cc_final: 0.7746 (p0) REVERT: E 267 HIS cc_start: 0.8091 (t70) cc_final: 0.7750 (t70) REVERT: A 90 GLN cc_start: 0.8987 (mt0) cc_final: 0.8604 (mp10) REVERT: A 165 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8508 (mm-30) REVERT: A 429 ILE cc_start: 0.8652 (pt) cc_final: 0.8341 (pp) REVERT: A 440 LEU cc_start: 0.8552 (tp) cc_final: 0.8323 (tt) outliers start: 53 outliers final: 29 residues processed: 355 average time/residue: 1.3554 time to fit residues: 538.7822 Evaluate side-chains 369 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 335 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 429 ILE 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 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 59 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 141 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 180 optimal weight: 0.3980 chunk 210 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.145958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.111081 restraints weight = 17637.579| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.86 r_work: 0.2817 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19280 Z= 0.138 Angle : 0.550 6.217 26265 Z= 0.290 Chirality : 0.045 0.163 2965 Planarity : 0.004 0.042 3235 Dihedral : 8.333 63.697 3170 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.08 % Allowed : 10.73 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2240 helix: 1.80 (0.22), residues: 615 sheet: 0.71 (0.19), residues: 665 loop : 0.30 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.002 0.001 HIS E 119 PHE 0.015 0.001 PHE A 98 TYR 0.028 0.002 TYR E 299 ARG 0.006 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 10) link_NAG-ASN : angle 2.64320 ( 30) link_ALPHA1-6 : bond 0.00614 ( 5) link_ALPHA1-6 : angle 1.34162 ( 15) link_BETA1-4 : bond 0.00403 ( 10) link_BETA1-4 : angle 2.35168 ( 30) link_ALPHA1-3 : bond 0.00613 ( 5) link_ALPHA1-3 : angle 1.55350 ( 15) hydrogen bonds : bond 0.04219 ( 885) hydrogen bonds : angle 4.48916 ( 2970) SS BOND : bond 0.00372 ( 10) SS BOND : angle 0.77129 ( 20) covalent geometry : bond 0.00297 (19240) covalent geometry : angle 0.53575 (26155) *********************** 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 385 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 1.948 Fit side-chains REVERT: B 18 LYS cc_start: 0.7736 (tttt) cc_final: 0.6991 (tmmt) REVERT: B 165 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8474 (mm-30) REVERT: B 267 HIS cc_start: 0.7904 (t70) cc_final: 0.7516 (m170) REVERT: B 268 LEU cc_start: 0.8516 (tp) cc_final: 0.8257 (tm) REVERT: K 415 THR cc_start: 0.8197 (m) cc_final: 0.7887 (t) REVERT: K 433 GLU cc_start: 0.7812 (tt0) cc_final: 0.6894 (tm-30) REVERT: O 468 LEU cc_start: 0.6585 (tp) cc_final: 0.6001 (tp) REVERT: N 415 THR cc_start: 0.8075 (m) cc_final: 0.7743 (t) REVERT: N 433 GLU cc_start: 0.7954 (tt0) cc_final: 0.6993 (tm-30) REVERT: C 18 LYS cc_start: 0.7794 (tttt) cc_final: 0.7067 (tmmt) REVERT: C 90 GLN cc_start: 0.9025 (mt0) cc_final: 0.8749 (mp10) REVERT: C 261 MET cc_start: 0.9228 (mmt) cc_final: 0.8808 (mmm) REVERT: C 440 LEU cc_start: 0.8623 (tp) cc_final: 0.8338 (tt) REVERT: D 18 LYS cc_start: 0.7581 (tttt) cc_final: 0.6900 (tmmt) REVERT: D 59 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8945 (tt) REVERT: D 165 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8379 (mm-30) REVERT: D 243 ASN cc_start: 0.8346 (t0) cc_final: 0.8054 (t0) REVERT: D 244 TYR cc_start: 0.8430 (p90) cc_final: 0.8176 (p90) REVERT: D 245 ASP cc_start: 0.7928 (p0) cc_final: 0.7646 (m-30) REVERT: D 267 HIS cc_start: 0.7965 (t70) cc_final: 0.7722 (t70) REVERT: D 440 LEU cc_start: 0.8746 (tp) cc_final: 0.8526 (tt) REVERT: E 18 LYS cc_start: 0.7960 (tttt) cc_final: 0.6996 (tmmt) REVERT: E 56 ASP cc_start: 0.9210 (p0) cc_final: 0.8999 (p0) REVERT: E 115 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8729 (tmm) REVERT: E 165 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8425 (mm-30) REVERT: E 215 LYS cc_start: 0.9145 (tttt) cc_final: 0.8632 (tptp) REVERT: E 243 ASN cc_start: 0.8390 (t0) cc_final: 0.7986 (t0) REVERT: E 245 ASP cc_start: 0.8362 (m-30) cc_final: 0.7723 (p0) REVERT: E 267 HIS cc_start: 0.8206 (t70) cc_final: 0.7924 (t70) REVERT: A 90 GLN cc_start: 0.9023 (mt0) cc_final: 0.8638 (mp10) REVERT: A 165 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: A 429 ILE cc_start: 0.8638 (pt) cc_final: 0.8403 (pp) REVERT: A 440 LEU cc_start: 0.8612 (tp) cc_final: 0.8359 (tt) outliers start: 41 outliers final: 25 residues processed: 358 average time/residue: 1.3969 time to fit residues: 558.2958 Evaluate side-chains 363 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 332 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER 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 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 78 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 0.0980 chunk 180 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 243 ASN C 265 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 = 0.3537 r_free = 0.3537 target = 0.143363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.104368 restraints weight = 17429.315| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.26 r_work: 0.2774 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 19280 Z= 0.288 Angle : 0.695 7.151 26265 Z= 0.363 Chirality : 0.051 0.161 2965 Planarity : 0.005 0.053 3235 Dihedral : 9.361 69.908 3170 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.78 % Allowed : 10.18 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 2240 helix: 1.59 (0.21), residues: 615 sheet: 0.63 (0.19), residues: 685 loop : 0.30 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 426 HIS 0.005 0.001 HIS D 107 PHE 0.022 0.002 PHE C 221 TYR 0.035 0.003 TYR D 299 ARG 0.010 0.001 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 10) link_NAG-ASN : angle 3.22366 ( 30) link_ALPHA1-6 : bond 0.00224 ( 5) link_ALPHA1-6 : angle 1.63384 ( 15) link_BETA1-4 : bond 0.01014 ( 10) link_BETA1-4 : angle 3.33113 ( 30) link_ALPHA1-3 : bond 0.00115 ( 5) link_ALPHA1-3 : angle 1.80701 ( 15) hydrogen bonds : bond 0.05335 ( 885) hydrogen bonds : angle 4.81358 ( 2970) SS BOND : bond 0.00357 ( 10) SS BOND : angle 1.43746 ( 20) covalent geometry : bond 0.00657 (19240) covalent geometry : angle 0.67506 (26155) *********************** 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 389 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 334 time to evaluate : 2.007 Fit side-chains REVERT: B 18 LYS cc_start: 0.7733 (tttt) cc_final: 0.6966 (tmmt) REVERT: B 165 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8474 (mm-30) REVERT: B 267 HIS cc_start: 0.7932 (t70) cc_final: 0.7475 (m170) REVERT: K 415 THR cc_start: 0.8344 (m) cc_final: 0.8044 (t) REVERT: K 447 TYR cc_start: 0.8579 (m-80) cc_final: 0.8333 (m-80) REVERT: O 468 LEU cc_start: 0.6501 (tp) cc_final: 0.5958 (tp) REVERT: N 415 THR cc_start: 0.8201 (m) cc_final: 0.7827 (t) REVERT: N 433 GLU cc_start: 0.7972 (tt0) cc_final: 0.7050 (tm-30) REVERT: L 433 GLU cc_start: 0.7875 (tt0) cc_final: 0.7304 (tt0) REVERT: C 18 LYS cc_start: 0.7786 (tttt) cc_final: 0.7066 (tmmt) REVERT: C 90 GLN cc_start: 0.9038 (mt0) cc_final: 0.8697 (mp10) REVERT: C 261 MET cc_start: 0.9257 (mmt) cc_final: 0.8947 (mmp) REVERT: C 267 HIS cc_start: 0.7852 (t70) cc_final: 0.7398 (m170) REVERT: C 440 LEU cc_start: 0.8661 (tp) cc_final: 0.8369 (tt) REVERT: D 18 LYS cc_start: 0.7830 (tttt) cc_final: 0.7159 (tmmt) REVERT: D 90 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8623 (mp10) REVERT: D 165 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8432 (mm-30) REVERT: D 243 ASN cc_start: 0.8420 (t0) cc_final: 0.8089 (t0) REVERT: D 244 TYR cc_start: 0.8494 (p90) cc_final: 0.8293 (p90) REVERT: D 267 HIS cc_start: 0.7955 (t70) cc_final: 0.7507 (t70) REVERT: D 440 LEU cc_start: 0.8767 (tp) cc_final: 0.8527 (tt) REVERT: E 18 LYS cc_start: 0.7832 (tttt) cc_final: 0.6915 (tmmt) REVERT: E 48 ASP cc_start: 0.7772 (m-30) cc_final: 0.7051 (m-30) REVERT: E 56 ASP cc_start: 0.9197 (p0) cc_final: 0.8979 (p0) REVERT: E 115 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8767 (tmm) REVERT: E 165 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8449 (mm-30) REVERT: E 215 LYS cc_start: 0.9148 (tttt) cc_final: 0.8596 (tptp) REVERT: E 243 ASN cc_start: 0.8470 (t0) cc_final: 0.8075 (t0) REVERT: E 245 ASP cc_start: 0.8478 (m-30) cc_final: 0.7806 (p0) REVERT: E 267 HIS cc_start: 0.8166 (t70) cc_final: 0.7892 (t70) REVERT: A 90 GLN cc_start: 0.9058 (mt0) cc_final: 0.8702 (mp10) REVERT: A 165 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: A 440 LEU cc_start: 0.8652 (tp) cc_final: 0.8387 (tt) outliers start: 55 outliers final: 31 residues processed: 354 average time/residue: 1.3770 time to fit residues: 544.8164 Evaluate side-chains 363 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 326 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET 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 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 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 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 59 LEU Chi-restraints excluded: chain D residue 90 GLN 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 97 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN C 243 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 = 0.3568 r_free = 0.3568 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.113031 restraints weight = 17756.366| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.72 r_work: 0.2829 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19280 Z= 0.128 Angle : 0.548 7.829 26265 Z= 0.289 Chirality : 0.045 0.171 2965 Planarity : 0.003 0.037 3235 Dihedral : 8.267 62.807 3170 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.92 % Allowed : 10.73 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2240 helix: 1.91 (0.22), residues: 610 sheet: 0.70 (0.19), residues: 665 loop : 0.30 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.003 0.001 HIS C 107 PHE 0.014 0.001 PHE A 98 TYR 0.026 0.002 TYR C 299 ARG 0.006 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 10) link_NAG-ASN : angle 2.56369 ( 30) link_ALPHA1-6 : bond 0.00632 ( 5) link_ALPHA1-6 : angle 1.31842 ( 15) link_BETA1-4 : bond 0.00344 ( 10) link_BETA1-4 : angle 2.22986 ( 30) link_ALPHA1-3 : bond 0.00711 ( 5) link_ALPHA1-3 : angle 1.45103 ( 15) hydrogen bonds : bond 0.04044 ( 885) hydrogen bonds : angle 4.46183 ( 2970) SS BOND : bond 0.00255 ( 10) SS BOND : angle 0.71926 ( 20) covalent geometry : bond 0.00274 (19240) covalent geometry : angle 0.53453 (26155) *********************** 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: 38 poor density : 340 time to evaluate : 1.906 Fit side-chains REVERT: B 18 LYS cc_start: 0.7712 (tttt) cc_final: 0.6967 (tmmt) REVERT: B 165 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8441 (mm-30) REVERT: B 224 GLN cc_start: 0.8837 (tp40) cc_final: 0.8624 (tp-100) REVERT: B 267 HIS cc_start: 0.7914 (t70) cc_final: 0.7425 (m170) REVERT: K 415 THR cc_start: 0.8158 (m) cc_final: 0.7853 (t) REVERT: K 433 GLU cc_start: 0.7835 (tt0) cc_final: 0.6798 (tm-30) REVERT: O 468 LEU cc_start: 0.6418 (tp) cc_final: 0.5859 (tp) REVERT: N 415 THR cc_start: 0.8044 (m) cc_final: 0.7697 (t) REVERT: N 433 GLU cc_start: 0.8029 (tt0) cc_final: 0.7017 (tm-30) REVERT: L 433 GLU cc_start: 0.7873 (tt0) cc_final: 0.7351 (tt0) REVERT: C 18 LYS cc_start: 0.7815 (tttt) cc_final: 0.7095 (tmmt) REVERT: C 20 LEU cc_start: 0.8877 (mt) cc_final: 0.8675 (mp) REVERT: C 90 GLN cc_start: 0.9020 (mt0) cc_final: 0.8746 (mp10) REVERT: C 261 MET cc_start: 0.9212 (mmt) cc_final: 0.8762 (mmm) REVERT: C 267 HIS cc_start: 0.7765 (t70) cc_final: 0.7461 (m170) REVERT: D 18 LYS cc_start: 0.7643 (tttt) cc_final: 0.6946 (tmmt) REVERT: D 59 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8926 (tt) REVERT: D 165 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: D 243 ASN cc_start: 0.8234 (t0) cc_final: 0.7881 (t0) REVERT: D 244 TYR cc_start: 0.8388 (p90) cc_final: 0.8140 (p90) REVERT: D 267 HIS cc_start: 0.7901 (t70) cc_final: 0.7458 (t70) REVERT: D 440 LEU cc_start: 0.8730 (tp) cc_final: 0.8519 (tt) REVERT: E 18 LYS cc_start: 0.7964 (tttt) cc_final: 0.7054 (tmmt) REVERT: E 48 ASP cc_start: 0.7742 (m-30) cc_final: 0.7023 (m-30) REVERT: E 56 ASP cc_start: 0.9186 (p0) cc_final: 0.8971 (p0) REVERT: E 115 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8694 (tmm) REVERT: E 165 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8362 (mm-30) REVERT: E 215 LYS cc_start: 0.9119 (tttt) cc_final: 0.8593 (tptp) REVERT: E 243 ASN cc_start: 0.8386 (t0) cc_final: 0.7992 (t0) REVERT: E 245 ASP cc_start: 0.8290 (m-30) cc_final: 0.7707 (p0) REVERT: E 267 HIS cc_start: 0.8148 (t70) cc_final: 0.7854 (t70) REVERT: A 90 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: A 165 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8471 (mm-30) REVERT: A 440 LEU cc_start: 0.8604 (tp) cc_final: 0.8348 (tt) outliers start: 38 outliers final: 23 residues processed: 352 average time/residue: 1.3713 time to fit residues: 540.4191 Evaluate side-chains 363 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 333 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET 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 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 C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS 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 59 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 A residue 90 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 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 = 0.3579 r_free = 0.3579 target = 0.146974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108553 restraints weight = 17606.953| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.18 r_work: 0.2801 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19280 Z= 0.128 Angle : 0.547 7.940 26265 Z= 0.287 Chirality : 0.045 0.183 2965 Planarity : 0.003 0.045 3235 Dihedral : 7.869 59.226 3170 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.03 % Allowed : 10.89 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2240 helix: 1.82 (0.22), residues: 615 sheet: 0.73 (0.19), residues: 665 loop : 0.29 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.002 0.001 HIS E 119 PHE 0.015 0.001 PHE A 98 TYR 0.028 0.002 TYR E 299 ARG 0.006 0.000 ARG E 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 10) link_NAG-ASN : angle 2.51220 ( 30) link_ALPHA1-6 : bond 0.00746 ( 5) link_ALPHA1-6 : angle 1.30489 ( 15) link_BETA1-4 : bond 0.00369 ( 10) link_BETA1-4 : angle 2.25637 ( 30) link_ALPHA1-3 : bond 0.00673 ( 5) link_ALPHA1-3 : angle 1.61923 ( 15) hydrogen bonds : bond 0.04020 ( 885) hydrogen bonds : angle 4.39810 ( 2970) SS BOND : bond 0.00227 ( 10) SS BOND : angle 0.66947 ( 20) covalent geometry : bond 0.00276 (19240) covalent geometry : angle 0.53394 (26155) *********************** 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 375 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 2.091 Fit side-chains REVERT: B 18 LYS cc_start: 0.7705 (tttt) cc_final: 0.6875 (tmmt) REVERT: B 165 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8505 (mm-30) REVERT: B 224 GLN cc_start: 0.8860 (tp40) cc_final: 0.8638 (tp-100) REVERT: B 267 HIS cc_start: 0.7930 (t70) cc_final: 0.7598 (t-170) REVERT: K 415 THR cc_start: 0.8112 (m) cc_final: 0.7791 (t) REVERT: K 433 GLU cc_start: 0.7881 (tt0) cc_final: 0.6898 (tm-30) REVERT: O 468 LEU cc_start: 0.6446 (tp) cc_final: 0.5804 (tp) REVERT: N 415 THR cc_start: 0.8024 (m) cc_final: 0.7662 (t) REVERT: N 433 GLU cc_start: 0.7995 (tt0) cc_final: 0.7036 (tm-30) REVERT: L 433 GLU cc_start: 0.7980 (tt0) cc_final: 0.7462 (tt0) REVERT: C 18 LYS cc_start: 0.7808 (tttt) cc_final: 0.7065 (tmmt) REVERT: C 90 GLN cc_start: 0.9040 (mt0) cc_final: 0.8719 (mp10) REVERT: C 115 MET cc_start: 0.9132 (ttm) cc_final: 0.8841 (tmm) REVERT: C 261 MET cc_start: 0.9248 (mmt) cc_final: 0.8844 (mmm) REVERT: C 267 HIS cc_start: 0.7907 (t70) cc_final: 0.7351 (m170) REVERT: C 440 LEU cc_start: 0.8700 (tt) cc_final: 0.8487 (tt) REVERT: D 18 LYS cc_start: 0.7622 (tttt) cc_final: 0.6900 (tmmt) REVERT: D 59 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8946 (tt) REVERT: D 115 MET cc_start: 0.9266 (tmm) cc_final: 0.9058 (ppp) REVERT: D 165 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8411 (mm-30) REVERT: D 243 ASN cc_start: 0.8122 (t0) cc_final: 0.7770 (t0) REVERT: D 244 TYR cc_start: 0.8393 (p90) cc_final: 0.8094 (p90) REVERT: D 267 HIS cc_start: 0.7969 (t70) cc_final: 0.7498 (t70) REVERT: D 301 PHE cc_start: 0.8798 (t80) cc_final: 0.8542 (t80) REVERT: D 440 LEU cc_start: 0.8712 (tp) cc_final: 0.8505 (tt) REVERT: E 18 LYS cc_start: 0.7906 (tttt) cc_final: 0.6917 (tmmt) REVERT: E 48 ASP cc_start: 0.7835 (m-30) cc_final: 0.7131 (m-30) REVERT: E 56 ASP cc_start: 0.9227 (p0) cc_final: 0.9021 (p0) REVERT: E 115 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8862 (tmm) REVERT: E 165 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: E 215 LYS cc_start: 0.9159 (tttt) cc_final: 0.8617 (tptp) REVERT: E 243 ASN cc_start: 0.8490 (t0) cc_final: 0.8115 (t0) REVERT: E 245 ASP cc_start: 0.8321 (m-30) cc_final: 0.7661 (p0) REVERT: E 267 HIS cc_start: 0.8181 (t70) cc_final: 0.7888 (t70) REVERT: A 90 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8673 (mp10) REVERT: A 165 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: A 429 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8387 (pp) REVERT: A 440 LEU cc_start: 0.8598 (tp) cc_final: 0.8352 (tt) outliers start: 40 outliers final: 29 residues processed: 349 average time/residue: 1.4003 time to fit residues: 546.2415 Evaluate side-chains 370 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 333 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET 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 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 C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS 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 59 LEU 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 D residue 302 VAL 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 90 GLN 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 208 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 153 optimal weight: 0.0770 chunk 9 optimal weight: 4.9990 chunk 190 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 B 265 ASN C 243 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 = 0.3617 r_free = 0.3617 target = 0.150135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.112305 restraints weight = 17572.777| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.15 r_work: 0.2864 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19280 Z= 0.100 Angle : 0.507 7.883 26265 Z= 0.265 Chirality : 0.044 0.222 2965 Planarity : 0.003 0.047 3235 Dihedral : 6.927 51.060 3170 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.52 % Allowed : 11.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2240 helix: 1.86 (0.22), residues: 615 sheet: 1.02 (0.20), residues: 625 loop : 0.13 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 168 HIS 0.002 0.000 HIS B 267 PHE 0.017 0.001 PHE C 301 TYR 0.023 0.001 TYR E 299 ARG 0.010 0.000 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 10) link_NAG-ASN : angle 2.08307 ( 30) link_ALPHA1-6 : bond 0.01010 ( 5) link_ALPHA1-6 : angle 1.20761 ( 15) link_BETA1-4 : bond 0.00323 ( 10) link_BETA1-4 : angle 1.68760 ( 30) link_ALPHA1-3 : bond 0.01032 ( 5) link_ALPHA1-3 : angle 1.45031 ( 15) hydrogen bonds : bond 0.03514 ( 885) hydrogen bonds : angle 4.21757 ( 2970) SS BOND : bond 0.00204 ( 10) SS BOND : angle 0.42745 ( 20) covalent geometry : bond 0.00208 (19240) covalent geometry : angle 0.49740 (26155) ********************** 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 384 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 354 time to evaluate : 2.765 Fit side-chains REVERT: B 18 LYS cc_start: 0.7740 (tttt) cc_final: 0.6894 (tmmt) REVERT: B 49 MET cc_start: 0.8194 (tmm) cc_final: 0.7988 (pp-130) REVERT: B 90 GLN cc_start: 0.9056 (mt0) cc_final: 0.8762 (mp10) REVERT: B 224 GLN cc_start: 0.8830 (tp40) cc_final: 0.8610 (tp-100) REVERT: K 415 THR cc_start: 0.8078 (m) cc_final: 0.7705 (t) REVERT: K 433 GLU cc_start: 0.7754 (tt0) cc_final: 0.6877 (tm-30) REVERT: O 415 THR cc_start: 0.7982 (m) cc_final: 0.7423 (t) REVERT: O 468 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5738 (tp) REVERT: N 415 THR cc_start: 0.7895 (m) cc_final: 0.7419 (t) REVERT: N 433 GLU cc_start: 0.8033 (tt0) cc_final: 0.7008 (tm-30) REVERT: C 18 LYS cc_start: 0.7731 (tttt) cc_final: 0.6991 (tmmt) REVERT: C 68 ARG cc_start: 0.8927 (ttm170) cc_final: 0.8662 (tpp80) REVERT: C 90 GLN cc_start: 0.9014 (mt0) cc_final: 0.8753 (mp10) REVERT: C 115 MET cc_start: 0.9069 (ttm) cc_final: 0.8780 (tmm) REVERT: C 261 MET cc_start: 0.9203 (mmt) cc_final: 0.8772 (mmm) REVERT: C 267 HIS cc_start: 0.7885 (t70) cc_final: 0.7394 (m170) REVERT: C 298 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8996 (tm-30) REVERT: D 18 LYS cc_start: 0.7613 (tttt) cc_final: 0.6888 (tmmt) REVERT: D 59 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8929 (tt) REVERT: D 243 ASN cc_start: 0.7978 (t0) cc_final: 0.7744 (t0) REVERT: D 244 TYR cc_start: 0.8314 (p90) cc_final: 0.7980 (p90) REVERT: D 267 HIS cc_start: 0.7945 (t70) cc_final: 0.7500 (t70) REVERT: D 301 PHE cc_start: 0.8782 (t80) cc_final: 0.8497 (t80) REVERT: E 18 LYS cc_start: 0.7842 (tttt) cc_final: 0.6897 (tmmt) REVERT: E 48 ASP cc_start: 0.7808 (m-30) cc_final: 0.7116 (m-30) REVERT: E 56 ASP cc_start: 0.9195 (p0) cc_final: 0.8985 (p0) REVERT: E 115 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8828 (tmm) REVERT: E 215 LYS cc_start: 0.9131 (tttt) cc_final: 0.8603 (tptp) REVERT: E 243 ASN cc_start: 0.8401 (t0) cc_final: 0.8018 (t0) REVERT: E 245 ASP cc_start: 0.8314 (m-30) cc_final: 0.7626 (p0) REVERT: E 267 HIS cc_start: 0.8079 (t70) cc_final: 0.7825 (t70) REVERT: A 68 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8557 (tpp80) REVERT: A 429 ILE cc_start: 0.8600 (pt) cc_final: 0.8370 (pp) REVERT: A 440 LEU cc_start: 0.8571 (tp) cc_final: 0.8341 (tt) outliers start: 30 outliers final: 21 residues processed: 363 average time/residue: 1.5059 time to fit residues: 611.7979 Evaluate side-chains 365 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU 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 C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS 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 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET 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 190 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 152 optimal weight: 0.0970 chunk 86 optimal weight: 7.9990 chunk 224 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 A 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 = 0.3566 r_free = 0.3566 target = 0.145884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107634 restraints weight = 17500.736| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.23 r_work: 0.2816 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19280 Z= 0.179 Angle : 0.597 8.178 26265 Z= 0.310 Chirality : 0.047 0.194 2965 Planarity : 0.004 0.057 3235 Dihedral : 7.585 54.798 3170 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.72 % Allowed : 12.05 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2240 helix: 1.81 (0.22), residues: 615 sheet: 0.84 (0.19), residues: 660 loop : 0.32 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 241 HIS 0.004 0.001 HIS E 119 PHE 0.018 0.002 PHE C 301 TYR 0.031 0.002 TYR E 299 ARG 0.006 0.001 ARG A 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 10) link_NAG-ASN : angle 2.81436 ( 30) link_ALPHA1-6 : bond 0.00725 ( 5) link_ALPHA1-6 : angle 1.33085 ( 15) link_BETA1-4 : bond 0.00567 ( 10) link_BETA1-4 : angle 2.49305 ( 30) link_ALPHA1-3 : bond 0.00539 ( 5) link_ALPHA1-3 : angle 1.82526 ( 15) hydrogen bonds : bond 0.04378 ( 885) hydrogen bonds : angle 4.45375 ( 2970) SS BOND : bond 0.00279 ( 10) SS BOND : angle 0.88456 ( 20) covalent geometry : bond 0.00398 (19240) covalent geometry : angle 0.58122 (26155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19261.26 seconds wall clock time: 332 minutes 32.86 seconds (19952.86 seconds total)