Starting phenix.real_space_refine on Sat Sep 12 22:07:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qfa_4542/09_2026/6qfa_4542.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 12130 2.51 5 N 3060 2.21 5 O 3465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18755 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "D" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "E" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "A" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.99, per 1000 atoms: 0.21 Number of scatterers: 18755 At special positions: 0 Unit cell: (143.38, 138.03, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3465 8.00 N 3060 7.00 C 12130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 80 " " NAG B 501 " - " ASN B 80 " " NAG C 501 " - " ASN C 80 " " NAG D 501 " - " ASN D 80 " " NAG E 501 " - " ASN E 80 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN C 149 " " NAG H 1 " - " ASN D 149 " " NAG I 1 " - " ASN E 149 " " NAG J 1 " - " ASN A 149 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 659.0 milliseconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 30 sheets defined 31.7% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 removed outlier: 3.620A pdb=" N ALA B 73 " --> pdb=" O LYS B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.581A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.687A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.841A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 447 removed outlier: 4.108A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.541A pdb=" N VAL B 447 " --> pdb=" O TRP B 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 497 No H-bonds generated for 'chain 'K' and resid 495 through 497' Processing helix chain 'O' and resid 495 through 497 No H-bonds generated for 'chain 'O' and resid 495 through 497' Processing helix chain 'N' and resid 495 through 497 No H-bonds generated for 'chain 'N' and resid 495 through 497' Processing helix chain 'M' and resid 495 through 497 No H-bonds generated for 'chain 'M' and resid 495 through 497' Processing helix chain 'L' and resid 495 through 497 No H-bonds generated for 'chain 'L' and resid 495 through 497' Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 removed outlier: 3.620A pdb=" N ALA C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.790A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 236 Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 246 through 271 removed outlier: 3.853A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 447 removed outlier: 4.108A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix removed outlier: 3.541A pdb=" N VAL C 447 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 21 Processing helix chain 'D' and resid 70 through 73 removed outlier: 3.620A pdb=" N ALA D 73 " --> pdb=" O LYS D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.687A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 246 through 271 removed outlier: 3.582A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 447 removed outlier: 4.108A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix removed outlier: 3.541A pdb=" N VAL D 447 " --> pdb=" O TRP D 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.621A pdb=" N ALA E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.687A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 246 through 271 removed outlier: 3.576A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR E 271 " --> pdb=" O HIS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 447 removed outlier: 4.109A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix removed outlier: 3.542A pdb=" N VAL E 447 " --> pdb=" O TRP E 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 70 through 73 removed outlier: 3.621A pdb=" N ALA A 73 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.580A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.688A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 246 through 271 removed outlier: 3.587A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 removed outlier: 3.579A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 447 removed outlier: 4.109A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.541A pdb=" N VAL A 447 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.873A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL B 106 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ARG B 129 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AA5, first strand: chain 'K' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR K 506 " --> pdb=" O TYR K 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'O' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 480 " --> pdb=" O GLN O 426 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR O 501 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 480 " --> pdb=" O GLN O 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR O 506 " --> pdb=" O TYR O 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 2 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 480 " --> pdb=" O GLN N 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 480 " --> pdb=" O GLN N 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR N 506 " --> pdb=" O TYR N 481 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AB5, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 445 through 447 removed outlier: 5.241A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR M 506 " --> pdb=" O TYR M 481 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 445 through 447 removed outlier: 5.242A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR L 506 " --> pdb=" O TYR L 481 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.259A pdb=" N ASP C 101 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA C 135 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.890A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL D 106 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ARG D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP D 56 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET D 49 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.868A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL E 106 " --> pdb=" O ARG E 129 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG E 129 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.520A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.852A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2970 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 2.05 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 - 17.43: 10414 17.43 - 34.86: 485 34.86 - 52.29: 66 52.29 - 69.72: 15 69.72 - 87.15: 10 Dihedral angle restraints: 10990 sinusoidal: 4345 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 10987 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'A' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'N' selection = chain 'M' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.280 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 10.797 87.147 6730 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.16), residues: 2240 helix: -3.79 (0.11), residues: 615 sheet: 0.39 (0.19), residues: 670 loop : -0.92 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.020 0.002 TYR D 299 PHE 0.011 0.002 PHE D 105 TRP 0.011 0.001 TRP C 426 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.36 (19240) covalent geometry : angle 0.79981 / 0.50 (26155) SS BOND : bond 0.00039 / 0.02 ( 10) SS BOND : angle 0.65645 / 0.44 ( 20) hydrogen bonds : bond 0.27035 / 17.93 ( 885) hydrogen bonds : angle 8.92379 / 6.12 ( 2970) link_ALPHA1-3 : bond 0.05915 / 3.24 ( 5) link_ALPHA1-3 : angle 1.98031 / 1.32 ( 15) link_ALPHA1-6 : bond 0.05998 / 3.29 ( 5) link_ALPHA1-6 : angle 1.92579 / 1.22 ( 15) link_BETA1-4 : bond 0.05984 / 3.49 ( 10) link_BETA1-4 : angle 3.28600 / 2.17 ( 30) link_NAG-ASN : bond 0.01554 / 0.86 ( 10) link_NAG-ASN : angle 4.37911 / 3.13 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.746 Fit side-chains REVERT: B 18 LYS cc_start: 0.7636 (tttt) cc_final: 0.7200 (tmmt) REVERT: B 137 MET cc_start: 0.8335 (mmp) cc_final: 0.8078 (mmp) REVERT: B 179 GLU cc_start: 0.8062 (pm20) cc_final: 0.7826 (pm20) REVERT: B 261 MET cc_start: 0.8936 (mmt) cc_final: 0.8675 (tpp) REVERT: K 425 ARG cc_start: 0.7749 (ptt180) cc_final: 0.7547 (ptt180) REVERT: N 447 TYR cc_start: 0.8366 (m-80) cc_final: 0.7743 (m-80) REVERT: C 18 LYS cc_start: 0.7631 (tttt) cc_final: 0.7125 (tmmt) REVERT: C 52 GLU cc_start: 0.8573 (mp0) cc_final: 0.8340 (mp0) REVERT: C 90 GLN cc_start: 0.8795 (mt0) cc_final: 0.8582 (mp10) REVERT: C 261 MET cc_start: 0.9027 (mmt) cc_final: 0.8640 (mmm) REVERT: C 298 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8626 (tm-30) REVERT: C 440 LEU cc_start: 0.8282 (tp) cc_final: 0.8033 (tt) REVERT: D 18 LYS cc_start: 0.7585 (tttt) cc_final: 0.7025 (tmmt) REVERT: D 48 ASP cc_start: 0.7187 (m-30) cc_final: 0.6931 (m-30) REVERT: D 52 GLU cc_start: 0.8570 (mp0) cc_final: 0.8326 (mp0) REVERT: D 115 MET cc_start: 0.8581 (ttm) cc_final: 0.8375 (tmm) REVERT: D 243 ASN cc_start: 0.7858 (t0) cc_final: 0.7219 (t0) REVERT: D 244 TYR cc_start: 0.7784 (p90) cc_final: 0.7551 (p90) REVERT: D 304 TYR cc_start: 0.8847 (t80) cc_final: 0.8469 (t80) REVERT: E 14 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6858 (mt-10) REVERT: E 56 ASP cc_start: 0.8763 (p0) cc_final: 0.8499 (p0) REVERT: E 90 GLN cc_start: 0.8782 (mt0) cc_final: 0.8466 (mp10) REVERT: E 115 MET cc_start: 0.8481 (ttm) cc_final: 0.7973 (tmm) REVERT: E 137 MET cc_start: 0.8428 (mmp) cc_final: 0.8017 (mmp) REVERT: E 215 LYS cc_start: 0.8619 (tttt) cc_final: 0.8390 (tptp) REVERT: E 243 ASN cc_start: 0.7594 (t0) cc_final: 0.7074 (t0) REVERT: E 244 TYR cc_start: 0.7806 (p90) cc_final: 0.7578 (p90) REVERT: E 245 ASP cc_start: 0.7627 (m-30) cc_final: 0.7320 (p0) REVERT: E 261 MET cc_start: 0.9010 (mmt) cc_final: 0.8764 (tpp) REVERT: E 283 MET cc_start: 0.8345 (mmm) cc_final: 0.8111 (mmm) REVERT: A 90 GLN cc_start: 0.8706 (mt0) cc_final: 0.8377 (mp10) REVERT: A 261 MET cc_start: 0.9017 (mmt) cc_final: 0.8742 (tpp) REVERT: A 283 MET cc_start: 0.8371 (mmm) cc_final: 0.8131 (mmm) REVERT: A 440 LEU cc_start: 0.8463 (tp) cc_final: 0.8190 (tt) outliers start: 0 outliers final: 2 residues processed: 353 average time/residue: 0.6025 time to fit residues: 239.4529 Evaluate side-chains 321 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN B 90 GLN B 185 GLN C 243 ASN C 265 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.145834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109700 restraints weight = 17669.117| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.25 r_work: 0.2834 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19280 Z= 0.203 Angle : 0.636 5.535 26265 Z= 0.341 Chirality : 0.047 0.155 2965 Planarity : 0.005 0.042 3235 Dihedral : 5.241 19.820 2574 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.82 % Allowed : 7.44 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2240 helix: -0.33 (0.18), residues: 615 sheet: 0.78 (0.20), residues: 645 loop : -0.40 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 269 TYR 0.028 0.002 TYR D 299 PHE 0.016 0.002 PHE C 221 TRP 0.009 0.002 TRP B 426 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (19240) covalent geometry : angle 0.61968 / 0.34 (26155) SS BOND : bond 0.00404 / 0.23 ( 10) SS BOND : angle 1.52404 / 1.11 ( 20) hydrogen bonds : bond 0.05969 / 3.89 ( 885) hydrogen bonds : angle 5.05648 / 3.51 ( 2970) link_ALPHA1-3 : bond 0.00197 / 0.10 ( 5) link_ALPHA1-3 : angle 1.57349 / 0.99 ( 15) link_ALPHA1-6 : bond 0.00321 / 0.17 ( 5) link_ALPHA1-6 : angle 1.73567 / 1.04 ( 15) link_BETA1-4 : bond 0.00761 / 0.46 ( 10) link_BETA1-4 : angle 2.43272 / 1.60 ( 30) link_NAG-ASN : bond 0.00294 / 0.16 ( 10) link_NAG-ASN : angle 3.10645 / 2.24 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 351 time to evaluate : 0.730 Fit side-chains REVERT: B 18 LYS cc_start: 0.7967 (tttt) cc_final: 0.7123 (tmmt) REVERT: B 70 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8613 (mmtt) REVERT: B 137 MET cc_start: 0.8972 (mmp) cc_final: 0.8643 (mmp) REVERT: B 261 MET cc_start: 0.9094 (mmt) cc_final: 0.8832 (tpp) REVERT: K 415 THR cc_start: 0.8499 (m) cc_final: 0.8096 (t) REVERT: K 447 TYR cc_start: 0.8527 (m-80) cc_final: 0.8250 (m-80) REVERT: N 421 MET cc_start: 0.9140 (mmt) cc_final: 0.8938 (tpp) REVERT: N 433 GLU cc_start: 0.7812 (tt0) cc_final: 0.6772 (tm-30) REVERT: N 447 TYR cc_start: 0.8526 (m-80) cc_final: 0.8084 (m-80) REVERT: L 425 ARG cc_start: 0.8183 (ptt180) cc_final: 0.7895 (ptt180) REVERT: L 433 GLU cc_start: 0.7658 (tt0) cc_final: 0.7458 (tt0) REVERT: C 18 LYS cc_start: 0.7713 (tttt) cc_final: 0.7035 (tmmt) REVERT: C 52 GLU cc_start: 0.8834 (mp0) cc_final: 0.8564 (mp0) REVERT: C 90 GLN cc_start: 0.8992 (mt0) cc_final: 0.8722 (mp10) REVERT: C 115 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8635 (tmm) REVERT: C 261 MET cc_start: 0.9212 (mmt) cc_final: 0.8721 (mmm) REVERT: C 429 ILE cc_start: 0.8567 (pt) cc_final: 0.8340 (pp) REVERT: C 440 LEU cc_start: 0.8529 (tp) cc_final: 0.8215 (tt) REVERT: D 18 LYS cc_start: 0.7718 (tttt) cc_final: 0.7036 (tmmt) REVERT: D 52 GLU cc_start: 0.8775 (mp0) cc_final: 0.8569 (mp0) REVERT: D 165 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: D 243 ASN cc_start: 0.8200 (t0) cc_final: 0.7683 (t0) REVERT: D 244 TYR cc_start: 0.8421 (p90) cc_final: 0.8074 (p90) REVERT: D 267 HIS cc_start: 0.7863 (t70) cc_final: 0.7443 (m90) REVERT: D 304 TYR cc_start: 0.8899 (t80) cc_final: 0.8639 (t80) REVERT: D 440 LEU cc_start: 0.8685 (tp) cc_final: 0.8397 (tt) REVERT: E 14 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7065 (mt-10) REVERT: E 18 LYS cc_start: 0.7793 (tttt) cc_final: 0.6892 (tmmt) REVERT: E 56 ASP cc_start: 0.9159 (p0) cc_final: 0.8945 (p0) REVERT: E 90 GLN cc_start: 0.8989 (mt0) cc_final: 0.8693 (mp10) REVERT: E 115 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8671 (tmm) REVERT: E 137 MET cc_start: 0.8932 (mmp) cc_final: 0.8623 (mmp) REVERT: E 165 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: E 215 LYS cc_start: 0.9102 (tttt) cc_final: 0.8568 (tptp) REVERT: E 243 ASN cc_start: 0.8203 (t0) cc_final: 0.7765 (t0) REVERT: E 244 TYR cc_start: 0.8373 (p90) cc_final: 0.8119 (p90) REVERT: E 245 ASP cc_start: 0.8331 (m-30) cc_final: 0.7661 (p0) REVERT: E 267 HIS cc_start: 0.7932 (t70) cc_final: 0.7553 (m170) REVERT: E 429 ILE cc_start: 0.8528 (pt) cc_final: 0.8325 (pp) REVERT: A 90 GLN cc_start: 0.8974 (mt0) cc_final: 0.8636 (mp10) REVERT: A 165 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8456 (mm-30) REVERT: A 429 ILE cc_start: 0.8586 (pt) cc_final: 0.8330 (pp) REVERT: A 440 LEU cc_start: 0.8649 (tp) cc_final: 0.8349 (tt) outliers start: 36 outliers final: 19 residues processed: 357 average time/residue: 0.6174 time to fit residues: 247.3348 Evaluate side-chains 350 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER 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 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 204 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3551 r_free = 0.3551 target = 0.144695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.101574 restraints weight = 17853.920| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.46 r_work: 0.2792 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19280 Z= 0.196 Angle : 0.606 5.925 26265 Z= 0.322 Chirality : 0.046 0.155 2965 Planarity : 0.004 0.045 3235 Dihedral : 5.258 20.038 2572 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.18 % Allowed : 8.41 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2240 helix: 1.14 (0.20), residues: 615 sheet: 0.69 (0.19), residues: 665 loop : -0.08 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 28 TYR 0.030 0.002 TYR A 299 PHE 0.016 0.002 PHE A 98 TRP 0.008 0.001 TRP B 426 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (19240) covalent geometry : angle 0.58824 / 0.32 (26155) SS BOND : bond 0.00284 / 0.18 ( 10) SS BOND : angle 1.06917 / 0.73 ( 20) hydrogen bonds : bond 0.05103 / 3.33 ( 885) hydrogen bonds : angle 4.72788 / 3.28 ( 2970) link_ALPHA1-3 : bond 0.00065 / 0.03 ( 5) link_ALPHA1-3 : angle 1.58676 / 1.01 ( 15) link_ALPHA1-6 : bond 0.00086 / 0.05 ( 5) link_ALPHA1-6 : angle 1.64274 / 0.99 ( 15) link_BETA1-4 : bond 0.00636 / 0.39 ( 10) link_BETA1-4 : angle 2.47585 / 1.64 ( 30) link_NAG-ASN : bond 0.00306 / 0.17 ( 10) link_NAG-ASN : angle 3.14494 / 2.28 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 0.700 Fit side-chains REVERT: B 18 LYS cc_start: 0.7839 (tttt) cc_final: 0.6993 (tmmt) REVERT: B 137 MET cc_start: 0.9002 (mmp) cc_final: 0.8780 (mmp) REVERT: B 165 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8400 (mm-30) REVERT: B 261 MET cc_start: 0.9169 (mmt) cc_final: 0.8927 (tpp) REVERT: B 267 HIS cc_start: 0.7849 (t70) cc_final: 0.7538 (m170) REVERT: K 415 THR cc_start: 0.8321 (m) cc_final: 0.7948 (t) REVERT: K 447 TYR cc_start: 0.8565 (m-80) cc_final: 0.8271 (m-80) REVERT: N 415 THR cc_start: 0.8351 (m) cc_final: 0.7905 (t) REVERT: N 421 MET cc_start: 0.9181 (mmt) cc_final: 0.8914 (tpp) REVERT: N 433 GLU cc_start: 0.7899 (tt0) cc_final: 0.6846 (tm-30) REVERT: L 425 ARG cc_start: 0.8221 (ptt180) cc_final: 0.7840 (ptt180) REVERT: L 433 GLU cc_start: 0.7714 (tt0) cc_final: 0.7489 (tt0) REVERT: C 18 LYS cc_start: 0.7790 (tttt) cc_final: 0.7080 (tmmt) REVERT: C 48 ASP cc_start: 0.7688 (m-30) cc_final: 0.7194 (m-30) REVERT: C 52 GLU cc_start: 0.8867 (mp0) cc_final: 0.8664 (mp0) REVERT: C 90 GLN cc_start: 0.8966 (mt0) cc_final: 0.8680 (mp10) REVERT: C 115 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8802 (tmm) REVERT: C 182 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8537 (mt-10) REVERT: C 261 MET cc_start: 0.9220 (mmt) cc_final: 0.8905 (mmp) REVERT: C 429 ILE cc_start: 0.8545 (pt) cc_final: 0.8339 (pp) REVERT: C 440 LEU cc_start: 0.8656 (tp) cc_final: 0.8346 (tt) REVERT: D 18 LYS cc_start: 0.7689 (tttt) cc_final: 0.7004 (tmmt) REVERT: D 165 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8371 (mm-30) REVERT: D 243 ASN cc_start: 0.8166 (t0) cc_final: 0.7803 (t0) REVERT: D 244 TYR cc_start: 0.8447 (p90) cc_final: 0.8131 (p90) REVERT: D 267 HIS cc_start: 0.7946 (t70) cc_final: 0.7644 (t70) REVERT: D 440 LEU cc_start: 0.8741 (tp) cc_final: 0.8465 (tt) REVERT: E 14 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7037 (mt-10) REVERT: E 18 LYS cc_start: 0.7837 (tttt) cc_final: 0.6912 (tmmt) REVERT: E 56 ASP cc_start: 0.9162 (p0) cc_final: 0.8952 (p0) REVERT: E 115 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8734 (tmm) REVERT: E 137 MET cc_start: 0.8979 (mmp) cc_final: 0.8702 (mmp) REVERT: E 165 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8401 (mm-30) REVERT: E 215 LYS cc_start: 0.9121 (tttt) cc_final: 0.8593 (tptp) REVERT: E 243 ASN cc_start: 0.8253 (t0) cc_final: 0.7838 (t0) REVERT: E 245 ASP cc_start: 0.8433 (m-30) cc_final: 0.7721 (p0) REVERT: E 267 HIS cc_start: 0.8035 (t70) cc_final: 0.7634 (t70) REVERT: A 90 GLN cc_start: 0.9001 (mt0) cc_final: 0.8623 (mp10) REVERT: A 165 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8507 (mm-30) REVERT: A 429 ILE cc_start: 0.8625 (pt) cc_final: 0.8379 (pp) REVERT: A 440 LEU cc_start: 0.8584 (tp) cc_final: 0.8327 (tt) outliers start: 43 outliers final: 24 residues processed: 362 average time/residue: 0.6491 time to fit residues: 263.2129 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 : 0.716 ------------------------------------------------------------------------------- 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 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 470 MET 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 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 93 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 201 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN C 113 ASN C 243 ASN C 265 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.146741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.110186 restraints weight = 17822.736| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.14 r_work: 0.2862 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19280 Z= 0.136 Angle : 0.539 5.656 26265 Z= 0.288 Chirality : 0.044 0.151 2965 Planarity : 0.004 0.041 3235 Dihedral : 5.010 18.313 2572 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.33 % Allowed : 9.11 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 2240 helix: 1.68 (0.21), residues: 610 sheet: 0.73 (0.19), residues: 660 loop : 0.04 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.028 0.002 TYR E 299 PHE 0.014 0.001 PHE A 98 TRP 0.008 0.001 TRP B 426 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (19240) covalent geometry : angle 0.52472 / 0.29 (26155) SS BOND : bond 0.00341 / 0.18 ( 10) SS BOND : angle 0.78290 / 0.53 ( 20) hydrogen bonds : bond 0.04291 / 2.81 ( 885) hydrogen bonds : angle 4.48642 / 3.12 ( 2970) link_ALPHA1-3 : bond 0.00197 / 0.12 ( 5) link_ALPHA1-3 : angle 1.55813 / 0.98 ( 15) link_ALPHA1-6 : bond 0.00060 / 0.03 ( 5) link_ALPHA1-6 : angle 1.54783 / 0.95 ( 15) link_BETA1-4 : bond 0.00372 / 0.22 ( 10) link_BETA1-4 : angle 2.07169 / 1.37 ( 30) link_NAG-ASN : bond 0.00125 / 0.07 ( 10) link_NAG-ASN : angle 2.72471 / 1.97 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.687 Fit side-chains REVERT: B 18 LYS cc_start: 0.7822 (tttt) cc_final: 0.6991 (tmmt) REVERT: B 137 MET cc_start: 0.8924 (mmp) cc_final: 0.8702 (mmp) REVERT: B 165 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8361 (mm-30) REVERT: B 261 MET cc_start: 0.9160 (mmt) cc_final: 0.8936 (tpp) REVERT: B 267 HIS cc_start: 0.7768 (t70) cc_final: 0.7495 (m170) REVERT: K 415 THR cc_start: 0.8213 (m) cc_final: 0.7885 (t) REVERT: K 433 GLU cc_start: 0.7763 (tt0) cc_final: 0.6760 (tm-30) REVERT: N 415 THR cc_start: 0.8199 (m) cc_final: 0.7783 (t) REVERT: N 433 GLU cc_start: 0.7906 (tt0) cc_final: 0.6839 (tm-30) REVERT: L 425 ARG cc_start: 0.8262 (ptt180) cc_final: 0.8060 (ptt180) REVERT: L 433 GLU cc_start: 0.7789 (tt0) cc_final: 0.7565 (tt0) REVERT: C 18 LYS cc_start: 0.7813 (tttt) cc_final: 0.7132 (tmmt) REVERT: C 90 GLN cc_start: 0.8951 (mt0) cc_final: 0.8681 (mp10) REVERT: C 115 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8699 (tmm) REVERT: C 261 MET cc_start: 0.9189 (mmt) cc_final: 0.8743 (mmm) REVERT: C 440 LEU cc_start: 0.8618 (tp) cc_final: 0.8321 (tt) REVERT: D 18 LYS cc_start: 0.7603 (tttt) cc_final: 0.6906 (tmmt) REVERT: D 243 ASN cc_start: 0.8051 (t0) cc_final: 0.7719 (t0) REVERT: D 244 TYR cc_start: 0.8376 (p90) cc_final: 0.8032 (p90) REVERT: D 267 HIS cc_start: 0.7932 (t70) cc_final: 0.7640 (t70) REVERT: D 440 LEU cc_start: 0.8736 (tp) cc_final: 0.8495 (tt) REVERT: E 14 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7058 (mt-10) REVERT: E 18 LYS cc_start: 0.7744 (tttt) cc_final: 0.6810 (tmmt) REVERT: E 56 ASP cc_start: 0.9166 (p0) cc_final: 0.8938 (p0) REVERT: E 115 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8662 (tmm) REVERT: E 137 MET cc_start: 0.8961 (mmp) cc_final: 0.8733 (mmp) REVERT: E 165 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8359 (mm-30) REVERT: E 215 LYS cc_start: 0.9099 (tttt) cc_final: 0.8588 (tptp) REVERT: E 243 ASN cc_start: 0.8260 (t0) cc_final: 0.7850 (t0) REVERT: E 245 ASP cc_start: 0.8345 (m-30) cc_final: 0.7693 (p0) REVERT: E 267 HIS cc_start: 0.7995 (t70) cc_final: 0.7744 (t70) REVERT: A 90 GLN cc_start: 0.8973 (mt0) cc_final: 0.8607 (mp10) REVERT: A 165 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8436 (mm-30) REVERT: A 429 ILE cc_start: 0.8611 (pt) cc_final: 0.8383 (pp) REVERT: A 440 LEU cc_start: 0.8592 (tp) cc_final: 0.8307 (tt) outliers start: 46 outliers final: 24 residues processed: 364 average time/residue: 0.5971 time to fit residues: 243.9263 Evaluate side-chains 363 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 334 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 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 E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 429 ILE 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 Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 244 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 107 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3559 r_free = 0.3559 target = 0.145036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107561 restraints weight = 17625.398| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.27 r_work: 0.2823 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 19280 Z= 0.212 Angle : 0.609 5.958 26265 Z= 0.322 Chirality : 0.047 0.154 2965 Planarity : 0.004 0.044 3235 Dihedral : 5.256 19.635 2570 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.38 % Allowed : 9.47 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2240 helix: 1.65 (0.21), residues: 615 sheet: 0.74 (0.19), residues: 660 loop : 0.13 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 28 TYR 0.030 0.002 TYR D 299 PHE 0.018 0.002 PHE A 98 TRP 0.010 0.002 TRP B 426 HIS 0.005 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (19240) covalent geometry : angle 0.59173 / 0.32 (26155) SS BOND : bond 0.00291 / 0.18 ( 10) SS BOND : angle 1.30530 / 0.84 ( 20) hydrogen bonds : bond 0.04826 / 3.15 ( 885) hydrogen bonds : angle 4.61230 / 3.20 ( 2970) link_ALPHA1-3 : bond 0.00076 / 0.04 ( 5) link_ALPHA1-3 : angle 1.58177 / 1.00 ( 15) link_ALPHA1-6 : bond 0.00110 / 0.06 ( 5) link_ALPHA1-6 : angle 1.66386 / 1.00 ( 15) link_BETA1-4 : bond 0.00717 / 0.44 ( 10) link_BETA1-4 : angle 2.55511 / 1.68 ( 30) link_NAG-ASN : bond 0.00340 / 0.18 ( 10) link_NAG-ASN : angle 3.09176 / 2.26 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 340 time to evaluate : 0.727 Fit side-chains REVERT: B 18 LYS cc_start: 0.7711 (tttt) cc_final: 0.6940 (tmmt) REVERT: B 165 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: B 261 MET cc_start: 0.9191 (mmt) cc_final: 0.8989 (tpp) REVERT: B 267 HIS cc_start: 0.7884 (t70) cc_final: 0.7516 (m170) REVERT: K 415 THR cc_start: 0.8234 (m) cc_final: 0.7921 (t) REVERT: K 447 TYR cc_start: 0.8548 (m-80) cc_final: 0.8295 (m-80) REVERT: O 468 LEU cc_start: 0.6483 (tp) cc_final: 0.6084 (tp) REVERT: N 415 THR cc_start: 0.8202 (m) cc_final: 0.7788 (t) REVERT: N 433 GLU cc_start: 0.7893 (tt0) cc_final: 0.6921 (tm-30) REVERT: L 433 GLU cc_start: 0.7789 (tt0) cc_final: 0.7551 (tt0) REVERT: C 18 LYS cc_start: 0.7786 (tttt) cc_final: 0.7074 (tmmt) REVERT: C 48 ASP cc_start: 0.7717 (m-30) cc_final: 0.7170 (m-30) REVERT: C 90 GLN cc_start: 0.9003 (mt0) cc_final: 0.8712 (mp10) REVERT: C 115 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8668 (tmm) REVERT: C 261 MET cc_start: 0.9227 (mmt) cc_final: 0.8778 (mmm) REVERT: C 440 LEU cc_start: 0.8634 (tp) cc_final: 0.8329 (tt) REVERT: D 18 LYS cc_start: 0.7643 (tttt) cc_final: 0.6959 (tmmt) REVERT: D 165 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8365 (mm-30) REVERT: D 243 ASN cc_start: 0.8118 (t0) cc_final: 0.7757 (t0) REVERT: D 244 TYR cc_start: 0.8410 (p90) cc_final: 0.8101 (p90) REVERT: D 267 HIS cc_start: 0.7902 (t70) cc_final: 0.7484 (t70) REVERT: D 282 ASP cc_start: 0.8647 (m-30) cc_final: 0.8425 (m-30) REVERT: D 440 LEU cc_start: 0.8753 (tp) cc_final: 0.8511 (tt) REVERT: E 18 LYS cc_start: 0.7802 (tttt) cc_final: 0.6906 (tmmt) REVERT: E 56 ASP cc_start: 0.9184 (p0) cc_final: 0.8963 (p0) REVERT: E 115 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8729 (tmm) REVERT: E 165 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8415 (mm-30) REVERT: E 215 LYS cc_start: 0.9118 (tttt) cc_final: 0.8568 (tptp) REVERT: E 243 ASN cc_start: 0.8382 (t0) cc_final: 0.7968 (t0) REVERT: E 245 ASP cc_start: 0.8441 (m-30) cc_final: 0.7742 (p0) REVERT: E 267 HIS cc_start: 0.8103 (t70) cc_final: 0.7850 (t70) REVERT: A 90 GLN cc_start: 0.8997 (mt0) cc_final: 0.8618 (mp10) REVERT: A 165 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: A 429 ILE cc_start: 0.8645 (pt) cc_final: 0.8394 (pp) REVERT: A 440 LEU cc_start: 0.8610 (tp) cc_final: 0.8336 (tt) outliers start: 47 outliers final: 28 residues processed: 353 average time/residue: 0.6167 time to fit residues: 244.4773 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 : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 95 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3586 r_free = 0.3586 target = 0.147353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.110338 restraints weight = 17548.895| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.15 r_work: 0.2806 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19280 Z= 0.126 Angle : 0.527 6.176 26265 Z= 0.281 Chirality : 0.044 0.155 2965 Planarity : 0.003 0.040 3235 Dihedral : 4.958 18.394 2570 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.33 % Allowed : 10.08 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2240 helix: 1.89 (0.22), residues: 610 sheet: 0.73 (0.19), residues: 660 loop : 0.14 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 269 TYR 0.027 0.002 TYR E 299 PHE 0.014 0.001 PHE A 98 TRP 0.008 0.001 TRP M 440 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (19240) covalent geometry : angle 0.51347 / 0.28 (26155) SS BOND : bond 0.00210 / 0.12 ( 10) SS BOND : angle 0.71402 / 0.53 ( 20) hydrogen bonds : bond 0.04062 / 2.66 ( 885) hydrogen bonds : angle 4.41163 / 3.06 ( 2970) link_ALPHA1-3 : bond 0.00135 / 0.08 ( 5) link_ALPHA1-3 : angle 1.53995 / 0.97 ( 15) link_ALPHA1-6 : bond 0.00068 / 0.03 ( 5) link_ALPHA1-6 : angle 1.53524 / 0.95 ( 15) link_BETA1-4 : bond 0.00325 / 0.19 ( 10) link_BETA1-4 : angle 2.02125 / 1.33 ( 30) link_NAG-ASN : bond 0.00102 / 0.05 ( 10) link_NAG-ASN : angle 2.63034 / 1.90 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 350 time to evaluate : 0.735 Fit side-chains REVERT: B 18 LYS cc_start: 0.7686 (tttt) cc_final: 0.6853 (tmmt) REVERT: B 165 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8490 (mm-30) REVERT: B 267 HIS cc_start: 0.7945 (t70) cc_final: 0.7513 (m170) REVERT: B 268 LEU cc_start: 0.8489 (tp) cc_final: 0.8263 (tm) REVERT: K 415 THR cc_start: 0.8130 (m) cc_final: 0.7818 (t) REVERT: K 433 GLU cc_start: 0.7776 (tt0) cc_final: 0.6745 (tm-30) REVERT: O 468 LEU cc_start: 0.6504 (tp) cc_final: 0.5908 (tp) REVERT: N 415 THR cc_start: 0.8031 (m) cc_final: 0.7685 (t) REVERT: N 433 GLU cc_start: 0.7958 (tt0) cc_final: 0.6980 (tm-30) REVERT: C 18 LYS cc_start: 0.7783 (tttt) cc_final: 0.7030 (tmmt) REVERT: C 48 ASP cc_start: 0.7864 (m-30) cc_final: 0.7312 (m-30) REVERT: C 90 GLN cc_start: 0.9029 (mt0) cc_final: 0.8765 (mp10) REVERT: C 115 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8804 (tmm) REVERT: C 261 MET cc_start: 0.9226 (mmt) cc_final: 0.8814 (mmm) REVERT: C 440 LEU cc_start: 0.8606 (tp) cc_final: 0.8313 (tt) REVERT: D 18 LYS cc_start: 0.7549 (tttt) cc_final: 0.6844 (tmmt) REVERT: D 49 MET cc_start: 0.8221 (tmm) cc_final: 0.7893 (pp-130) REVERT: D 165 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8401 (mm-30) REVERT: D 243 ASN cc_start: 0.8123 (t0) cc_final: 0.7773 (t0) REVERT: D 244 TYR cc_start: 0.8415 (p90) cc_final: 0.8090 (p90) REVERT: D 267 HIS cc_start: 0.7991 (t70) cc_final: 0.7555 (t70) REVERT: D 440 LEU cc_start: 0.8725 (tp) cc_final: 0.8506 (tt) REVERT: E 18 LYS cc_start: 0.7806 (tttt) cc_final: 0.6836 (tmmt) REVERT: E 48 ASP cc_start: 0.7821 (m-30) cc_final: 0.7194 (m-30) REVERT: E 56 ASP cc_start: 0.9231 (p0) cc_final: 0.9024 (p0) REVERT: E 115 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8738 (tmm) REVERT: E 165 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8479 (mm-30) REVERT: E 215 LYS cc_start: 0.9150 (tttt) cc_final: 0.8615 (tptp) REVERT: E 243 ASN cc_start: 0.8388 (t0) cc_final: 0.7983 (t0) REVERT: E 245 ASP cc_start: 0.8393 (m-30) cc_final: 0.7690 (p0) REVERT: E 267 HIS cc_start: 0.8176 (t70) cc_final: 0.7871 (t70) REVERT: A 90 GLN cc_start: 0.9035 (mt0) cc_final: 0.8644 (mp10) REVERT: A 165 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8579 (mm-30) REVERT: A 269 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8296 (tpp80) REVERT: A 429 ILE cc_start: 0.8652 (pt) cc_final: 0.8413 (pp) REVERT: A 440 LEU cc_start: 0.8600 (tp) cc_final: 0.8341 (tt) outliers start: 46 outliers final: 26 residues processed: 365 average time/residue: 0.5810 time to fit residues: 238.4630 Evaluate side-chains 368 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 336 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain 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 M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 468 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 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 429 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 198 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.146661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.108336 restraints weight = 17555.063| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.12 r_work: 0.2798 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19280 Z= 0.147 Angle : 0.549 6.734 26265 Z= 0.290 Chirality : 0.045 0.158 2965 Planarity : 0.004 0.038 3235 Dihedral : 4.991 18.422 2570 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.53 % Allowed : 10.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2240 helix: 1.90 (0.22), residues: 610 sheet: 0.72 (0.19), residues: 660 loop : 0.13 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 269 TYR 0.028 0.002 TYR E 299 PHE 0.015 0.002 PHE A 98 TRP 0.008 0.001 TRP B 426 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (19240) covalent geometry : angle 0.53455 / 0.29 (26155) SS BOND : bond 0.00251 / 0.15 ( 10) SS BOND : angle 0.79507 / 0.59 ( 20) hydrogen bonds : bond 0.04213 / 2.76 ( 885) hydrogen bonds : angle 4.43054 / 3.08 ( 2970) link_ALPHA1-3 : bond 0.00074 / 0.04 ( 5) link_ALPHA1-3 : angle 1.53271 / 0.97 ( 15) link_ALPHA1-6 : bond 0.00048 / 0.02 ( 5) link_ALPHA1-6 : angle 1.56562 / 0.96 ( 15) link_BETA1-4 : bond 0.00416 / 0.25 ( 10) link_BETA1-4 : angle 2.19273 / 1.44 ( 30) link_NAG-ASN : bond 0.00148 / 0.08 ( 10) link_NAG-ASN : angle 2.73226 / 1.99 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 0.705 Fit side-chains REVERT: B 18 LYS cc_start: 0.7745 (tttt) cc_final: 0.6916 (tmmt) REVERT: B 165 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8515 (mm-30) REVERT: B 267 HIS cc_start: 0.8022 (t70) cc_final: 0.7482 (m170) REVERT: K 415 THR cc_start: 0.8143 (m) cc_final: 0.7825 (t) REVERT: K 433 GLU cc_start: 0.7806 (tt0) cc_final: 0.6795 (tm-30) REVERT: O 468 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.5880 (tp) REVERT: N 415 THR cc_start: 0.8047 (m) cc_final: 0.7693 (t) REVERT: N 433 GLU cc_start: 0.7968 (tt0) cc_final: 0.6969 (tm-30) REVERT: C 18 LYS cc_start: 0.7766 (tttt) cc_final: 0.7013 (tmmt) REVERT: C 48 ASP cc_start: 0.7895 (m-30) cc_final: 0.7322 (m-30) REVERT: C 90 GLN cc_start: 0.9033 (mt0) cc_final: 0.8738 (mp10) REVERT: C 115 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8831 (tmm) REVERT: C 261 MET cc_start: 0.9245 (mmt) cc_final: 0.8827 (mmm) REVERT: C 440 LEU cc_start: 0.8617 (tp) cc_final: 0.8328 (tt) REVERT: D 18 LYS cc_start: 0.7633 (tttt) cc_final: 0.6907 (tmmt) REVERT: D 165 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8431 (mm-30) REVERT: D 243 ASN cc_start: 0.8142 (t0) cc_final: 0.7786 (t0) REVERT: D 244 TYR cc_start: 0.8441 (p90) cc_final: 0.8111 (p90) REVERT: D 267 HIS cc_start: 0.7993 (t70) cc_final: 0.7562 (t70) REVERT: D 440 LEU cc_start: 0.8734 (tp) cc_final: 0.8506 (tt) REVERT: E 18 LYS cc_start: 0.7837 (tttt) cc_final: 0.6825 (tmmt) REVERT: E 48 ASP cc_start: 0.7889 (m-30) cc_final: 0.7230 (m-30) REVERT: E 56 ASP cc_start: 0.9228 (p0) cc_final: 0.9025 (p0) REVERT: E 115 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8736 (tmm) REVERT: E 165 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: E 215 LYS cc_start: 0.9167 (tttt) cc_final: 0.8626 (tptp) REVERT: E 243 ASN cc_start: 0.8483 (t0) cc_final: 0.8086 (t0) REVERT: E 244 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8139 (p90) REVERT: E 245 ASP cc_start: 0.8438 (m-30) cc_final: 0.7683 (p0) REVERT: E 267 HIS cc_start: 0.8213 (t70) cc_final: 0.7897 (t70) REVERT: A 90 GLN cc_start: 0.9036 (mt0) cc_final: 0.8640 (mp10) REVERT: A 165 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8593 (mm-30) REVERT: A 269 ARG cc_start: 0.8458 (tpp80) cc_final: 0.8243 (tpp80) REVERT: A 429 ILE cc_start: 0.8645 (pt) cc_final: 0.8421 (pp) REVERT: A 440 LEU cc_start: 0.8612 (tp) cc_final: 0.8357 (tt) outliers start: 50 outliers final: 31 residues processed: 357 average time/residue: 0.5919 time to fit residues: 237.5782 Evaluate side-chains 367 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 328 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 468 LEU Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 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 E residue 429 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 7 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110639 restraints weight = 17620.276| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.15 r_work: 0.2847 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19280 Z= 0.109 Angle : 0.509 7.266 26265 Z= 0.269 Chirality : 0.043 0.159 2965 Planarity : 0.003 0.040 3235 Dihedral : 4.774 17.342 2570 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.77 % Allowed : 11.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2240 helix: 1.92 (0.22), residues: 615 sheet: 0.84 (0.19), residues: 650 loop : 0.09 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.026 0.002 TYR E 299 PHE 0.012 0.001 PHE A 98 TRP 0.008 0.001 TRP A 168 HIS 0.002 0.001 HIS C 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (19240) covalent geometry : angle 0.49652 / 0.27 (26155) SS BOND : bond 0.00212 / 0.11 ( 10) SS BOND : angle 0.51095 / 0.37 ( 20) hydrogen bonds : bond 0.03773 / 2.48 ( 885) hydrogen bonds : angle 4.29581 / 2.98 ( 2970) link_ALPHA1-3 : bond 0.00197 / 0.11 ( 5) link_ALPHA1-3 : angle 1.48268 / 0.94 ( 15) link_ALPHA1-6 : bond 0.00140 / 0.07 ( 5) link_ALPHA1-6 : angle 1.49269 / 0.92 ( 15) link_BETA1-4 : bond 0.00264 / 0.15 ( 10) link_BETA1-4 : angle 1.85871 / 1.22 ( 30) link_NAG-ASN : bond 0.00084 / 0.05 ( 10) link_NAG-ASN : angle 2.37310 / 1.71 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 344 time to evaluate : 0.576 Fit side-chains REVERT: B 18 LYS cc_start: 0.7651 (tttt) cc_final: 0.6855 (tmmt) REVERT: B 165 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8440 (mm-30) REVERT: B 267 HIS cc_start: 0.7911 (t70) cc_final: 0.7494 (m170) REVERT: B 268 LEU cc_start: 0.8552 (tp) cc_final: 0.8285 (tm) REVERT: K 415 THR cc_start: 0.8087 (m) cc_final: 0.7778 (t) REVERT: K 433 GLU cc_start: 0.7728 (tt0) cc_final: 0.6870 (tm-30) REVERT: O 468 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5685 (tp) REVERT: N 415 THR cc_start: 0.7952 (m) cc_final: 0.7586 (t) REVERT: N 425 ARG cc_start: 0.8135 (ptt-90) cc_final: 0.7617 (ptt-90) REVERT: N 433 GLU cc_start: 0.7909 (tt0) cc_final: 0.6930 (tm-30) REVERT: C 18 LYS cc_start: 0.7785 (tttt) cc_final: 0.7048 (tmmt) REVERT: C 48 ASP cc_start: 0.7825 (m-30) cc_final: 0.7260 (m-30) REVERT: C 90 GLN cc_start: 0.9014 (mt0) cc_final: 0.8692 (mp10) REVERT: C 115 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8766 (tmm) REVERT: C 261 MET cc_start: 0.9197 (mmt) cc_final: 0.8750 (mmm) REVERT: C 267 HIS cc_start: 0.7773 (t70) cc_final: 0.7452 (m170) REVERT: C 298 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8983 (tm-30) REVERT: C 440 LEU cc_start: 0.8604 (tp) cc_final: 0.8337 (tt) REVERT: D 9 MET cc_start: 0.7323 (mtp) cc_final: 0.6986 (mtm) REVERT: D 18 LYS cc_start: 0.7622 (tttt) cc_final: 0.6906 (tmmt) REVERT: D 165 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8343 (mm-30) REVERT: D 243 ASN cc_start: 0.8029 (t0) cc_final: 0.7703 (t0) REVERT: D 244 TYR cc_start: 0.8358 (p90) cc_final: 0.7991 (p90) REVERT: D 267 HIS cc_start: 0.7931 (t70) cc_final: 0.7519 (t70) REVERT: D 301 PHE cc_start: 0.8844 (t80) cc_final: 0.8566 (t80) REVERT: E 18 LYS cc_start: 0.7830 (tttt) cc_final: 0.6904 (tmmt) REVERT: E 48 ASP cc_start: 0.7809 (m-30) cc_final: 0.7127 (m-30) REVERT: E 49 MET cc_start: 0.8216 (tmm) cc_final: 0.7921 (pp-130) REVERT: E 115 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8835 (tmm) REVERT: E 215 LYS cc_start: 0.9129 (tttt) cc_final: 0.8600 (tptp) REVERT: E 243 ASN cc_start: 0.8416 (t0) cc_final: 0.8047 (t0) REVERT: E 245 ASP cc_start: 0.8299 (m-30) cc_final: 0.7612 (p0) REVERT: E 267 HIS cc_start: 0.8161 (t70) cc_final: 0.7844 (t70) REVERT: A 269 ARG cc_start: 0.8437 (tpp80) cc_final: 0.8228 (tpp80) REVERT: A 429 ILE cc_start: 0.8614 (pt) cc_final: 0.8387 (pp) REVERT: A 440 LEU cc_start: 0.8590 (tp) cc_final: 0.8349 (tt) outliers start: 35 outliers final: 22 residues processed: 354 average time/residue: 0.5941 time to fit residues: 235.9011 Evaluate side-chains 361 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 190 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 168 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3551 r_free = 0.3551 target = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.107152 restraints weight = 17544.199| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.03 r_work: 0.2780 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19280 Z= 0.219 Angle : 0.622 8.037 26265 Z= 0.326 Chirality : 0.047 0.165 2965 Planarity : 0.004 0.049 3235 Dihedral : 5.227 19.560 2570 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.23 % Allowed : 11.04 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2240 helix: 1.78 (0.22), residues: 615 sheet: 0.71 (0.19), residues: 685 loop : 0.21 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 28 TYR 0.032 0.002 TYR D 299 PHE 0.019 0.002 PHE A 98 TRP 0.010 0.002 TRP B 426 HIS 0.004 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (19240) covalent geometry : angle 0.60408 / 0.32 (26155) SS BOND : bond 0.00283 / 0.17 ( 10) SS BOND : angle 1.19922 / 0.90 ( 20) hydrogen bonds : bond 0.04767 / 3.11 ( 885) hydrogen bonds : angle 4.59571 / 3.19 ( 2970) link_ALPHA1-3 : bond 0.00080 / 0.04 ( 5) link_ALPHA1-3 : angle 1.57544 / 1.00 ( 15) link_ALPHA1-6 : bond 0.00116 / 0.06 ( 5) link_ALPHA1-6 : angle 1.68688 / 1.01 ( 15) link_BETA1-4 : bond 0.00735 / 0.45 ( 10) link_BETA1-4 : angle 2.62140 / 1.72 ( 30) link_NAG-ASN : bond 0.00347 / 0.19 ( 10) link_NAG-ASN : angle 3.19748 / 2.34 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 0.742 Fit side-chains REVERT: B 18 LYS cc_start: 0.7797 (tttt) cc_final: 0.6978 (tmmt) REVERT: B 165 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8492 (mm-30) REVERT: B 267 HIS cc_start: 0.8000 (t70) cc_final: 0.7534 (m170) REVERT: K 415 THR cc_start: 0.8248 (m) cc_final: 0.7944 (t) REVERT: K 447 TYR cc_start: 0.8554 (m-80) cc_final: 0.8330 (m-80) REVERT: O 468 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.5923 (tp) REVERT: N 415 THR cc_start: 0.8127 (m) cc_final: 0.7777 (t) REVERT: N 433 GLU cc_start: 0.7960 (tt0) cc_final: 0.7032 (tm-30) REVERT: C 18 LYS cc_start: 0.7798 (tttt) cc_final: 0.7073 (tmmt) REVERT: C 48 ASP cc_start: 0.7869 (m-30) cc_final: 0.7282 (m-30) REVERT: C 90 GLN cc_start: 0.9043 (mt0) cc_final: 0.8731 (mp10) REVERT: C 115 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8863 (tmm) REVERT: C 261 MET cc_start: 0.9250 (mmt) cc_final: 0.8936 (mmp) REVERT: C 267 HIS cc_start: 0.7851 (t70) cc_final: 0.7471 (m170) REVERT: C 440 LEU cc_start: 0.8639 (tp) cc_final: 0.8360 (tt) REVERT: D 18 LYS cc_start: 0.7783 (tttt) cc_final: 0.7080 (tmmt) REVERT: D 165 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8452 (mm-30) REVERT: D 243 ASN cc_start: 0.8189 (t0) cc_final: 0.7812 (t0) REVERT: D 244 TYR cc_start: 0.8415 (p90) cc_final: 0.8074 (p90) REVERT: D 267 HIS cc_start: 0.7952 (t70) cc_final: 0.7517 (t70) REVERT: E 18 LYS cc_start: 0.8000 (tttt) cc_final: 0.7040 (tmmt) REVERT: E 48 ASP cc_start: 0.7800 (m-30) cc_final: 0.7080 (m-30) REVERT: E 115 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8770 (tmm) REVERT: E 165 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8474 (mm-30) REVERT: E 215 LYS cc_start: 0.9165 (tttt) cc_final: 0.8628 (tptp) REVERT: E 243 ASN cc_start: 0.8443 (t0) cc_final: 0.8040 (t0) REVERT: E 245 ASP cc_start: 0.8489 (m-30) cc_final: 0.7781 (p0) REVERT: E 267 HIS cc_start: 0.8219 (t70) cc_final: 0.7929 (t70) REVERT: A 90 GLN cc_start: 0.9026 (mt0) cc_final: 0.8651 (mp10) REVERT: A 165 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8559 (mm-30) REVERT: A 429 ILE cc_start: 0.8638 (pt) cc_final: 0.8331 (pp) REVERT: A 440 LEU cc_start: 0.8629 (tp) cc_final: 0.8376 (tt) outliers start: 44 outliers final: 29 residues processed: 354 average time/residue: 0.6282 time to fit residues: 249.6073 Evaluate side-chains 366 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 330 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain L residue 468 LEU Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain 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 429 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN B 265 ASN C 243 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.144676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.108868 restraints weight = 17587.078| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.94 r_work: 0.2818 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2352 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= 0.173 Angle : 0.583 8.466 26265 Z= 0.306 Chirality : 0.046 0.168 2965 Planarity : 0.004 0.056 3235 Dihedral : 5.142 20.182 2570 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.08 % Allowed : 11.24 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 2240 helix: 1.73 (0.21), residues: 620 sheet: 0.74 (0.19), residues: 660 loop : 0.21 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 269 TYR 0.029 0.002 TYR E 299 PHE 0.017 0.002 PHE A 98 TRP 0.008 0.001 TRP C 426 HIS 0.003 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (19240) covalent geometry : angle 0.56731 / 0.30 (26155) SS BOND : bond 0.00269 / 0.15 ( 10) SS BOND : angle 1.02138 / 0.73 ( 20) hydrogen bonds : bond 0.04402 / 2.88 ( 885) hydrogen bonds : angle 4.52284 / 3.14 ( 2970) link_ALPHA1-3 : bond 0.00043 / 0.03 ( 5) link_ALPHA1-3 : angle 1.56048 / 0.98 ( 15) link_ALPHA1-6 : bond 0.00058 / 0.03 ( 5) link_ALPHA1-6 : angle 1.60987 / 0.98 ( 15) link_BETA1-4 : bond 0.00521 / 0.31 ( 10) link_BETA1-4 : angle 2.32084 / 1.53 ( 30) link_NAG-ASN : bond 0.00209 / 0.11 ( 10) link_NAG-ASN : angle 2.94806 / 2.15 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 0.697 Fit side-chains REVERT: B 18 LYS cc_start: 0.7716 (tttt) cc_final: 0.6992 (tmmt) REVERT: B 165 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8427 (mm-30) REVERT: B 224 GLN cc_start: 0.8873 (tp40) cc_final: 0.8625 (tp40) REVERT: B 267 HIS cc_start: 0.7958 (t70) cc_final: 0.7531 (m170) REVERT: B 268 LEU cc_start: 0.8548 (tp) cc_final: 0.8303 (tm) REVERT: K 415 THR cc_start: 0.8154 (m) cc_final: 0.7838 (t) REVERT: O 468 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.5867 (tp) REVERT: N 415 THR cc_start: 0.8098 (m) cc_final: 0.7740 (t) REVERT: N 433 GLU cc_start: 0.7935 (tt0) cc_final: 0.6996 (tm-30) REVERT: C 18 LYS cc_start: 0.7807 (tttt) cc_final: 0.7084 (tmmt) REVERT: C 48 ASP cc_start: 0.7805 (m-30) cc_final: 0.7219 (m-30) REVERT: C 90 GLN cc_start: 0.9029 (mt0) cc_final: 0.8755 (mp10) REVERT: C 115 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8801 (tmm) REVERT: C 261 MET cc_start: 0.9217 (mmt) cc_final: 0.8804 (mmm) REVERT: C 267 HIS cc_start: 0.7828 (t70) cc_final: 0.7365 (m170) REVERT: C 440 LEU cc_start: 0.8631 (tp) cc_final: 0.8351 (tt) REVERT: D 18 LYS cc_start: 0.7638 (tttt) cc_final: 0.6946 (tmmt) REVERT: D 90 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8617 (mp10) REVERT: D 165 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: D 243 ASN cc_start: 0.8124 (t0) cc_final: 0.7762 (t0) REVERT: D 244 TYR cc_start: 0.8351 (p90) cc_final: 0.8013 (p90) REVERT: D 267 HIS cc_start: 0.7896 (t70) cc_final: 0.7642 (t70) REVERT: E 18 LYS cc_start: 0.7996 (tttt) cc_final: 0.7050 (tmmt) REVERT: E 48 ASP cc_start: 0.7752 (m-30) cc_final: 0.7021 (m-30) REVERT: E 115 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8742 (tmm) REVERT: E 215 LYS cc_start: 0.9132 (tttt) cc_final: 0.8598 (tptp) REVERT: E 243 ASN cc_start: 0.8416 (t0) cc_final: 0.8034 (t0) REVERT: E 245 ASP cc_start: 0.8358 (m-30) cc_final: 0.7734 (p0) REVERT: E 267 HIS cc_start: 0.8133 (t70) cc_final: 0.7861 (t70) REVERT: A 90 GLN cc_start: 0.9024 (mt0) cc_final: 0.8651 (mp10) REVERT: A 165 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8495 (mm-30) REVERT: A 440 LEU cc_start: 0.8616 (tp) cc_final: 0.8366 (tt) outliers start: 41 outliers final: 30 residues processed: 350 average time/residue: 0.6283 time to fit residues: 246.9472 Evaluate side-chains 366 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 329 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain L residue 468 LEU Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 30 ASP 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 E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 429 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 105 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN B 265 ASN C 243 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.108792 restraints weight = 17638.191| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.21 r_work: 0.2817 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19280 Z= 0.134 Angle : 0.547 8.266 26265 Z= 0.288 Chirality : 0.044 0.166 2965 Planarity : 0.004 0.057 3235 Dihedral : 4.975 20.729 2570 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.87 % Allowed : 11.54 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2240 helix: 1.84 (0.22), residues: 615 sheet: 0.77 (0.19), residues: 660 loop : 0.19 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.028 0.002 TYR E 299 PHE 0.015 0.001 PHE C 301 TRP 0.007 0.001 TRP A 426 HIS 0.002 0.001 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (19240) covalent geometry : angle 0.53298 / 0.29 (26155) SS BOND : bond 0.00278 / 0.15 ( 10) SS BOND : angle 0.80102 / 0.56 ( 20) hydrogen bonds : bond 0.04052 / 2.65 ( 885) hydrogen bonds : angle 4.41065 / 3.06 ( 2970) link_ALPHA1-3 : bond 0.00123 / 0.07 ( 5) link_ALPHA1-3 : angle 1.52529 / 0.96 ( 15) link_ALPHA1-6 : bond 0.00057 / 0.03 ( 5) link_ALPHA1-6 : angle 1.53820 / 0.95 ( 15) link_BETA1-4 : bond 0.00329 / 0.20 ( 10) link_BETA1-4 : angle 2.06486 / 1.36 ( 30) link_NAG-ASN : bond 0.00100 / 0.05 ( 10) link_NAG-ASN : angle 2.64049 / 1.92 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8386.78 seconds wall clock time: 143 minutes 13.03 seconds (8593.03 seconds total)