Starting phenix.real_space_refine on Thu Mar 5 12:24:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mly_23913/03_2026/7mly_23913_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mly_23913/03_2026/7mly_23913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mly_23913/03_2026/7mly_23913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mly_23913/03_2026/7mly_23913.map" model { file = "/net/cci-nas-00/data/ceres_data/7mly_23913/03_2026/7mly_23913_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mly_23913/03_2026/7mly_23913_trim.cif" } resolution = 2.7 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 13597 2.51 5 N 3398 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20982 Number of models: 1 Model: "" Number of chains: 27 Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "K" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2724 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2771 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2732 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2819 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2686 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 1 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 66 Unusual residues: {'D10': 1, 'DD9': 1, 'HP6': 2, 'LNK': 2, 'MYS': 1, 'NBU': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Unusual residues: {'D12': 1, 'DD9': 1, 'HEX': 1, 'HP6': 2, 'LNK': 2, 'OCT': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 51 Unusual residues: {'DD9': 1, 'HEX': 1, 'HP6': 2, 'LNK': 2, 'NBU': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 52 Unusual residues: {'D12': 1, 'HEX': 1, 'LNK': 2, 'NBU': 4, 'OCT': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 42 Unusual residues: {'HP6': 3, 'LNK': 2, 'UND': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.04, per 1000 atoms: 0.24 Number of scatterers: 20982 At special positions: 0 Unit cell: (154.462, 130.508, 141.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 3852 8.00 N 3398 7.00 C 13597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.04 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.04 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.04 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN T 4 " - " MAN T 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 5 " " BMA f 3 " - " MAN f 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " NAG-ASN " NAG T 1 " - " ASN D 38 " " NAG Z 1 " - " ASN A 38 " " NAG f 1 " - " ASN B 38 " " NAG l 1 " - " ASN C 38 " " NAG r 1 " - " ASN E 220 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 811.4 milliseconds 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4786 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 36 sheets defined 26.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.829A pdb=" N LEU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.608A pdb=" N LYS G 65 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.513A pdb=" N ASP M 82 " --> pdb=" O GLN M 79 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 79 through 83' Processing helix chain 'L' and resid 62 through 65 removed outlier: 3.758A pdb=" N LYS L 65 " --> pdb=" O GLU L 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.585A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.584A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'D' and resid 12 through 18 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.797A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.690A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.888A pdb=" N TRP D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 248 through 271 removed outlier: 3.747A pdb=" N VAL D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 308 removed outlier: 3.900A pdb=" N VAL D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 415 removed outlier: 3.505A pdb=" N SER D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix removed outlier: 3.846A pdb=" N TRP D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.658A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.771A pdb=" N ALA A 74 " --> pdb=" O PRO A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.700A pdb=" N SER A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.888A pdb=" N THR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 309 removed outlier: 3.613A pdb=" N VAL A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 418 removed outlier: 4.144A pdb=" N ARG A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 3.689A pdb=" N TRP A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 18 removed outlier: 3.669A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 removed outlier: 3.806A pdb=" N ALA B 74 " --> pdb=" O PRO B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 91 removed outlier: 4.047A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.542A pdb=" N SER B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 248 through 269 removed outlier: 3.550A pdb=" N SER B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 309 removed outlier: 3.649A pdb=" N VAL B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 removed outlier: 4.186A pdb=" N ASP B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 418 Proline residue: B 403 - end of helix removed outlier: 3.669A pdb=" N LEU B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 18 removed outlier: 3.598A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 4.098A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.889A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 227 removed outlier: 3.531A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.658A pdb=" N SER C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 248 through 273 removed outlier: 3.772A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 314 removed outlier: 3.880A pdb=" N VAL C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.632A pdb=" N ARG C 384 " --> pdb=" O GLU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 417 removed outlier: 4.288A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix removed outlier: 3.730A pdb=" N LEU C 407 " --> pdb=" O PRO C 403 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 415 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 417 " --> pdb=" O TYR C 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 43 removed outlier: 4.615A pdb=" N LEU E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 removed outlier: 3.587A pdb=" N LYS E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 109 through 116 removed outlier: 3.595A pdb=" N TYR E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.668A pdb=" N MET E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 263 removed outlier: 3.742A pdb=" N TRP E 263 " --> pdb=" O VAL E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 removed outlier: 3.694A pdb=" N TRP E 267 " --> pdb=" O LEU E 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 264 through 267' Processing helix chain 'E' and resid 272 through 296 removed outlier: 3.520A pdb=" N ARG E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 278 - end of helix removed outlier: 4.033A pdb=" N SER E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 295 " --> pdb=" O CYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 333 removed outlier: 3.572A pdb=" N LEU E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 333 " --> pdb=" O GLN E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 removed outlier: 3.646A pdb=" N ASP E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 475 removed outlier: 3.826A pdb=" N PHE E 466 " --> pdb=" O CYS E 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'J' and resid 19 through 20 removed outlier: 3.632A pdb=" N THR J 72 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.514A pdb=" N TYR J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.504A pdb=" N THR G 78 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.712A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE G 34 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.702A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE K 75 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.352A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.557A pdb=" N ILE F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER F 57 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.364A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU M 85 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 62 through 67 removed outlier: 3.720A pdb=" N THR M 72 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.291A pdb=" N LYS L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP L 47 " --> pdb=" O LYS L 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 19 through 22 removed outlier: 4.022A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR I 72 " --> pdb=" O SER I 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.738A pdb=" N LEU I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.832A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 37 through 47 removed outlier: 3.789A pdb=" N PHE D 44 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 67 current: chain 'D' and resid 126 through 136 Processing sheet with id=AC3, first strand: chain 'D' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 98 through 100 current: chain 'D' and resid 209 through 218 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 200 through 202 Processing sheet with id=AC5, first strand: chain 'A' and resid 37 through 45 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 37 through 45 current: chain 'A' and resid 57 through 69 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 57 through 69 current: chain 'A' and resid 125 through 134 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 158 current: chain 'A' and resid 211 through 218 Processing sheet with id=AC7, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AC8, first strand: chain 'B' and resid 37 through 47 removed outlier: 6.756A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 44 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 69 current: chain 'B' and resid 125 through 137 Processing sheet with id=AC9, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AD1, first strand: chain 'B' and resid 149 through 152 removed outlier: 3.527A pdb=" N GLU B 217 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 200 through 202 Processing sheet with id=AD3, first strand: chain 'C' and resid 37 through 52 removed outlier: 6.504A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 67 current: chain 'C' and resid 116 through 120 Processing sheet with id=AD4, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.650A pdb=" N HIS C 215 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU C 192 " --> pdb=" O HIS C 215 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N GLU C 217 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS C 190 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 200 through 202 Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 143 removed outlier: 6.953A pdb=" N ASP E 78 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER E 71 " --> pdb=" O ASP E 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG E 80 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE E 69 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 121 through 123 Processing sheet with id=AD8, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AD9, first strand: chain 'E' and resid 223 through 225 629 hydrogen bonds defined for protein. 1665 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: 3.34 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3241 1.31 - 1.44: 6108 1.44 - 1.57: 11870 1.57 - 1.70: 1 1.70 - 1.82: 222 Bond restraints: 21442 Sorted by residual: bond pdb=" C ARG D 399 " pdb=" O ARG D 399 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.25e-02 6.40e+03 1.69e+01 bond pdb=" CA ARG D 399 " pdb=" CB ARG D 399 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.64e-02 3.72e+03 1.47e+01 bond pdb=" C1 NAG r 2 " pdb=" O5 NAG r 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 BMA l 3 " pdb=" C2 BMA l 3 " ideal model delta sigma weight residual 1.519 1.582 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" NE ARG D 399 " pdb=" CZ ARG D 399 " ideal model delta sigma weight residual 1.326 1.294 0.032 1.10e-02 8.26e+03 8.40e+00 ... (remaining 21437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 28262 1.97 - 3.94: 512 3.94 - 5.91: 128 5.91 - 7.88: 27 7.88 - 9.85: 3 Bond angle restraints: 28932 Sorted by residual: angle pdb=" C SER A 308 " pdb=" N ARG A 309 " pdb=" CA ARG A 309 " ideal model delta sigma weight residual 123.20 117.38 5.82 1.38e+00 5.25e-01 1.78e+01 angle pdb=" NE ARG D 399 " pdb=" CZ ARG D 399 " pdb=" NH1 ARG D 399 " ideal model delta sigma weight residual 121.50 117.64 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.17 110.32 3.85 1.14e+00 7.69e-01 1.14e+01 angle pdb=" N ALA I 51 " pdb=" CA ALA I 51 " pdb=" CB ALA I 51 " ideal model delta sigma weight residual 114.17 110.32 3.85 1.14e+00 7.69e-01 1.14e+01 angle pdb=" N ALA M 51 " pdb=" CA ALA M 51 " pdb=" CB ALA M 51 " ideal model delta sigma weight residual 114.17 110.40 3.77 1.14e+00 7.69e-01 1.09e+01 ... (remaining 28927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 12547 24.56 - 49.12: 279 49.12 - 73.68: 67 73.68 - 98.24: 41 98.24 - 122.81: 46 Dihedral angle restraints: 12980 sinusoidal: 5529 harmonic: 7451 Sorted by residual: dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 39.49 53.51 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 40.48 52.52 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 42.64 50.36 1 1.00e+01 1.00e-02 3.48e+01 ... (remaining 12977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3162 0.115 - 0.229: 60 0.229 - 0.344: 10 0.344 - 0.458: 1 0.458 - 0.573: 1 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG r 1 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG r 1 " pdb=" O5 NAG r 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ARG D 399 " pdb=" N ARG D 399 " pdb=" C ARG D 399 " pdb=" CB ARG D 399 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3231 not shown) Planarity restraints: 3579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 308 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C SER A 308 " -0.053 2.00e-02 2.50e+03 pdb=" O SER A 308 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 309 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 98 " -0.007 2.00e-02 2.50e+03 1.41e-02 3.49e+00 pdb=" CG PHE J 98 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE J 98 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE J 98 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 98 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE J 98 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 98 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 98 " 0.008 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE K 98 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE K 98 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE K 98 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE K 98 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE K 98 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 98 " 0.001 2.00e-02 2.50e+03 ... (remaining 3576 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 256 2.61 - 3.18: 19168 3.18 - 3.76: 30501 3.76 - 4.33: 47341 4.33 - 4.90: 75246 Nonbonded interactions: 172512 Sorted by model distance: nonbonded pdb=" O SER I 30 " pdb=" OH TYR I 71 " model vdw 2.040 3.040 nonbonded pdb=" O LEU A 98 " pdb=" OG1 THR B 112 " model vdw 2.046 3.040 nonbonded pdb=" O LYS D 16 " pdb=" OG SER D 22 " model vdw 2.053 3.040 nonbonded pdb=" OG SER J 43 " pdb=" O GLY G 109 " model vdw 2.063 3.040 nonbonded pdb=" O SER J 30 " pdb=" OH TYR J 71 " model vdw 2.067 3.040 ... (remaining 172507 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 309 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 386 or (resid 387 and (name N or name CA or name \ C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 309 or resid 386 through 419)) selection = (chain 'D' and (resid 9 through 386 or (resid 387 and (name N or name CA or name \ C or name O or name CB )) or resid 388 through 419)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and resid 2 through 102) selection = chain 'J' selection = (chain 'K' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) selection = (chain 'M' and resid 2 through 102) } ncs_group { reference = chain 'T' selection = chain 'Z' } ncs_group { reference = chain 'f' selection = chain 'l' } 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: 0.010 Normalize map: mean=0, sd=1: 8.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.300 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.004 0.064 21481 Z= 0.184 Angle : 0.730 15.919 29031 Z= 0.348 Chirality : 0.046 0.573 3234 Planarity : 0.004 0.043 3574 Dihedral : 14.567 122.805 8140 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 29.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.13 % Allowed : 1.75 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.15), residues: 2522 helix: -2.70 (0.17), residues: 511 sheet: -2.98 (0.15), residues: 759 loop : -2.55 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 252 TYR 0.014 0.002 TYR A 301 PHE 0.030 0.002 PHE J 98 TRP 0.022 0.002 TRP L 108 HIS 0.009 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00391 (21442) covalent geometry : angle 0.69661 (28932) SS BOND : bond 0.00288 ( 18) SS BOND : angle 1.31238 ( 36) hydrogen bonds : bond 0.25998 ( 629) hydrogen bonds : angle 10.20096 ( 1665) link_ALPHA1-2 : bond 0.00402 ( 1) link_ALPHA1-2 : angle 1.78462 ( 3) link_ALPHA1-3 : bond 0.00516 ( 2) link_ALPHA1-3 : angle 3.37184 ( 6) link_ALPHA1-6 : bond 0.00723 ( 3) link_ALPHA1-6 : angle 1.96900 ( 9) link_BETA1-4 : bond 0.00586 ( 10) link_BETA1-4 : angle 3.75677 ( 30) link_NAG-ASN : bond 0.01272 ( 5) link_NAG-ASN : angle 7.47085 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 463 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8688 (mt0) cc_final: 0.8439 (pm20) REVERT: F 23 LYS cc_start: 0.9238 (tptp) cc_final: 0.8898 (tppp) REVERT: D 235 VAL cc_start: 0.9654 (t) cc_final: 0.9170 (t) REVERT: D 399 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8082 (mpp80) REVERT: A 220 MET cc_start: 0.7769 (ptm) cc_final: 0.7421 (ttp) REVERT: B 287 MET cc_start: 0.8744 (mmm) cc_final: 0.8405 (mmm) REVERT: C 407 LEU cc_start: 0.9413 (tt) cc_final: 0.9078 (tm) REVERT: C 412 PHE cc_start: 0.8239 (t80) cc_final: 0.7987 (t80) REVERT: E 77 MET cc_start: 0.8871 (mmt) cc_final: 0.8382 (mmm) REVERT: E 263 TRP cc_start: 0.8949 (m-10) cc_final: 0.8740 (m-10) REVERT: E 329 GLN cc_start: 0.8804 (tp40) cc_final: 0.8319 (tp-100) outliers start: 3 outliers final: 0 residues processed: 465 average time/residue: 0.7370 time to fit residues: 380.3614 Evaluate side-chains 263 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 399 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 107 HIS D 125 ASN D 150 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 305 ASN A 61 ASN A 125 ASN A 150 GLN A 186 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 266 GLN B 67 GLN B 107 HIS ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN C 46 ASN C 125 ASN C 164 ASN C 177 GLN C 186 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN E 90 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.066142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050474 restraints weight = 78402.336| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.58 r_work: 0.2976 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21481 Z= 0.231 Angle : 0.861 16.651 29031 Z= 0.403 Chirality : 0.049 0.477 3234 Planarity : 0.005 0.044 3574 Dihedral : 15.607 107.441 3369 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.82 % Allowed : 11.78 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.19 (0.16), residues: 2522 helix: -1.29 (0.21), residues: 543 sheet: -2.42 (0.16), residues: 759 loop : -2.22 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 54 TYR 0.021 0.002 TYR E 454 PHE 0.034 0.002 PHE B 409 TRP 0.025 0.002 TRP A 239 HIS 0.009 0.002 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00530 (21442) covalent geometry : angle 0.83166 (28932) SS BOND : bond 0.00320 ( 18) SS BOND : angle 1.17150 ( 36) hydrogen bonds : bond 0.05119 ( 629) hydrogen bonds : angle 6.47769 ( 1665) link_ALPHA1-2 : bond 0.00364 ( 1) link_ALPHA1-2 : angle 2.08740 ( 3) link_ALPHA1-3 : bond 0.00968 ( 2) link_ALPHA1-3 : angle 4.69446 ( 6) link_ALPHA1-6 : bond 0.01690 ( 3) link_ALPHA1-6 : angle 3.25987 ( 9) link_BETA1-4 : bond 0.00805 ( 10) link_BETA1-4 : angle 3.69706 ( 30) link_NAG-ASN : bond 0.01276 ( 5) link_NAG-ASN : angle 7.41764 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8625 (mmpt) REVERT: G 107 TYR cc_start: 0.8924 (m-80) cc_final: 0.8620 (m-80) REVERT: F 5 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8589 (tm-30) REVERT: F 13 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6609 (mmtt) REVERT: F 23 LYS cc_start: 0.9116 (tptp) cc_final: 0.8889 (tppp) REVERT: M 11 MET cc_start: 0.8912 (mtt) cc_final: 0.8642 (mmt) REVERT: L 82 GLN cc_start: 0.9463 (tt0) cc_final: 0.9232 (tt0) REVERT: I 4 MET cc_start: 0.8969 (mmm) cc_final: 0.8762 (mtm) REVERT: I 9 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8708 (mmmt) REVERT: I 45 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8558 (mmpt) REVERT: H 89 GLU cc_start: 0.9111 (tp30) cc_final: 0.8802 (tp30) REVERT: D 140 MET cc_start: 0.9508 (mtt) cc_final: 0.9280 (mpp) REVERT: D 227 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8969 (mtm) REVERT: D 239 TRP cc_start: 0.8474 (m-10) cc_final: 0.8120 (m-10) REVERT: D 293 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8970 (m-80) REVERT: D 399 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8560 (mpp80) REVERT: A 220 MET cc_start: 0.8611 (ptm) cc_final: 0.7883 (ttp) REVERT: B 287 MET cc_start: 0.9468 (mmm) cc_final: 0.9153 (mmm) REVERT: B 412 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8562 (t80) REVERT: C 56 MET cc_start: 0.9193 (mmm) cc_final: 0.8944 (mmm) REVERT: C 412 PHE cc_start: 0.8904 (t80) cc_final: 0.8553 (t80) REVERT: E 77 MET cc_start: 0.9419 (mmt) cc_final: 0.8707 (mmm) REVERT: E 120 ASP cc_start: 0.8864 (p0) cc_final: 0.8551 (p0) REVERT: E 217 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: E 263 TRP cc_start: 0.9362 (m-10) cc_final: 0.9008 (m-10) REVERT: E 290 GLU cc_start: 0.9327 (tp30) cc_final: 0.9057 (tp30) REVERT: E 294 LEU cc_start: 0.9415 (mm) cc_final: 0.9108 (mm) REVERT: E 329 GLN cc_start: 0.9636 (tp40) cc_final: 0.8818 (tp-100) REVERT: E 331 MET cc_start: 0.8775 (mmp) cc_final: 0.8486 (mmp) outliers start: 63 outliers final: 18 residues processed: 336 average time/residue: 0.6721 time to fit residues: 253.1892 Evaluate side-chains 273 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 399 ARG Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 59 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 HIS F 6 GLN F 27 HIS M 91 HIS L 6 GLN I 79 GLN H 27 HIS D 67 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 125 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.064191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048107 restraints weight = 78953.218| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.61 r_work: 0.2903 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 21481 Z= 0.303 Angle : 0.869 16.824 29031 Z= 0.405 Chirality : 0.050 0.525 3234 Planarity : 0.005 0.047 3574 Dihedral : 13.875 98.277 3369 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.13 % Allowed : 13.57 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.16), residues: 2522 helix: -0.59 (0.22), residues: 548 sheet: -2.06 (0.17), residues: 744 loop : -1.94 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 399 TYR 0.021 0.002 TYR E 231 PHE 0.027 0.002 PHE A 409 TRP 0.018 0.002 TRP A 243 HIS 0.012 0.002 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00687 (21442) covalent geometry : angle 0.83930 (28932) SS BOND : bond 0.00337 ( 18) SS BOND : angle 1.13356 ( 36) hydrogen bonds : bond 0.04269 ( 629) hydrogen bonds : angle 5.75310 ( 1665) link_ALPHA1-2 : bond 0.00275 ( 1) link_ALPHA1-2 : angle 2.03955 ( 3) link_ALPHA1-3 : bond 0.01068 ( 2) link_ALPHA1-3 : angle 4.45249 ( 6) link_ALPHA1-6 : bond 0.01997 ( 3) link_ALPHA1-6 : angle 3.54739 ( 9) link_BETA1-4 : bond 0.00717 ( 10) link_BETA1-4 : angle 3.81680 ( 30) link_NAG-ASN : bond 0.01199 ( 5) link_NAG-ASN : angle 7.35980 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 269 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 ASP cc_start: 0.7004 (m-30) cc_final: 0.6761 (m-30) REVERT: G 89 GLU cc_start: 0.8860 (mp0) cc_final: 0.8066 (pp20) REVERT: G 107 TYR cc_start: 0.8987 (m-80) cc_final: 0.8736 (m-80) REVERT: F 5 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8615 (tm-30) REVERT: F 13 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6727 (mmtt) REVERT: M 11 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8520 (mmt) REVERT: L 19 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8738 (ttmm) REVERT: L 82 GLN cc_start: 0.9543 (tt0) cc_final: 0.8947 (tt0) REVERT: I 45 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8591 (mmpt) REVERT: I 79 GLN cc_start: 0.6919 (mp10) cc_final: 0.6692 (mp10) REVERT: I 82 ASP cc_start: 0.7320 (m-30) cc_final: 0.6984 (m-30) REVERT: H 59 ASN cc_start: 0.8950 (t0) cc_final: 0.8626 (t160) REVERT: H 74 LYS cc_start: 0.9336 (mtmm) cc_final: 0.8999 (mppt) REVERT: D 392 LYS cc_start: 0.8860 (pttm) cc_final: 0.8633 (ptpp) REVERT: D 399 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8326 (pmm-80) REVERT: A 21 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 220 MET cc_start: 0.8672 (ptm) cc_final: 0.8136 (ttp) REVERT: A 305 ASN cc_start: 0.9566 (OUTLIER) cc_final: 0.9083 (t0) REVERT: B 192 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: B 412 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8615 (t80) REVERT: C 56 MET cc_start: 0.9217 (mmm) cc_final: 0.8927 (mmm) REVERT: C 263 MET cc_start: 0.9387 (mmm) cc_final: 0.8976 (mmm) REVERT: C 290 CYS cc_start: 0.9414 (m) cc_final: 0.9106 (m) REVERT: C 407 LEU cc_start: 0.9549 (tm) cc_final: 0.9237 (mt) REVERT: C 411 MET cc_start: 0.9250 (ptt) cc_final: 0.8829 (ppp) REVERT: C 412 PHE cc_start: 0.8936 (t80) cc_final: 0.8733 (t80) REVERT: E 77 MET cc_start: 0.9459 (mmt) cc_final: 0.8706 (mmm) REVERT: E 153 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8666 (mtt) REVERT: E 217 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6786 (pp20) REVERT: E 263 TRP cc_start: 0.9423 (m-10) cc_final: 0.9030 (m-10) REVERT: E 285 LEU cc_start: 0.9330 (tp) cc_final: 0.9120 (mm) REVERT: E 290 GLU cc_start: 0.9388 (tp30) cc_final: 0.9159 (tp30) REVERT: E 329 GLN cc_start: 0.9646 (tp40) cc_final: 0.8888 (tp-100) REVERT: E 331 MET cc_start: 0.8762 (mmp) cc_final: 0.8472 (mmp) outliers start: 70 outliers final: 23 residues processed: 313 average time/residue: 0.6572 time to fit residues: 231.5890 Evaluate side-chains 275 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 399 ARG Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 199 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.065641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.049684 restraints weight = 78052.404| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.60 r_work: 0.2954 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21481 Z= 0.158 Angle : 0.795 16.327 29031 Z= 0.362 Chirality : 0.048 0.496 3234 Planarity : 0.004 0.049 3574 Dihedral : 12.553 93.506 3369 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.09 % Allowed : 15.14 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.16), residues: 2522 helix: -0.41 (0.22), residues: 558 sheet: -1.75 (0.17), residues: 728 loop : -1.81 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 18 TYR 0.015 0.001 TYR E 325 PHE 0.028 0.002 PHE A 409 TRP 0.011 0.001 TRP K 50 HIS 0.011 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00360 (21442) covalent geometry : angle 0.76645 (28932) SS BOND : bond 0.00288 ( 18) SS BOND : angle 0.88001 ( 36) hydrogen bonds : bond 0.03700 ( 629) hydrogen bonds : angle 5.32548 ( 1665) link_ALPHA1-2 : bond 0.00338 ( 1) link_ALPHA1-2 : angle 1.58169 ( 3) link_ALPHA1-3 : bond 0.01069 ( 2) link_ALPHA1-3 : angle 4.30544 ( 6) link_ALPHA1-6 : bond 0.01341 ( 3) link_ALPHA1-6 : angle 3.24430 ( 9) link_BETA1-4 : bond 0.00683 ( 10) link_BETA1-4 : angle 3.55608 ( 30) link_NAG-ASN : bond 0.01223 ( 5) link_NAG-ASN : angle 7.07102 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8527 (mmpt) REVERT: J 82 ASP cc_start: 0.7046 (m-30) cc_final: 0.6746 (m-30) REVERT: G 73 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: G 89 GLU cc_start: 0.8854 (mp0) cc_final: 0.8024 (pp20) REVERT: G 90 ASP cc_start: 0.8733 (m-30) cc_final: 0.8097 (m-30) REVERT: G 107 TYR cc_start: 0.8956 (m-80) cc_final: 0.8715 (m-80) REVERT: K 18 ARG cc_start: 0.8772 (ttm110) cc_final: 0.8543 (ttm110) REVERT: K 24 LYS cc_start: 0.7926 (tppt) cc_final: 0.7615 (tppt) REVERT: F 5 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8577 (tm-30) REVERT: F 74 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: L 19 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8650 (mmmm) REVERT: L 52 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8975 (tt) REVERT: L 82 GLN cc_start: 0.9545 (tt0) cc_final: 0.9197 (tt0) REVERT: I 9 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8699 (mmmt) REVERT: I 45 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8543 (mmpt) REVERT: I 79 GLN cc_start: 0.7010 (mp10) cc_final: 0.6789 (mp-120) REVERT: I 82 ASP cc_start: 0.7308 (m-30) cc_final: 0.6942 (m-30) REVERT: H 3 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8426 (tp-100) REVERT: H 59 ASN cc_start: 0.8936 (t0) cc_final: 0.8611 (t160) REVERT: H 74 LYS cc_start: 0.9363 (mtmm) cc_final: 0.8994 (mppt) REVERT: H 81 MET cc_start: 0.9372 (ttp) cc_final: 0.9142 (ttp) REVERT: H 89 GLU cc_start: 0.9107 (tp30) cc_final: 0.8872 (tp30) REVERT: D 55 THR cc_start: 0.9700 (m) cc_final: 0.9482 (p) REVERT: D 140 MET cc_start: 0.9545 (mtt) cc_final: 0.9341 (mpp) REVERT: D 239 TRP cc_start: 0.8771 (m-10) cc_final: 0.8449 (m-10) REVERT: D 287 MET cc_start: 0.9084 (mmm) cc_final: 0.8308 (mmm) REVERT: D 399 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8539 (pmm-80) REVERT: A 309 ARG cc_start: 0.8820 (tmt170) cc_final: 0.8611 (ttp-170) REVERT: A 412 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8942 (m-80) REVERT: B 287 MET cc_start: 0.9457 (mmm) cc_final: 0.9245 (mmm) REVERT: B 412 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8546 (t80) REVERT: C 56 MET cc_start: 0.9254 (mmm) cc_final: 0.8951 (mmm) REVERT: C 140 MET cc_start: 0.9477 (mtp) cc_final: 0.9146 (mtp) REVERT: C 213 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8404 (mmm-85) REVERT: C 263 MET cc_start: 0.9428 (mmm) cc_final: 0.8842 (mmm) REVERT: C 290 CYS cc_start: 0.9421 (m) cc_final: 0.9051 (m) REVERT: C 407 LEU cc_start: 0.9514 (tm) cc_final: 0.9250 (mt) REVERT: C 411 MET cc_start: 0.9219 (ptt) cc_final: 0.8878 (pp-130) REVERT: C 412 PHE cc_start: 0.8888 (t80) cc_final: 0.8648 (t80) REVERT: E 77 MET cc_start: 0.9472 (mmt) cc_final: 0.8784 (mmm) REVERT: E 120 ASP cc_start: 0.9023 (p0) cc_final: 0.8611 (p0) REVERT: E 263 TRP cc_start: 0.9288 (m-10) cc_final: 0.8878 (m-10) REVERT: E 285 LEU cc_start: 0.9322 (tp) cc_final: 0.9108 (mm) REVERT: E 290 GLU cc_start: 0.9393 (tp30) cc_final: 0.9162 (tp30) REVERT: E 329 GLN cc_start: 0.9654 (tp40) cc_final: 0.8957 (tp-100) REVERT: E 331 MET cc_start: 0.8708 (mmp) cc_final: 0.8387 (mmp) outliers start: 69 outliers final: 24 residues processed: 327 average time/residue: 0.6388 time to fit residues: 236.3705 Evaluate side-chains 284 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 399 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 138 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.064980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049037 restraints weight = 78173.194| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.59 r_work: 0.2930 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21481 Z= 0.192 Angle : 0.802 16.315 29031 Z= 0.365 Chirality : 0.047 0.499 3234 Planarity : 0.004 0.045 3574 Dihedral : 11.770 92.193 3369 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.40 % Allowed : 16.70 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2522 helix: -0.21 (0.22), residues: 562 sheet: -1.64 (0.17), residues: 737 loop : -1.68 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 40 TYR 0.015 0.001 TYR E 325 PHE 0.026 0.002 PHE A 409 TRP 0.025 0.001 TRP A 243 HIS 0.009 0.002 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00436 (21442) covalent geometry : angle 0.77329 (28932) SS BOND : bond 0.00299 ( 18) SS BOND : angle 1.05170 ( 36) hydrogen bonds : bond 0.03579 ( 629) hydrogen bonds : angle 5.15920 ( 1665) link_ALPHA1-2 : bond 0.00293 ( 1) link_ALPHA1-2 : angle 1.55252 ( 3) link_ALPHA1-3 : bond 0.01092 ( 2) link_ALPHA1-3 : angle 4.29506 ( 6) link_ALPHA1-6 : bond 0.01084 ( 3) link_ALPHA1-6 : angle 3.02423 ( 9) link_BETA1-4 : bond 0.00673 ( 10) link_BETA1-4 : angle 3.48239 ( 30) link_NAG-ASN : bond 0.01220 ( 5) link_NAG-ASN : angle 7.13493 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 261 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 89 GLU cc_start: 0.8854 (mp0) cc_final: 0.8119 (pp20) REVERT: K 24 LYS cc_start: 0.7899 (tppt) cc_final: 0.7546 (tppt) REVERT: K 81 GLU cc_start: 0.8462 (mp0) cc_final: 0.8108 (pm20) REVERT: F 5 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8559 (tm-30) REVERT: F 74 LYS cc_start: 0.8959 (mttm) cc_final: 0.8694 (mttm) REVERT: M 42 GLN cc_start: 0.9253 (mt0) cc_final: 0.8936 (mt0) REVERT: M 83 LEU cc_start: 0.8828 (mm) cc_final: 0.8460 (mm) REVERT: M 90 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8627 (pp30) REVERT: L 19 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8660 (mmmm) REVERT: L 52 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8957 (tt) REVERT: L 82 GLN cc_start: 0.9530 (tt0) cc_final: 0.9209 (tt0) REVERT: I 9 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8953 (mmmm) REVERT: I 45 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8533 (mmpt) REVERT: H 59 ASN cc_start: 0.8936 (t0) cc_final: 0.8631 (t160) REVERT: H 74 LYS cc_start: 0.9366 (mtmm) cc_final: 0.9050 (mppt) REVERT: D 399 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8600 (pmm-80) REVERT: A 21 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8990 (p) REVERT: A 220 MET cc_start: 0.8670 (ptm) cc_final: 0.8221 (ttp) REVERT: A 412 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8833 (t80) REVERT: B 246 MET cc_start: 0.8245 (pmm) cc_final: 0.7391 (ppp) REVERT: B 287 MET cc_start: 0.9480 (mmm) cc_final: 0.9148 (mmm) REVERT: B 412 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8551 (t80) REVERT: C 56 MET cc_start: 0.9263 (mmm) cc_final: 0.8980 (mmp) REVERT: C 140 MET cc_start: 0.9474 (mtp) cc_final: 0.8961 (mtt) REVERT: C 213 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8193 (mmm-85) REVERT: C 263 MET cc_start: 0.9437 (mmm) cc_final: 0.9229 (mmm) REVERT: C 290 CYS cc_start: 0.9428 (m) cc_final: 0.9210 (m) REVERT: C 293 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8696 (m-10) REVERT: C 407 LEU cc_start: 0.9554 (tm) cc_final: 0.9239 (mt) REVERT: C 411 MET cc_start: 0.9228 (ptt) cc_final: 0.8806 (pp-130) REVERT: E 77 MET cc_start: 0.9461 (mmt) cc_final: 0.8763 (mmm) REVERT: E 120 ASP cc_start: 0.9034 (p0) cc_final: 0.8587 (p0) REVERT: E 214 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7993 (pp20) REVERT: E 217 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: E 232 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7824 (p) REVERT: E 263 TRP cc_start: 0.9333 (m-10) cc_final: 0.8777 (m-10) REVERT: E 285 LEU cc_start: 0.9320 (tp) cc_final: 0.9114 (mm) REVERT: E 290 GLU cc_start: 0.9442 (tp30) cc_final: 0.9065 (tp30) REVERT: E 294 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9147 (mm) REVERT: E 329 GLN cc_start: 0.9672 (tp40) cc_final: 0.8893 (tp-100) REVERT: E 331 MET cc_start: 0.8701 (mmp) cc_final: 0.8396 (mmp) REVERT: E 454 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7902 (t80) outliers start: 76 outliers final: 29 residues processed: 310 average time/residue: 0.6410 time to fit residues: 224.2158 Evaluate side-chains 289 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 399 ARG Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN I 79 GLN H 6 GLN D 186 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.064805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048855 restraints weight = 77854.812| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.56 r_work: 0.2926 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21481 Z= 0.196 Angle : 0.811 16.374 29031 Z= 0.368 Chirality : 0.047 0.510 3234 Planarity : 0.004 0.046 3574 Dihedral : 11.016 91.296 3369 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.81 % Allowed : 16.93 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2522 helix: -0.04 (0.23), residues: 566 sheet: -1.55 (0.18), residues: 737 loop : -1.59 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 18 TYR 0.014 0.002 TYR E 325 PHE 0.026 0.002 PHE A 409 TRP 0.013 0.001 TRP A 243 HIS 0.008 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00448 (21442) covalent geometry : angle 0.78017 (28932) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.02212 ( 36) hydrogen bonds : bond 0.03495 ( 629) hydrogen bonds : angle 5.02577 ( 1665) link_ALPHA1-2 : bond 0.00269 ( 1) link_ALPHA1-2 : angle 1.54996 ( 3) link_ALPHA1-3 : bond 0.01075 ( 2) link_ALPHA1-3 : angle 4.34022 ( 6) link_ALPHA1-6 : bond 0.01189 ( 3) link_ALPHA1-6 : angle 2.99589 ( 9) link_BETA1-4 : bond 0.00630 ( 10) link_BETA1-4 : angle 3.42599 ( 30) link_NAG-ASN : bond 0.01280 ( 5) link_NAG-ASN : angle 7.62658 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 257 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 89 GLU cc_start: 0.8868 (mp0) cc_final: 0.8148 (pp20) REVERT: K 24 LYS cc_start: 0.7900 (tppt) cc_final: 0.7593 (tppt) REVERT: K 81 GLU cc_start: 0.8479 (mp0) cc_final: 0.8115 (pm20) REVERT: F 5 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8558 (tm-30) REVERT: F 74 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8791 (mttm) REVERT: F 82 GLN cc_start: 0.9494 (tt0) cc_final: 0.9125 (tt0) REVERT: M 83 LEU cc_start: 0.8845 (mm) cc_final: 0.8486 (mm) REVERT: M 94 THR cc_start: 0.9098 (m) cc_final: 0.8793 (p) REVERT: L 3 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: L 19 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8625 (mmmm) REVERT: L 52 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8909 (tt) REVERT: L 74 LYS cc_start: 0.8942 (mppt) cc_final: 0.8545 (mptt) REVERT: L 82 GLN cc_start: 0.9543 (tt0) cc_final: 0.9212 (tt0) REVERT: I 9 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8972 (mmmm) REVERT: I 45 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8533 (mmpt) REVERT: I 75 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7668 (tp) REVERT: H 59 ASN cc_start: 0.8934 (t0) cc_final: 0.8627 (t160) REVERT: H 74 LYS cc_start: 0.9371 (mtmm) cc_final: 0.9053 (mppt) REVERT: H 89 GLU cc_start: 0.9084 (tp30) cc_final: 0.8665 (tp30) REVERT: D 140 MET cc_start: 0.9607 (mtt) cc_final: 0.9365 (mpp) REVERT: D 287 MET cc_start: 0.9067 (mmm) cc_final: 0.8535 (mtm) REVERT: D 399 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8620 (pmm-80) REVERT: A 21 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9000 (p) REVERT: A 29 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.6792 (ptm-80) REVERT: A 55 THR cc_start: 0.9604 (OUTLIER) cc_final: 0.9359 (p) REVERT: A 110 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8381 (tp30) REVERT: A 220 MET cc_start: 0.8719 (ptm) cc_final: 0.8269 (ttp) REVERT: A 276 LYS cc_start: 0.9348 (mtmm) cc_final: 0.9134 (mttm) REVERT: A 305 ASN cc_start: 0.9593 (OUTLIER) cc_final: 0.9147 (t0) REVERT: A 412 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8970 (m-80) REVERT: B 246 MET cc_start: 0.8314 (pmm) cc_final: 0.7570 (ppp) REVERT: B 287 MET cc_start: 0.9516 (mmm) cc_final: 0.9135 (mmm) REVERT: B 412 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8541 (t80) REVERT: C 55 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9319 (m) REVERT: C 56 MET cc_start: 0.9240 (mmm) cc_final: 0.8942 (mmp) REVERT: C 140 MET cc_start: 0.9465 (mtp) cc_final: 0.9042 (mtt) REVERT: C 213 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8224 (mmm-85) REVERT: C 263 MET cc_start: 0.9436 (mmm) cc_final: 0.9199 (mmm) REVERT: C 290 CYS cc_start: 0.9404 (m) cc_final: 0.9188 (m) REVERT: C 293 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8717 (m-10) REVERT: C 407 LEU cc_start: 0.9540 (tm) cc_final: 0.9230 (mt) REVERT: E 77 MET cc_start: 0.9464 (mmt) cc_final: 0.8788 (mmm) REVERT: E 120 ASP cc_start: 0.9050 (p0) cc_final: 0.8614 (p0) REVERT: E 214 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8017 (pp20) REVERT: E 217 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7309 (pp20) REVERT: E 232 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7870 (p) REVERT: E 263 TRP cc_start: 0.9345 (m-10) cc_final: 0.8927 (m-10) REVERT: E 267 TRP cc_start: 0.9073 (m-90) cc_final: 0.8614 (m100) REVERT: E 285 LEU cc_start: 0.9319 (tp) cc_final: 0.9112 (mm) REVERT: E 290 GLU cc_start: 0.9447 (tp30) cc_final: 0.9048 (tp30) REVERT: E 294 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9144 (mm) REVERT: E 329 GLN cc_start: 0.9682 (tp40) cc_final: 0.9028 (tp-100) REVERT: E 331 MET cc_start: 0.8691 (mmp) cc_final: 0.8380 (mmp) REVERT: E 454 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7953 (t80) outliers start: 85 outliers final: 36 residues processed: 313 average time/residue: 0.6271 time to fit residues: 222.4264 Evaluate side-chains 305 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 399 ARG Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 454 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 185 optimal weight: 0.0670 chunk 139 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 134 optimal weight: 0.0020 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.066194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050383 restraints weight = 77889.603| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.58 r_work: 0.2973 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21481 Z= 0.129 Angle : 0.781 16.285 29031 Z= 0.354 Chirality : 0.046 0.467 3234 Planarity : 0.004 0.047 3574 Dihedral : 10.051 88.879 3369 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.54 % Allowed : 17.20 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.17), residues: 2522 helix: 0.11 (0.23), residues: 559 sheet: -1.39 (0.18), residues: 740 loop : -1.53 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 101 TYR 0.020 0.001 TYR G 107 PHE 0.025 0.001 PHE A 409 TRP 0.035 0.001 TRP A 243 HIS 0.008 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00292 (21442) covalent geometry : angle 0.75250 (28932) SS BOND : bond 0.00277 ( 18) SS BOND : angle 0.95554 ( 36) hydrogen bonds : bond 0.03364 ( 629) hydrogen bonds : angle 4.84463 ( 1665) link_ALPHA1-2 : bond 0.00333 ( 1) link_ALPHA1-2 : angle 1.54321 ( 3) link_ALPHA1-3 : bond 0.01094 ( 2) link_ALPHA1-3 : angle 4.38275 ( 6) link_ALPHA1-6 : bond 0.01473 ( 3) link_ALPHA1-6 : angle 2.57195 ( 9) link_BETA1-4 : bond 0.00620 ( 10) link_BETA1-4 : angle 3.25413 ( 30) link_NAG-ASN : bond 0.01334 ( 5) link_NAG-ASN : angle 7.20639 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 273 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 19 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8430 (m) REVERT: G 23 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.9023 (tppt) REVERT: G 89 GLU cc_start: 0.8846 (mp0) cc_final: 0.8257 (pp20) REVERT: G 90 ASP cc_start: 0.8753 (m-30) cc_final: 0.8150 (m-30) REVERT: K 24 LYS cc_start: 0.7906 (tppt) cc_final: 0.7591 (tppt) REVERT: K 81 GLU cc_start: 0.8486 (mp0) cc_final: 0.8059 (pm20) REVERT: F 5 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8482 (tm-30) REVERT: F 12 MET cc_start: 0.8485 (mmm) cc_final: 0.8248 (mpm) REVERT: F 74 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8726 (mttm) REVERT: F 82 GLN cc_start: 0.9521 (tt0) cc_final: 0.9173 (tt0) REVERT: M 42 GLN cc_start: 0.9179 (mt0) cc_final: 0.8798 (pt0) REVERT: M 83 LEU cc_start: 0.8838 (mm) cc_final: 0.8507 (mm) REVERT: M 90 GLN cc_start: 0.9228 (pp30) cc_final: 0.8759 (pp30) REVERT: M 94 THR cc_start: 0.9095 (m) cc_final: 0.8797 (p) REVERT: L 3 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8594 (tm-30) REVERT: L 19 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8530 (mmmm) REVERT: L 74 LYS cc_start: 0.8905 (mppt) cc_final: 0.8528 (mptt) REVERT: L 82 GLN cc_start: 0.9479 (tt0) cc_final: 0.9126 (tt0) REVERT: I 9 LYS cc_start: 0.9255 (mmmm) cc_final: 0.9014 (mmmm) REVERT: I 45 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8488 (mmpt) REVERT: H 59 ASN cc_start: 0.8915 (t0) cc_final: 0.8616 (t160) REVERT: H 74 LYS cc_start: 0.9358 (mtmm) cc_final: 0.9030 (mppt) REVERT: H 89 GLU cc_start: 0.9087 (tp30) cc_final: 0.8715 (tp30) REVERT: D 140 MET cc_start: 0.9618 (mtt) cc_final: 0.9383 (mpp) REVERT: A 21 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8966 (p) REVERT: A 55 THR cc_start: 0.9647 (OUTLIER) cc_final: 0.9406 (p) REVERT: A 110 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: A 220 MET cc_start: 0.8712 (ptm) cc_final: 0.8234 (ttp) REVERT: A 412 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: B 246 MET cc_start: 0.8330 (pmm) cc_final: 0.7618 (ppp) REVERT: B 404 MET cc_start: 0.9424 (tmm) cc_final: 0.9174 (ptt) REVERT: C 55 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9346 (m) REVERT: C 56 MET cc_start: 0.9249 (mmm) cc_final: 0.8971 (mmp) REVERT: C 140 MET cc_start: 0.9453 (mtp) cc_final: 0.9042 (mtt) REVERT: C 213 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8213 (mmm-85) REVERT: C 263 MET cc_start: 0.9409 (mmm) cc_final: 0.9177 (mmm) REVERT: C 293 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8645 (m-10) REVERT: C 407 LEU cc_start: 0.9537 (tm) cc_final: 0.9284 (mt) REVERT: E 77 MET cc_start: 0.9453 (mmt) cc_final: 0.8807 (mmm) REVERT: E 120 ASP cc_start: 0.8949 (p0) cc_final: 0.8496 (p0) REVERT: E 214 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: E 217 GLU cc_start: 0.7345 (pp20) cc_final: 0.6636 (pp20) REVERT: E 263 TRP cc_start: 0.9279 (m-10) cc_final: 0.8757 (m-10) REVERT: E 285 LEU cc_start: 0.9301 (tp) cc_final: 0.9050 (mt) REVERT: E 290 GLU cc_start: 0.9454 (tp30) cc_final: 0.9015 (mm-30) REVERT: E 294 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9004 (mm) REVERT: E 329 GLN cc_start: 0.9684 (tp40) cc_final: 0.8957 (tp-100) REVERT: E 331 MET cc_start: 0.8658 (mmp) cc_final: 0.8335 (mmp) outliers start: 79 outliers final: 29 residues processed: 324 average time/residue: 0.6333 time to fit residues: 232.0015 Evaluate side-chains 276 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 186 GLN Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 231 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN B 186 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.065583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049567 restraints weight = 78152.892| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.61 r_work: 0.2951 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21481 Z= 0.164 Angle : 0.812 16.268 29031 Z= 0.367 Chirality : 0.047 0.489 3234 Planarity : 0.004 0.044 3574 Dihedral : 9.395 83.675 3365 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.40 % Allowed : 17.78 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.17), residues: 2522 helix: 0.27 (0.23), residues: 557 sheet: -1.34 (0.18), residues: 740 loop : -1.50 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 40 TYR 0.017 0.001 TYR D 301 PHE 0.025 0.001 PHE B 187 TRP 0.032 0.001 TRP A 243 HIS 0.007 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00380 (21442) covalent geometry : angle 0.78681 (28932) SS BOND : bond 0.00275 ( 18) SS BOND : angle 1.03367 ( 36) hydrogen bonds : bond 0.03409 ( 629) hydrogen bonds : angle 4.85556 ( 1665) link_ALPHA1-2 : bond 0.00220 ( 1) link_ALPHA1-2 : angle 1.61515 ( 3) link_ALPHA1-3 : bond 0.00990 ( 2) link_ALPHA1-3 : angle 4.43600 ( 6) link_ALPHA1-6 : bond 0.01380 ( 3) link_ALPHA1-6 : angle 2.15703 ( 9) link_BETA1-4 : bond 0.00642 ( 10) link_BETA1-4 : angle 3.28972 ( 30) link_NAG-ASN : bond 0.01289 ( 5) link_NAG-ASN : angle 6.92493 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 239 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8875 (tppt) REVERT: G 65 LYS cc_start: 0.9058 (mptt) cc_final: 0.8838 (mppt) REVERT: G 74 LYS cc_start: 0.8593 (mppt) cc_final: 0.8319 (tppt) REVERT: G 89 GLU cc_start: 0.8896 (mp0) cc_final: 0.8290 (pp20) REVERT: G 90 ASP cc_start: 0.8756 (m-30) cc_final: 0.8157 (m-30) REVERT: K 24 LYS cc_start: 0.7899 (tppt) cc_final: 0.7600 (tppt) REVERT: K 81 GLU cc_start: 0.8493 (mp0) cc_final: 0.8066 (pm20) REVERT: F 5 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8501 (tm-30) REVERT: F 74 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8760 (mttm) REVERT: F 82 GLN cc_start: 0.9517 (tt0) cc_final: 0.9160 (tt0) REVERT: M 11 MET cc_start: 0.8110 (mmt) cc_final: 0.7831 (mpt) REVERT: M 42 GLN cc_start: 0.9193 (mt0) cc_final: 0.8751 (pt0) REVERT: M 83 LEU cc_start: 0.8856 (mm) cc_final: 0.8515 (mm) REVERT: M 94 THR cc_start: 0.9080 (m) cc_final: 0.8787 (p) REVERT: L 3 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8589 (tm-30) REVERT: L 19 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8537 (mmmm) REVERT: L 46 GLU cc_start: 0.9012 (tt0) cc_final: 0.8764 (mt-10) REVERT: L 74 LYS cc_start: 0.8931 (mppt) cc_final: 0.8536 (mptt) REVERT: L 82 GLN cc_start: 0.9494 (tt0) cc_final: 0.9154 (tt0) REVERT: I 9 LYS cc_start: 0.9300 (mmmm) cc_final: 0.9008 (mmmm) REVERT: I 11 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7590 (mmp) REVERT: I 45 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8520 (mmpt) REVERT: I 75 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7592 (tp) REVERT: H 59 ASN cc_start: 0.8910 (t0) cc_final: 0.8597 (t160) REVERT: H 74 LYS cc_start: 0.9375 (mtmm) cc_final: 0.9052 (mppt) REVERT: H 89 GLU cc_start: 0.9139 (tp30) cc_final: 0.8787 (tp30) REVERT: D 140 MET cc_start: 0.9619 (mtt) cc_final: 0.9390 (mpp) REVERT: D 287 MET cc_start: 0.8891 (mmm) cc_final: 0.8674 (mtm) REVERT: A 21 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9000 (p) REVERT: A 55 THR cc_start: 0.9635 (OUTLIER) cc_final: 0.9395 (p) REVERT: A 110 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: A 220 MET cc_start: 0.8699 (ptm) cc_final: 0.8207 (ttp) REVERT: A 246 MET cc_start: 0.8853 (ppp) cc_final: 0.8538 (ppp) REVERT: A 305 ASN cc_start: 0.9607 (OUTLIER) cc_final: 0.9170 (t0) REVERT: B 8 MET cc_start: 0.7999 (ppp) cc_final: 0.7658 (mmm) REVERT: B 18 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8492 (ptp) REVERT: B 192 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: B 246 MET cc_start: 0.8282 (pmm) cc_final: 0.7542 (ppp) REVERT: B 287 MET cc_start: 0.9546 (mmm) cc_final: 0.9114 (mmm) REVERT: B 412 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8497 (t80) REVERT: C 55 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9334 (m) REVERT: C 56 MET cc_start: 0.9257 (mmm) cc_final: 0.8950 (mmp) REVERT: C 140 MET cc_start: 0.9435 (mtp) cc_final: 0.8996 (mtt) REVERT: C 213 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8174 (mmm-85) REVERT: C 239 TRP cc_start: 0.8631 (m-10) cc_final: 0.8384 (m-10) REVERT: C 263 MET cc_start: 0.9418 (mmm) cc_final: 0.9193 (mmm) REVERT: C 293 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8677 (m-10) REVERT: C 407 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9288 (mt) REVERT: E 77 MET cc_start: 0.9427 (mmt) cc_final: 0.8750 (mmm) REVERT: E 120 ASP cc_start: 0.8958 (p0) cc_final: 0.8533 (p0) REVERT: E 214 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: E 217 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7168 (pp20) REVERT: E 263 TRP cc_start: 0.9319 (m-10) cc_final: 0.8936 (m-10) REVERT: E 285 LEU cc_start: 0.9290 (tp) cc_final: 0.9043 (mt) REVERT: E 290 GLU cc_start: 0.9469 (tp30) cc_final: 0.9039 (mm-30) REVERT: E 294 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9006 (mm) REVERT: E 329 GLN cc_start: 0.9685 (tp40) cc_final: 0.8996 (tp-100) REVERT: E 331 MET cc_start: 0.8674 (mmp) cc_final: 0.8344 (mmp) outliers start: 76 outliers final: 35 residues processed: 284 average time/residue: 0.6027 time to fit residues: 194.5615 Evaluate side-chains 286 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 19 LYS Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 39 optimal weight: 0.3980 chunk 222 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 0.0030 chunk 145 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN I 27 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.066351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050352 restraints weight = 77776.974| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.60 r_work: 0.2968 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21481 Z= 0.133 Angle : 0.799 16.191 29031 Z= 0.361 Chirality : 0.046 0.468 3234 Planarity : 0.004 0.047 3574 Dihedral : 8.752 76.004 3365 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.82 % Allowed : 18.58 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2522 helix: 0.31 (0.23), residues: 561 sheet: -1.23 (0.18), residues: 742 loop : -1.51 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 18 TYR 0.015 0.001 TYR D 301 PHE 0.020 0.001 PHE A 409 TRP 0.025 0.001 TRP A 243 HIS 0.007 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00307 (21442) covalent geometry : angle 0.77469 (28932) SS BOND : bond 0.00258 ( 18) SS BOND : angle 0.94928 ( 36) hydrogen bonds : bond 0.03338 ( 629) hydrogen bonds : angle 4.76549 ( 1665) link_ALPHA1-2 : bond 0.00240 ( 1) link_ALPHA1-2 : angle 1.66536 ( 3) link_ALPHA1-3 : bond 0.00836 ( 2) link_ALPHA1-3 : angle 4.46456 ( 6) link_ALPHA1-6 : bond 0.01380 ( 3) link_ALPHA1-6 : angle 1.83710 ( 9) link_BETA1-4 : bond 0.00628 ( 10) link_BETA1-4 : angle 3.21815 ( 30) link_NAG-ASN : bond 0.01331 ( 5) link_NAG-ASN : angle 6.71080 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8884 (tppt) REVERT: G 74 LYS cc_start: 0.8677 (mppt) cc_final: 0.8407 (tppt) REVERT: G 89 GLU cc_start: 0.8921 (mp0) cc_final: 0.8309 (pp20) REVERT: K 81 GLU cc_start: 0.8491 (mp0) cc_final: 0.8049 (pm20) REVERT: F 5 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8459 (tm-30) REVERT: F 12 MET cc_start: 0.8421 (mmm) cc_final: 0.8147 (mpm) REVERT: F 23 LYS cc_start: 0.9190 (tptp) cc_final: 0.8944 (mmmm) REVERT: F 74 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8761 (mttm) REVERT: F 82 GLN cc_start: 0.9517 (tt0) cc_final: 0.9066 (tp-100) REVERT: M 11 MET cc_start: 0.7985 (mmt) cc_final: 0.7687 (mpt) REVERT: M 42 GLN cc_start: 0.9144 (mt0) cc_final: 0.8728 (pt0) REVERT: M 83 LEU cc_start: 0.8855 (mm) cc_final: 0.8604 (mm) REVERT: M 90 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8398 (pp30) REVERT: M 94 THR cc_start: 0.9080 (m) cc_final: 0.8789 (p) REVERT: L 3 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8576 (tm-30) REVERT: L 46 GLU cc_start: 0.9021 (tt0) cc_final: 0.8716 (mt-10) REVERT: L 74 LYS cc_start: 0.8918 (mppt) cc_final: 0.8533 (mptt) REVERT: L 82 GLN cc_start: 0.9473 (tt0) cc_final: 0.8947 (tm-30) REVERT: I 9 LYS cc_start: 0.9298 (mmmm) cc_final: 0.9006 (mmmm) REVERT: I 45 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8535 (mmpt) REVERT: I 48 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8266 (pp) REVERT: H 59 ASN cc_start: 0.8928 (t0) cc_final: 0.8618 (t160) REVERT: H 74 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9040 (mppt) REVERT: H 89 GLU cc_start: 0.9119 (tp30) cc_final: 0.8768 (tp30) REVERT: D 140 MET cc_start: 0.9616 (mtt) cc_final: 0.9378 (mpp) REVERT: D 287 MET cc_start: 0.8890 (mmm) cc_final: 0.8645 (mtm) REVERT: A 21 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8983 (p) REVERT: A 55 THR cc_start: 0.9650 (OUTLIER) cc_final: 0.9413 (p) REVERT: A 110 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8207 (tp30) REVERT: A 220 MET cc_start: 0.8717 (ptm) cc_final: 0.8258 (ttp) REVERT: A 246 MET cc_start: 0.8878 (ppp) cc_final: 0.8494 (ppp) REVERT: B 8 MET cc_start: 0.7960 (ppp) cc_final: 0.7696 (tpp) REVERT: B 18 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8521 (ptp) REVERT: B 110 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8162 (tp30) REVERT: B 239 TRP cc_start: 0.8197 (m-10) cc_final: 0.7646 (m-10) REVERT: B 246 MET cc_start: 0.8346 (pmm) cc_final: 0.7603 (ppp) REVERT: B 287 MET cc_start: 0.9553 (mmm) cc_final: 0.9111 (mmm) REVERT: B 404 MET cc_start: 0.9465 (tmm) cc_final: 0.9218 (ptt) REVERT: B 412 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8454 (t80) REVERT: C 55 THR cc_start: 0.9567 (OUTLIER) cc_final: 0.9328 (m) REVERT: C 56 MET cc_start: 0.9255 (mmm) cc_final: 0.8890 (mmm) REVERT: C 213 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8200 (mmm-85) REVERT: C 239 TRP cc_start: 0.8635 (m-10) cc_final: 0.8391 (m-10) REVERT: C 263 MET cc_start: 0.9397 (mmm) cc_final: 0.9166 (mmm) REVERT: C 293 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8637 (m-10) REVERT: C 407 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9215 (mp) REVERT: C 411 MET cc_start: 0.9188 (ptt) cc_final: 0.8758 (pmt) REVERT: E 77 MET cc_start: 0.9394 (mmt) cc_final: 0.8732 (mmm) REVERT: E 120 ASP cc_start: 0.8913 (p0) cc_final: 0.8485 (p0) REVERT: E 214 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8150 (pp20) REVERT: E 263 TRP cc_start: 0.9289 (m-10) cc_final: 0.8930 (m-10) REVERT: E 267 TRP cc_start: 0.9105 (m-90) cc_final: 0.8639 (m100) REVERT: E 285 LEU cc_start: 0.9301 (tp) cc_final: 0.9054 (mt) REVERT: E 290 GLU cc_start: 0.9483 (tp30) cc_final: 0.9044 (mm-30) REVERT: E 294 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9033 (mm) REVERT: E 329 GLN cc_start: 0.9704 (tp40) cc_final: 0.8990 (tp-100) REVERT: E 331 MET cc_start: 0.8641 (mmp) cc_final: 0.8316 (mmp) outliers start: 63 outliers final: 29 residues processed: 298 average time/residue: 0.6813 time to fit residues: 228.0224 Evaluate side-chains 277 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain M residue 90 GLN Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 182 optimal weight: 20.0000 chunk 229 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 35 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN I 27 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.066208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050310 restraints weight = 78149.640| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.61 r_work: 0.2966 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 21481 Z= 0.218 Angle : 0.944 59.200 29031 Z= 0.469 Chirality : 0.049 0.617 3234 Planarity : 0.004 0.110 3574 Dihedral : 8.747 75.914 3365 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.55 % Allowed : 19.17 % Favored : 78.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2522 helix: 0.33 (0.23), residues: 562 sheet: -1.21 (0.18), residues: 743 loop : -1.52 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.001 ARG C 252 TYR 0.078 0.001 TYR C 301 PHE 0.020 0.001 PHE A 409 TRP 0.021 0.001 TRP A 243 HIS 0.015 0.001 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00496 (21442) covalent geometry : angle 0.92421 (28932) SS BOND : bond 0.00291 ( 18) SS BOND : angle 0.97262 ( 36) hydrogen bonds : bond 0.03355 ( 629) hydrogen bonds : angle 4.76641 ( 1665) link_ALPHA1-2 : bond 0.00212 ( 1) link_ALPHA1-2 : angle 1.66257 ( 3) link_ALPHA1-3 : bond 0.00806 ( 2) link_ALPHA1-3 : angle 4.49372 ( 6) link_ALPHA1-6 : bond 0.00951 ( 3) link_ALPHA1-6 : angle 1.80492 ( 9) link_BETA1-4 : bond 0.00627 ( 10) link_BETA1-4 : angle 3.22579 ( 30) link_NAG-ASN : bond 0.01342 ( 5) link_NAG-ASN : angle 6.70825 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8867 (tppt) REVERT: G 74 LYS cc_start: 0.8690 (mppt) cc_final: 0.8414 (tppt) REVERT: G 89 GLU cc_start: 0.8925 (mp0) cc_final: 0.8326 (pp20) REVERT: G 90 ASP cc_start: 0.8735 (m-30) cc_final: 0.8158 (m-30) REVERT: K 81 GLU cc_start: 0.8489 (mp0) cc_final: 0.8048 (pm20) REVERT: F 5 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8467 (tm-30) REVERT: F 12 MET cc_start: 0.8414 (mmm) cc_final: 0.8127 (mpm) REVERT: F 23 LYS cc_start: 0.9181 (tptp) cc_final: 0.8936 (mmmm) REVERT: F 74 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8772 (mttm) REVERT: F 82 GLN cc_start: 0.9526 (tt0) cc_final: 0.9065 (tp-100) REVERT: M 11 MET cc_start: 0.7984 (mmt) cc_final: 0.7685 (mpt) REVERT: M 42 GLN cc_start: 0.9144 (mt0) cc_final: 0.8718 (pt0) REVERT: M 83 LEU cc_start: 0.8893 (mm) cc_final: 0.8593 (mm) REVERT: M 94 THR cc_start: 0.9083 (m) cc_final: 0.8793 (p) REVERT: L 3 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: L 46 GLU cc_start: 0.9030 (tt0) cc_final: 0.8723 (mt-10) REVERT: L 74 LYS cc_start: 0.8921 (mppt) cc_final: 0.8539 (mptt) REVERT: L 82 GLN cc_start: 0.9436 (tt0) cc_final: 0.8930 (tm-30) REVERT: I 9 LYS cc_start: 0.9306 (mmmm) cc_final: 0.8998 (mmmm) REVERT: I 45 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8534 (mmpt) REVERT: I 48 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8263 (pp) REVERT: H 59 ASN cc_start: 0.8925 (t0) cc_final: 0.8615 (t160) REVERT: H 74 LYS cc_start: 0.9365 (mtmm) cc_final: 0.9046 (mppt) REVERT: H 89 GLU cc_start: 0.9132 (tp30) cc_final: 0.8850 (tp30) REVERT: D 140 MET cc_start: 0.9607 (mtt) cc_final: 0.9379 (mpp) REVERT: D 287 MET cc_start: 0.8896 (mmm) cc_final: 0.8582 (mtm) REVERT: A 21 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8987 (p) REVERT: A 55 THR cc_start: 0.9650 (OUTLIER) cc_final: 0.9406 (p) REVERT: A 110 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8205 (tp30) REVERT: A 220 MET cc_start: 0.8763 (ptm) cc_final: 0.8260 (ttp) REVERT: A 246 MET cc_start: 0.8880 (ppp) cc_final: 0.8481 (ppp) REVERT: A 306 PHE cc_start: 0.8931 (t80) cc_final: 0.8480 (t80) REVERT: B 8 MET cc_start: 0.7954 (ppp) cc_final: 0.7697 (tpp) REVERT: B 18 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8522 (ptp) REVERT: B 110 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8156 (tp30) REVERT: B 192 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: B 239 TRP cc_start: 0.8177 (m-10) cc_final: 0.7645 (m-10) REVERT: B 246 MET cc_start: 0.8342 (pmm) cc_final: 0.7604 (ppp) REVERT: B 287 MET cc_start: 0.9562 (mmm) cc_final: 0.9117 (mmm) REVERT: B 404 MET cc_start: 0.9467 (tmm) cc_final: 0.9213 (ptt) REVERT: C 55 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9330 (m) REVERT: C 56 MET cc_start: 0.9278 (mmm) cc_final: 0.8934 (mmp) REVERT: C 140 MET cc_start: 0.9514 (mtp) cc_final: 0.9133 (mtt) REVERT: C 213 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8203 (mmm-85) REVERT: C 239 TRP cc_start: 0.8632 (m-10) cc_final: 0.8411 (m-10) REVERT: C 263 MET cc_start: 0.9394 (mmm) cc_final: 0.9162 (mmm) REVERT: C 293 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8640 (m-10) REVERT: E 77 MET cc_start: 0.9394 (mmt) cc_final: 0.8733 (mmm) REVERT: E 120 ASP cc_start: 0.8921 (p0) cc_final: 0.8490 (p0) REVERT: E 263 TRP cc_start: 0.9334 (m-10) cc_final: 0.8923 (m-10) REVERT: E 267 TRP cc_start: 0.9075 (m-90) cc_final: 0.8620 (m100) REVERT: E 285 LEU cc_start: 0.9301 (tp) cc_final: 0.9054 (mt) REVERT: E 290 GLU cc_start: 0.9489 (tp30) cc_final: 0.9054 (mm-30) REVERT: E 294 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9038 (mm) REVERT: E 329 GLN cc_start: 0.9704 (tp40) cc_final: 0.8992 (tp-100) REVERT: E 331 MET cc_start: 0.8651 (mmp) cc_final: 0.8325 (mmp) outliers start: 57 outliers final: 33 residues processed: 268 average time/residue: 0.6173 time to fit residues: 187.4529 Evaluate side-chains 278 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain G residue 23 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 45 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 218 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.066180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.050345 restraints weight = 77999.448| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.59 r_work: 0.2965 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 21481 Z= 0.218 Angle : 0.944 59.200 29031 Z= 0.469 Chirality : 0.049 0.617 3234 Planarity : 0.004 0.110 3574 Dihedral : 8.747 75.914 3365 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.15 % Allowed : 19.53 % Favored : 78.33 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2522 helix: 0.33 (0.23), residues: 562 sheet: -1.21 (0.18), residues: 743 loop : -1.52 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.001 ARG C 252 TYR 0.078 0.001 TYR C 301 PHE 0.020 0.001 PHE A 409 TRP 0.021 0.001 TRP A 243 HIS 0.015 0.001 HIS F 27 Details of bonding type rmsd covalent geometry : bond 0.00496 (21442) covalent geometry : angle 0.92421 (28932) SS BOND : bond 0.00291 ( 18) SS BOND : angle 0.97262 ( 36) hydrogen bonds : bond 0.03355 ( 629) hydrogen bonds : angle 4.76641 ( 1665) link_ALPHA1-2 : bond 0.00212 ( 1) link_ALPHA1-2 : angle 1.66257 ( 3) link_ALPHA1-3 : bond 0.00806 ( 2) link_ALPHA1-3 : angle 4.49372 ( 6) link_ALPHA1-6 : bond 0.00951 ( 3) link_ALPHA1-6 : angle 1.80492 ( 9) link_BETA1-4 : bond 0.00627 ( 10) link_BETA1-4 : angle 3.22579 ( 30) link_NAG-ASN : bond 0.01342 ( 5) link_NAG-ASN : angle 6.70825 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7974.02 seconds wall clock time: 136 minutes 23.81 seconds (8183.81 seconds total)