Starting phenix.real_space_refine on Sat Jul 4 09:50:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md6_48169/07_2026/9md6_48169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md6_48169/07_2026/9md6_48169.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 { model { file = "/net/cci-nas-00/data/ceres_data/9md6_48169/07_2026/9md6_48169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md6_48169/07_2026/9md6_48169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9md6_48169/07_2026/9md6_48169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md6_48169/07_2026/9md6_48169.map" } 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 124 5.16 5 C 12148 2.51 5 N 3332 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19528 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "B" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "E" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "I" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "C" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "J" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "D" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 833 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.95, per 1000 atoms: 0.20 Number of scatterers: 19528 At special positions: 0 Unit cell: (154.37, 154.37, 79.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 124 16.00 O 3920 8.00 N 3332 7.00 C 12148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 6 " " BMA O 3 " - " MAN O 6 " " BMA P 3 " - " MAN P 6 " BETA1-2 " MAN M 4 " - " NAG M 5 " " MAN N 4 " - " NAG N 5 " " MAN O 4 " - " NAG O 5 " " MAN P 4 " - " NAG P 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 501 " - " ASN A 146 " " NAG A 502 " - " ASN A 367 " " NAG B 501 " - " ASN B 146 " " NAG B 502 " - " ASN B 367 " " NAG C 501 " - " ASN C 146 " " NAG C 502 " - " ASN C 367 " " NAG D 501 " - " ASN D 146 " " NAG D 502 " - " ASN D 367 " " NAG M 1 " - " ASN A 200 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN C 200 " " NAG P 1 " - " ASN D 200 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 854.0 milliseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4456 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.2% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 463 through 467 removed outlier: 3.580A pdb=" N MET A 467 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.885A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 100C removed outlier: 4.390A pdb=" N TYR H 100C" --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.682A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.581A pdb=" N MET B 467 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.885A pdb=" N SER E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 100C removed outlier: 4.390A pdb=" N TYR E 100C" --> pdb=" O TYR E 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.682A pdb=" N ASP I 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 79 through 83' Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 463 through 467 removed outlier: 3.580A pdb=" N MET C 467 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.885A pdb=" N SER F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 100C removed outlier: 4.374A pdb=" N TYR F 100C" --> pdb=" O TYR F 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.682A pdb=" N ASP J 82 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 79 through 83' Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 463 through 467 removed outlier: 3.580A pdb=" N MET D 467 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.885A pdb=" N SER G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 100C removed outlier: 4.390A pdb=" N TYR G 100C" --> pdb=" O TYR G 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.682A pdb=" N ASP K 82 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.638A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.874A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.587A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.595A pdb=" N HIS A 264 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.901A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS A 280 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU A 372 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU A 399 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 380 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN A 391 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.175A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.898A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.352A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.793A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.638A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.874A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS B 175 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET B 160 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN B 173 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.587A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB8, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.595A pdb=" N HIS B 264 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.901A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS B 280 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU B 372 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU B 399 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 378 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 380 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN B 391 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.175A pdb=" N ILE E 34 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 18 through 19 Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.898A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.352A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.793A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.638A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.874A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS C 175 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET C 160 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN C 173 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.587A pdb=" N ASP C 213 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AD2, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.595A pdb=" N HIS C 264 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 276 through 283 removed outlier: 4.901A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS C 280 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU C 372 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU C 399 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS C 378 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE C 380 " --> pdb=" O GLN C 391 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN C 391 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 9 through 11 removed outlier: 6.181A pdb=" N ILE F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AD7, first strand: chain 'J' and resid 4 through 5 removed outlier: 3.899A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.348A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.796A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.638A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.874A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS D 175 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET D 160 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN D 173 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.587A pdb=" N ASP D 213 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 223 through 224 Processing sheet with id=AE5, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.595A pdb=" N HIS D 264 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 276 through 283 removed outlier: 4.901A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS D 280 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU D 372 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU D 399 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS D 378 " --> pdb=" O ASN D 393 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE D 380 " --> pdb=" O GLN D 391 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN D 391 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 9 through 11 removed outlier: 6.175A pdb=" N ILE G 34 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.898A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.352A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.793A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6296 1.34 - 1.46: 5059 1.46 - 1.58: 8457 1.58 - 1.70: 0 1.70 - 1.82: 160 Bond restraints: 19972 Sorted by residual: bond pdb=" CA THR G 24 " pdb=" CB THR G 24 " ideal model delta sigma weight residual 1.527 1.558 -0.031 2.48e-02 1.63e+03 1.57e+00 bond pdb=" CA THR H 24 " pdb=" CB THR H 24 " ideal model delta sigma weight residual 1.527 1.558 -0.031 2.48e-02 1.63e+03 1.57e+00 bond pdb=" CA THR E 24 " pdb=" CB THR E 24 " ideal model delta sigma weight residual 1.527 1.558 -0.031 2.48e-02 1.63e+03 1.57e+00 bond pdb=" CA THR F 24 " pdb=" CB THR F 24 " ideal model delta sigma weight residual 1.527 1.556 -0.028 2.48e-02 1.63e+03 1.32e+00 bond pdb=" CA ASP B 125 " pdb=" CB ASP B 125 " ideal model delta sigma weight residual 1.526 1.542 -0.016 1.50e-02 4.44e+03 1.09e+00 ... (remaining 19967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 25799 1.14 - 2.29: 999 2.29 - 3.43: 251 3.43 - 4.58: 43 4.58 - 5.72: 12 Bond angle restraints: 27104 Sorted by residual: angle pdb=" C ASN C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta sigma weight residual 122.62 117.65 4.97 1.63e+00 3.76e-01 9.30e+00 angle pdb=" C ASN B 199 " pdb=" N ASN B 200 " pdb=" CA ASN B 200 " ideal model delta sigma weight residual 122.62 117.65 4.97 1.63e+00 3.76e-01 9.30e+00 angle pdb=" C ASN D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta sigma weight residual 122.62 117.65 4.97 1.63e+00 3.76e-01 9.30e+00 angle pdb=" C ASN A 199 " pdb=" N ASN A 200 " pdb=" CA ASN A 200 " ideal model delta sigma weight residual 122.62 117.65 4.97 1.63e+00 3.76e-01 9.30e+00 angle pdb=" CA ASP A 125 " pdb=" C ASP A 125 " pdb=" N PRO A 126 " ideal model delta sigma weight residual 117.47 120.17 -2.70 1.16e+00 7.43e-01 5.42e+00 ... (remaining 27099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 11012 17.90 - 35.79: 942 35.79 - 53.69: 215 53.69 - 71.59: 35 71.59 - 89.48: 16 Dihedral angle restraints: 12220 sinusoidal: 5204 harmonic: 7016 Sorted by residual: dihedral pdb=" CA TYR C 336 " pdb=" C TYR C 336 " pdb=" N CYS C 337 " pdb=" CA CYS C 337 " ideal model delta harmonic sigma weight residual 180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TYR D 336 " pdb=" C TYR D 336 " pdb=" N CYS D 337 " pdb=" CA CYS D 337 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TYR B 336 " pdb=" C TYR B 336 " pdb=" N CYS B 337 " pdb=" CA CYS B 337 " ideal model delta harmonic sigma weight residual 180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 12217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2106 0.039 - 0.077: 615 0.077 - 0.116: 245 0.116 - 0.154: 42 0.154 - 0.192: 12 Chirality restraints: 3020 Sorted by residual: chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 1.59e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.08 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.08 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 3017 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 125 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO B 126 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 125 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO C 126 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 125 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO D 126 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.025 5.00e-02 4.00e+02 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 418 2.67 - 3.23: 17274 3.23 - 3.79: 32455 3.79 - 4.34: 47763 4.34 - 4.90: 76682 Nonbonded interactions: 174592 Sorted by model distance: nonbonded pdb=" O GLY E 104 " pdb=" OG SER I 43 " model vdw 2.114 3.040 nonbonded pdb=" O GLY H 104 " pdb=" OG SER L 43 " model vdw 2.114 3.040 nonbonded pdb=" O GLY G 104 " pdb=" OG SER K 43 " model vdw 2.114 3.040 nonbonded pdb=" O GLY F 104 " pdb=" OG SER J 43 " model vdw 2.115 3.040 nonbonded pdb=" O VAL A 317 " pdb=" OG SER A 335 " model vdw 2.249 3.040 ... (remaining 174587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.960 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 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 : 0.002 0.031 20048 Z= 0.109 Angle : 0.578 6.160 27288 Z= 0.309 Chirality : 0.044 0.192 3020 Planarity : 0.005 0.045 3448 Dihedral : 13.943 89.485 7632 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.15 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2444 helix: -4.33 (0.21), residues: 24 sheet: -0.27 (0.16), residues: 1016 loop : -1.07 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 152 TYR 0.010 0.001 TYR G 102 PHE 0.013 0.002 PHE C 354 TRP 0.013 0.001 TRP G 47 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (19972) covalent geometry : angle 0.56099 / 0.31 (27104) SS BOND : bond 0.00242 / 0.15 ( 44) SS BOND : angle 0.86001 / 0.61 ( 88) hydrogen bonds : bond 0.24485 / 15.97 ( 580) hydrogen bonds : angle 9.91830 / 6.95 ( 1563) link_ALPHA1-3 : bond 0.01345 / 0.81 ( 4) link_ALPHA1-3 : angle 1.15375 / 0.57 ( 12) link_ALPHA1-6 : bond 0.01072 / 0.65 ( 4) link_ALPHA1-6 : angle 1.32187 / 0.67 ( 12) link_BETA1-2 : bond 0.00517 / 0.31 ( 4) link_BETA1-2 : angle 1.09068 / 0.53 ( 12) link_BETA1-4 : bond 0.00725 / 0.50 ( 8) link_BETA1-4 : angle 1.63278 / 0.99 ( 24) link_NAG-ASN : bond 0.00227 / 0.14 ( 12) link_NAG-ASN : angle 3.29900 / 2.21 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.670 Fit side-chains REVERT: A 125 ASP cc_start: 0.7876 (p0) cc_final: 0.7505 (p0) REVERT: A 150 HIS cc_start: 0.7269 (m-70) cc_final: 0.6457 (p90) REVERT: A 197 ASN cc_start: 0.7721 (p0) cc_final: 0.7400 (m110) REVERT: H 100 ASP cc_start: 0.7864 (t70) cc_final: 0.7344 (m-30) REVERT: B 125 ASP cc_start: 0.7818 (p0) cc_final: 0.7500 (p0) REVERT: B 150 HIS cc_start: 0.7356 (m-70) cc_final: 0.6497 (p90) REVERT: E 100 ASP cc_start: 0.7981 (t70) cc_final: 0.7451 (m-30) REVERT: C 125 ASP cc_start: 0.7898 (p0) cc_final: 0.7558 (p0) REVERT: C 150 HIS cc_start: 0.7257 (m-70) cc_final: 0.6413 (p90) REVERT: F 100 ASP cc_start: 0.7859 (t70) cc_final: 0.7360 (m-30) REVERT: D 125 ASP cc_start: 0.7878 (p0) cc_final: 0.7568 (p0) REVERT: D 150 HIS cc_start: 0.7239 (m-70) cc_final: 0.6421 (p90) REVERT: G 100 ASP cc_start: 0.7814 (t70) cc_final: 0.7328 (m-30) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.4868 time to fit residues: 170.7759 Evaluate side-chains 260 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN A 441 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 6 GLN B 131 GLN B 197 ASN B 441 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN I 6 GLN C 131 GLN C 197 ASN C 441 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 6 GLN D 131 GLN D 197 ASN D 441 ASN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN K 6 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.113125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.091404 restraints weight = 22737.385| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.42 r_work: 0.2818 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20048 Z= 0.265 Angle : 0.715 5.636 27288 Z= 0.388 Chirality : 0.050 0.203 3020 Planarity : 0.005 0.040 3448 Dihedral : 7.928 55.104 3324 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.26 % Favored : 95.42 % Rotamer: Outliers : 1.88 % Allowed : 7.50 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % 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: -1.00 (0.17), residues: 2444 helix: -3.56 (0.30), residues: 24 sheet: -0.21 (0.16), residues: 1020 loop : -0.92 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 61 TYR 0.017 0.003 TYR C 121 PHE 0.015 0.002 PHE B 354 TRP 0.016 0.002 TRP G 47 HIS 0.004 0.001 HIS D 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (19972) covalent geometry : angle 0.70361 / 0.39 (27104) SS BOND : bond 0.00485 / 0.29 ( 44) SS BOND : angle 1.10891 / 0.78 ( 88) hydrogen bonds : bond 0.05742 / 3.72 ( 580) hydrogen bonds : angle 7.12619 / 4.95 ( 1563) link_ALPHA1-3 : bond 0.01064 / 0.65 ( 4) link_ALPHA1-3 : angle 1.57367 / 0.79 ( 12) link_ALPHA1-6 : bond 0.00881 / 0.54 ( 4) link_ALPHA1-6 : angle 1.34429 / 0.67 ( 12) link_BETA1-2 : bond 0.00869 / 0.53 ( 4) link_BETA1-2 : angle 1.43526 / 0.71 ( 12) link_BETA1-4 : bond 0.00449 / 0.33 ( 8) link_BETA1-4 : angle 2.11021 / 1.22 ( 24) link_NAG-ASN : bond 0.00576 / 0.35 ( 12) link_NAG-ASN : angle 2.56920 / 1.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.761 Fit side-chains REVERT: A 150 HIS cc_start: 0.7817 (m-70) cc_final: 0.6714 (p-80) REVERT: A 434 THR cc_start: 0.9123 (m) cc_final: 0.8887 (p) REVERT: H 70 THR cc_start: 0.8701 (m) cc_final: 0.8433 (p) REVERT: B 150 HIS cc_start: 0.7814 (m-70) cc_final: 0.6705 (p-80) REVERT: B 434 THR cc_start: 0.9125 (m) cc_final: 0.8888 (p) REVERT: E 70 THR cc_start: 0.8697 (m) cc_final: 0.8434 (p) REVERT: C 150 HIS cc_start: 0.7811 (m-70) cc_final: 0.6710 (p-80) REVERT: C 434 THR cc_start: 0.9120 (m) cc_final: 0.8875 (p) REVERT: F 70 THR cc_start: 0.8702 (m) cc_final: 0.8443 (p) REVERT: D 150 HIS cc_start: 0.7806 (m-70) cc_final: 0.6714 (p-80) REVERT: D 434 THR cc_start: 0.9114 (m) cc_final: 0.8874 (p) REVERT: G 70 THR cc_start: 0.8703 (m) cc_final: 0.8441 (p) outliers start: 40 outliers final: 25 residues processed: 289 average time/residue: 0.5548 time to fit residues: 184.1359 Evaluate side-chains 286 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN E 105 GLN F 105 GLN G 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.115203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.092755 restraints weight = 22819.354| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.54 r_work: 0.2856 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20048 Z= 0.149 Angle : 0.585 4.624 27288 Z= 0.319 Chirality : 0.046 0.180 3020 Planarity : 0.004 0.038 3448 Dihedral : 7.317 50.668 3324 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 2.25 % Allowed : 9.38 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2444 helix: -2.52 (0.66), residues: 24 sheet: -0.17 (0.16), residues: 1016 loop : -0.70 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.014 0.002 TYR D 121 PHE 0.014 0.002 PHE D 410 TRP 0.013 0.001 TRP F 47 HIS 0.003 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (19972) covalent geometry : angle 0.57752 / 0.32 (27104) SS BOND : bond 0.00305 / 0.18 ( 44) SS BOND : angle 0.68191 / 0.47 ( 88) hydrogen bonds : bond 0.04823 / 3.12 ( 580) hydrogen bonds : angle 6.47396 / 4.49 ( 1563) link_ALPHA1-3 : bond 0.01230 / 0.75 ( 4) link_ALPHA1-3 : angle 1.35454 / 0.67 ( 12) link_ALPHA1-6 : bond 0.00891 / 0.54 ( 4) link_ALPHA1-6 : angle 1.35436 / 0.68 ( 12) link_BETA1-2 : bond 0.00645 / 0.39 ( 4) link_BETA1-2 : angle 1.25189 / 0.62 ( 12) link_BETA1-4 : bond 0.00555 / 0.41 ( 8) link_BETA1-4 : angle 1.76109 / 1.09 ( 24) link_NAG-ASN : bond 0.00246 / 0.15 ( 12) link_NAG-ASN : angle 1.85966 / 1.21 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 HIS cc_start: 0.7772 (m-70) cc_final: 0.6497 (p90) REVERT: A 434 THR cc_start: 0.9129 (m) cc_final: 0.8922 (p) REVERT: H 70 THR cc_start: 0.8633 (m) cc_final: 0.8308 (p) REVERT: L 3 VAL cc_start: 0.8837 (m) cc_final: 0.8540 (t) REVERT: B 150 HIS cc_start: 0.7758 (m-70) cc_final: 0.6473 (p90) REVERT: B 434 THR cc_start: 0.9120 (m) cc_final: 0.8911 (p) REVERT: E 70 THR cc_start: 0.8631 (m) cc_final: 0.8305 (p) REVERT: I 3 VAL cc_start: 0.8836 (m) cc_final: 0.8543 (t) REVERT: C 150 HIS cc_start: 0.7765 (m-70) cc_final: 0.6499 (p90) REVERT: C 434 THR cc_start: 0.9124 (m) cc_final: 0.8918 (p) REVERT: F 70 THR cc_start: 0.8636 (m) cc_final: 0.8315 (p) REVERT: J 3 VAL cc_start: 0.8833 (m) cc_final: 0.8548 (t) REVERT: D 150 HIS cc_start: 0.7764 (m-70) cc_final: 0.6511 (p90) REVERT: D 434 THR cc_start: 0.9124 (m) cc_final: 0.8914 (p) REVERT: G 70 THR cc_start: 0.8631 (m) cc_final: 0.8309 (p) REVERT: K 3 VAL cc_start: 0.8829 (m) cc_final: 0.8545 (t) outliers start: 48 outliers final: 28 residues processed: 300 average time/residue: 0.6052 time to fit residues: 206.3214 Evaluate side-chains 288 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 123 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 239 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN H 105 GLN B 441 ASN E 105 GLN C 441 ASN F 105 GLN D 441 ASN G 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.091644 restraints weight = 22743.901| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.54 r_work: 0.2827 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20048 Z= 0.175 Angle : 0.598 4.822 27288 Z= 0.325 Chirality : 0.046 0.184 3020 Planarity : 0.004 0.040 3448 Dihedral : 7.462 52.657 3324 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.76 % Favored : 96.07 % Rotamer: Outliers : 2.58 % Allowed : 9.80 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2444 helix: -2.08 (0.86), residues: 24 sheet: -0.19 (0.16), residues: 1016 loop : -0.68 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 54 TYR 0.015 0.002 TYR C 121 PHE 0.014 0.002 PHE D 354 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (19972) covalent geometry : angle 0.58936 / 0.32 (27104) SS BOND : bond 0.00338 / 0.20 ( 44) SS BOND : angle 0.74257 / 0.52 ( 88) hydrogen bonds : bond 0.04659 / 3.02 ( 580) hydrogen bonds : angle 6.27738 / 4.34 ( 1563) link_ALPHA1-3 : bond 0.01156 / 0.71 ( 4) link_ALPHA1-3 : angle 1.41623 / 0.71 ( 12) link_ALPHA1-6 : bond 0.00884 / 0.54 ( 4) link_ALPHA1-6 : angle 1.34251 / 0.67 ( 12) link_BETA1-2 : bond 0.00724 / 0.44 ( 4) link_BETA1-2 : angle 1.22116 / 0.61 ( 12) link_BETA1-4 : bond 0.00552 / 0.40 ( 8) link_BETA1-4 : angle 1.89064 / 1.13 ( 24) link_NAG-ASN : bond 0.00369 / 0.23 ( 12) link_NAG-ASN : angle 2.02489 / 1.32 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7858 (tt0) cc_final: 0.7512 (tp30) REVERT: A 150 HIS cc_start: 0.7776 (m-70) cc_final: 0.6498 (p90) REVERT: H 70 THR cc_start: 0.8631 (m) cc_final: 0.8300 (p) REVERT: L 61 ARG cc_start: 0.8322 (ttm170) cc_final: 0.8046 (ttm170) REVERT: B 83 GLU cc_start: 0.7851 (tt0) cc_final: 0.7502 (tp30) REVERT: B 150 HIS cc_start: 0.7773 (m-70) cc_final: 0.6489 (p90) REVERT: E 70 THR cc_start: 0.8619 (m) cc_final: 0.8292 (p) REVERT: I 61 ARG cc_start: 0.8318 (ttm170) cc_final: 0.8043 (ttm170) REVERT: C 83 GLU cc_start: 0.7866 (tt0) cc_final: 0.7526 (tp30) REVERT: C 150 HIS cc_start: 0.7770 (m-70) cc_final: 0.6499 (p90) REVERT: F 70 THR cc_start: 0.8627 (m) cc_final: 0.8310 (p) REVERT: J 61 ARG cc_start: 0.8322 (ttm170) cc_final: 0.8042 (ttm170) REVERT: D 83 GLU cc_start: 0.7845 (tt0) cc_final: 0.7511 (tp30) REVERT: D 150 HIS cc_start: 0.7776 (m-70) cc_final: 0.6515 (p90) REVERT: G 70 THR cc_start: 0.8631 (m) cc_final: 0.8307 (p) REVERT: K 61 ARG cc_start: 0.8314 (ttm170) cc_final: 0.8041 (ttm170) outliers start: 55 outliers final: 35 residues processed: 296 average time/residue: 0.5715 time to fit residues: 193.1386 Evaluate side-chains 296 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 168 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN H 39 GLN H 105 GLN B 441 ASN E 39 GLN E 105 GLN C 441 ASN F 105 GLN D 441 ASN G 39 GLN G 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.091428 restraints weight = 22702.490| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.53 r_work: 0.2823 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20048 Z= 0.164 Angle : 0.583 4.787 27288 Z= 0.317 Chirality : 0.046 0.181 3020 Planarity : 0.004 0.040 3448 Dihedral : 7.389 52.025 3324 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.58 % Favored : 97.26 % Rotamer: Outliers : 2.58 % Allowed : 10.27 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 2444 helix: -1.81 (0.97), residues: 24 sheet: -0.18 (0.16), residues: 1016 loop : -0.69 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.015 0.002 TYR D 121 PHE 0.013 0.002 PHE A 354 TRP 0.014 0.001 TRP C 178 HIS 0.003 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (19972) covalent geometry : angle 0.57533 / 0.32 (27104) SS BOND : bond 0.00321 / 0.19 ( 44) SS BOND : angle 0.67670 / 0.47 ( 88) hydrogen bonds : bond 0.04459 / 2.90 ( 580) hydrogen bonds : angle 6.17358 / 4.27 ( 1563) link_ALPHA1-3 : bond 0.01182 / 0.72 ( 4) link_ALPHA1-3 : angle 1.39054 / 0.69 ( 12) link_ALPHA1-6 : bond 0.00893 / 0.54 ( 4) link_ALPHA1-6 : angle 1.35066 / 0.68 ( 12) link_BETA1-2 : bond 0.00678 / 0.41 ( 4) link_BETA1-2 : angle 1.20967 / 0.60 ( 12) link_BETA1-4 : bond 0.00542 / 0.40 ( 8) link_BETA1-4 : angle 1.81282 / 1.10 ( 24) link_NAG-ASN : bond 0.00345 / 0.22 ( 12) link_NAG-ASN : angle 1.93443 / 1.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7866 (tt0) cc_final: 0.7529 (tp30) REVERT: A 150 HIS cc_start: 0.7766 (m-70) cc_final: 0.6489 (p90) REVERT: H 70 THR cc_start: 0.8609 (m) cc_final: 0.8293 (p) REVERT: B 83 GLU cc_start: 0.7860 (tt0) cc_final: 0.7523 (tp30) REVERT: B 150 HIS cc_start: 0.7754 (m-70) cc_final: 0.6481 (p90) REVERT: E 70 THR cc_start: 0.8602 (m) cc_final: 0.8286 (p) REVERT: C 83 GLU cc_start: 0.7871 (tt0) cc_final: 0.7543 (tp30) REVERT: C 150 HIS cc_start: 0.7747 (m-70) cc_final: 0.6489 (p90) REVERT: F 70 THR cc_start: 0.8606 (m) cc_final: 0.8301 (p) REVERT: D 83 GLU cc_start: 0.7862 (tt0) cc_final: 0.7536 (tp30) REVERT: D 150 HIS cc_start: 0.7759 (m-70) cc_final: 0.6506 (p90) REVERT: G 70 THR cc_start: 0.8615 (m) cc_final: 0.8306 (p) outliers start: 55 outliers final: 36 residues processed: 291 average time/residue: 0.5618 time to fit residues: 186.5927 Evaluate side-chains 295 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 187 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 chunk 8 optimal weight: 0.6980 chunk 223 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN E 105 GLN F 39 GLN F 105 GLN G 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.116525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.093981 restraints weight = 22394.607| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.57 r_work: 0.2851 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20048 Z= 0.124 Angle : 0.546 4.416 27288 Z= 0.296 Chirality : 0.045 0.184 3020 Planarity : 0.004 0.038 3448 Dihedral : 6.932 47.484 3324 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.60 % Rotamer: Outliers : 2.11 % Allowed : 11.59 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2444 helix: -1.64 (1.04), residues: 24 sheet: -0.05 (0.16), residues: 1016 loop : -0.62 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 54 TYR 0.013 0.001 TYR B 121 PHE 0.012 0.001 PHE D 354 TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS J 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19972) covalent geometry : angle 0.53926 / 0.29 (27104) SS BOND : bond 0.00262 / 0.16 ( 44) SS BOND : angle 0.54152 / 0.38 ( 88) hydrogen bonds : bond 0.04010 / 2.61 ( 580) hydrogen bonds : angle 5.96390 / 4.13 ( 1563) link_ALPHA1-3 : bond 0.01312 / 0.80 ( 4) link_ALPHA1-3 : angle 1.24296 / 0.62 ( 12) link_ALPHA1-6 : bond 0.00975 / 0.59 ( 4) link_ALPHA1-6 : angle 1.33407 / 0.67 ( 12) link_BETA1-2 : bond 0.00615 / 0.38 ( 4) link_BETA1-2 : angle 1.16331 / 0.58 ( 12) link_BETA1-4 : bond 0.00597 / 0.44 ( 8) link_BETA1-4 : angle 1.63478 / 1.01 ( 24) link_NAG-ASN : bond 0.00199 / 0.13 ( 12) link_NAG-ASN : angle 1.77352 / 1.14 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7866 (tt0) cc_final: 0.7519 (tp30) REVERT: A 150 HIS cc_start: 0.7743 (m-70) cc_final: 0.6474 (p90) REVERT: A 197 ASN cc_start: 0.8228 (p0) cc_final: 0.7489 (m110) REVERT: H 70 THR cc_start: 0.8587 (m) cc_final: 0.8301 (p) REVERT: B 83 GLU cc_start: 0.7878 (tt0) cc_final: 0.7531 (tp30) REVERT: B 150 HIS cc_start: 0.7745 (m-70) cc_final: 0.6485 (p90) REVERT: E 70 THR cc_start: 0.8579 (m) cc_final: 0.8292 (p) REVERT: C 83 GLU cc_start: 0.7875 (tt0) cc_final: 0.7541 (tp30) REVERT: C 150 HIS cc_start: 0.7740 (m-70) cc_final: 0.6495 (p90) REVERT: F 70 THR cc_start: 0.8587 (m) cc_final: 0.8310 (p) REVERT: D 83 GLU cc_start: 0.7874 (tt0) cc_final: 0.7539 (tp30) REVERT: D 150 HIS cc_start: 0.7742 (m-70) cc_final: 0.6508 (p90) REVERT: G 70 THR cc_start: 0.8593 (m) cc_final: 0.8314 (p) outliers start: 45 outliers final: 36 residues processed: 285 average time/residue: 0.5630 time to fit residues: 183.4884 Evaluate side-chains 292 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 115 optimal weight: 0.1980 chunk 143 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN E 105 GLN F 105 GLN G 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.089627 restraints weight = 22829.233| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.47 r_work: 0.2796 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20048 Z= 0.261 Angle : 0.661 5.592 27288 Z= 0.356 Chirality : 0.050 0.194 3020 Planarity : 0.005 0.043 3448 Dihedral : 7.978 57.992 3324 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.11 % Rotamer: Outliers : 2.11 % Allowed : 11.96 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2444 helix: -1.98 (0.87), residues: 24 sheet: -0.13 (0.16), residues: 1016 loop : -0.76 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 85 TYR 0.018 0.002 TYR C 121 PHE 0.015 0.002 PHE D 354 TRP 0.016 0.002 TRP G 103 HIS 0.004 0.001 HIS I 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (19972) covalent geometry : angle 0.65036 / 0.35 (27104) SS BOND : bond 0.00460 / 0.27 ( 44) SS BOND : angle 0.94423 / 0.66 ( 88) hydrogen bonds : bond 0.04986 / 3.25 ( 580) hydrogen bonds : angle 6.26033 / 4.31 ( 1563) link_ALPHA1-3 : bond 0.00951 / 0.58 ( 4) link_ALPHA1-3 : angle 1.62635 / 0.82 ( 12) link_ALPHA1-6 : bond 0.00823 / 0.50 ( 4) link_ALPHA1-6 : angle 1.39146 / 0.69 ( 12) link_BETA1-2 : bond 0.00812 / 0.49 ( 4) link_BETA1-2 : angle 1.33622 / 0.68 ( 12) link_BETA1-4 : bond 0.00471 / 0.35 ( 8) link_BETA1-4 : angle 2.15518 / 1.25 ( 24) link_NAG-ASN : bond 0.00590 / 0.37 ( 12) link_NAG-ASN : angle 2.28188 / 1.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7934 (tt0) cc_final: 0.7619 (tp30) REVERT: A 150 HIS cc_start: 0.7821 (m-70) cc_final: 0.6720 (p-80) REVERT: H 70 THR cc_start: 0.8595 (m) cc_final: 0.8321 (p) REVERT: L 61 ARG cc_start: 0.8446 (ttm170) cc_final: 0.8100 (ttm170) REVERT: B 83 GLU cc_start: 0.7908 (tt0) cc_final: 0.7599 (tp30) REVERT: B 150 HIS cc_start: 0.7816 (m-70) cc_final: 0.6717 (p-80) REVERT: E 70 THR cc_start: 0.8588 (m) cc_final: 0.8321 (p) REVERT: I 61 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8100 (ttm170) REVERT: C 83 GLU cc_start: 0.7937 (tt0) cc_final: 0.7626 (tp30) REVERT: C 150 HIS cc_start: 0.7806 (m-70) cc_final: 0.6712 (p-80) REVERT: F 70 THR cc_start: 0.8623 (m) cc_final: 0.8359 (p) REVERT: J 61 ARG cc_start: 0.8441 (ttm170) cc_final: 0.8093 (ttm170) REVERT: D 83 GLU cc_start: 0.7936 (tt0) cc_final: 0.7626 (tp30) REVERT: D 150 HIS cc_start: 0.7820 (m-70) cc_final: 0.6724 (p-80) REVERT: G 70 THR cc_start: 0.8593 (m) cc_final: 0.8330 (p) REVERT: K 61 ARG cc_start: 0.8446 (ttm170) cc_final: 0.8099 (ttm170) outliers start: 45 outliers final: 33 residues processed: 281 average time/residue: 0.5832 time to fit residues: 186.6020 Evaluate side-chains 299 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 GLN H 105 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.092558 restraints weight = 22742.159| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.54 r_work: 0.2844 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20048 Z= 0.135 Angle : 0.560 4.562 27288 Z= 0.304 Chirality : 0.045 0.177 3020 Planarity : 0.004 0.040 3448 Dihedral : 7.242 51.023 3324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.56 % Favored : 96.28 % Rotamer: Outliers : 2.30 % Allowed : 12.34 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.17), residues: 2444 helix: -1.55 (1.01), residues: 24 sheet: -0.06 (0.16), residues: 1016 loop : -0.65 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 85 TYR 0.014 0.001 TYR C 121 PHE 0.013 0.001 PHE A 354 TRP 0.015 0.001 TRP D 178 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (19972) covalent geometry : angle 0.55281 / 0.30 (27104) SS BOND : bond 0.00291 / 0.17 ( 44) SS BOND : angle 0.56729 / 0.40 ( 88) hydrogen bonds : bond 0.04093 / 2.67 ( 580) hydrogen bonds : angle 6.00655 / 4.16 ( 1563) link_ALPHA1-3 : bond 0.01218 / 0.75 ( 4) link_ALPHA1-3 : angle 1.34458 / 0.67 ( 12) link_ALPHA1-6 : bond 0.00911 / 0.55 ( 4) link_ALPHA1-6 : angle 1.34871 / 0.68 ( 12) link_BETA1-2 : bond 0.00622 / 0.38 ( 4) link_BETA1-2 : angle 1.17043 / 0.58 ( 12) link_BETA1-4 : bond 0.00555 / 0.41 ( 8) link_BETA1-4 : angle 1.70754 / 1.07 ( 24) link_NAG-ASN : bond 0.00244 / 0.15 ( 12) link_NAG-ASN : angle 1.82238 / 1.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7853 (tt0) cc_final: 0.7544 (tp30) REVERT: A 150 HIS cc_start: 0.7751 (m-70) cc_final: 0.6484 (p90) REVERT: H 70 THR cc_start: 0.8606 (m) cc_final: 0.8328 (p) REVERT: B 83 GLU cc_start: 0.7861 (tt0) cc_final: 0.7549 (tp30) REVERT: B 150 HIS cc_start: 0.7748 (m-70) cc_final: 0.6480 (p90) REVERT: E 70 THR cc_start: 0.8594 (m) cc_final: 0.8316 (p) REVERT: C 83 GLU cc_start: 0.7873 (tt0) cc_final: 0.7572 (tp30) REVERT: C 150 HIS cc_start: 0.7736 (m-70) cc_final: 0.6477 (p90) REVERT: F 70 THR cc_start: 0.8608 (m) cc_final: 0.8339 (p) REVERT: D 83 GLU cc_start: 0.7871 (tt0) cc_final: 0.7569 (tp30) REVERT: D 150 HIS cc_start: 0.7745 (m-70) cc_final: 0.6489 (p90) REVERT: G 70 THR cc_start: 0.8606 (m) cc_final: 0.8331 (p) outliers start: 49 outliers final: 43 residues processed: 296 average time/residue: 0.5641 time to fit residues: 190.9473 Evaluate side-chains 303 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 88 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN F 81 GLN F 105 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.092832 restraints weight = 22605.225| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.53 r_work: 0.2850 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20048 Z= 0.140 Angle : 0.563 4.563 27288 Z= 0.305 Chirality : 0.045 0.181 3020 Planarity : 0.004 0.041 3448 Dihedral : 7.104 49.633 3324 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 2.06 % Allowed : 12.48 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2444 helix: -1.60 (1.00), residues: 24 sheet: -0.02 (0.16), residues: 1016 loop : -0.59 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 54 TYR 0.014 0.002 TYR D 121 PHE 0.012 0.002 PHE D 354 TRP 0.014 0.001 TRP D 178 HIS 0.002 0.001 HIS J 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (19972) covalent geometry : angle 0.55534 / 0.30 (27104) SS BOND : bond 0.00292 / 0.18 ( 44) SS BOND : angle 0.64766 / 0.49 ( 88) hydrogen bonds : bond 0.04088 / 2.67 ( 580) hydrogen bonds : angle 5.93670 / 4.11 ( 1563) link_ALPHA1-3 : bond 0.01232 / 0.75 ( 4) link_ALPHA1-3 : angle 1.31176 / 0.65 ( 12) link_ALPHA1-6 : bond 0.00928 / 0.56 ( 4) link_ALPHA1-6 : angle 1.33532 / 0.67 ( 12) link_BETA1-2 : bond 0.00647 / 0.39 ( 4) link_BETA1-2 : angle 1.14972 / 0.57 ( 12) link_BETA1-4 : bond 0.00569 / 0.42 ( 8) link_BETA1-4 : angle 1.73177 / 1.05 ( 24) link_NAG-ASN : bond 0.00279 / 0.18 ( 12) link_NAG-ASN : angle 1.89625 / 1.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7864 (tt0) cc_final: 0.7540 (tp30) REVERT: A 150 HIS cc_start: 0.7740 (m-70) cc_final: 0.6478 (p90) REVERT: H 70 THR cc_start: 0.8595 (m) cc_final: 0.8328 (p) REVERT: B 83 GLU cc_start: 0.7870 (tt0) cc_final: 0.7544 (tp30) REVERT: B 150 HIS cc_start: 0.7743 (m-70) cc_final: 0.6483 (p90) REVERT: E 70 THR cc_start: 0.8587 (m) cc_final: 0.8326 (p) REVERT: C 83 GLU cc_start: 0.7887 (tt0) cc_final: 0.7568 (tp30) REVERT: C 150 HIS cc_start: 0.7738 (m-70) cc_final: 0.6488 (p90) REVERT: F 70 THR cc_start: 0.8596 (m) cc_final: 0.8343 (p) REVERT: D 83 GLU cc_start: 0.7883 (tt0) cc_final: 0.7563 (tp30) REVERT: D 150 HIS cc_start: 0.7747 (m-70) cc_final: 0.6503 (p90) REVERT: G 70 THR cc_start: 0.8595 (m) cc_final: 0.8337 (p) outliers start: 44 outliers final: 39 residues processed: 280 average time/residue: 0.5590 time to fit residues: 178.4011 Evaluate side-chains 298 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN F 105 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.090071 restraints weight = 22814.892| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.54 r_work: 0.2803 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20048 Z= 0.199 Angle : 0.612 5.108 27288 Z= 0.331 Chirality : 0.047 0.186 3020 Planarity : 0.004 0.042 3448 Dihedral : 7.589 54.491 3324 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 2.35 % Allowed : 12.99 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2444 helix: -1.79 (0.92), residues: 24 sheet: -0.07 (0.16), residues: 1016 loop : -0.67 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.016 0.002 TYR C 121 PHE 0.014 0.002 PHE C 354 TRP 0.015 0.002 TRP G 103 HIS 0.003 0.001 HIS K 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (19972) covalent geometry : angle 0.60264 / 0.33 (27104) SS BOND : bond 0.00373 / 0.22 ( 44) SS BOND : angle 0.81581 / 0.59 ( 88) hydrogen bonds : bond 0.04543 / 2.96 ( 580) hydrogen bonds : angle 6.11476 / 4.22 ( 1563) link_ALPHA1-3 : bond 0.01065 / 0.65 ( 4) link_ALPHA1-3 : angle 1.49596 / 0.75 ( 12) link_ALPHA1-6 : bond 0.00863 / 0.53 ( 4) link_ALPHA1-6 : angle 1.37474 / 0.69 ( 12) link_BETA1-2 : bond 0.00740 / 0.45 ( 4) link_BETA1-2 : angle 1.23372 / 0.62 ( 12) link_BETA1-4 : bond 0.00486 / 0.36 ( 8) link_BETA1-4 : angle 1.93307 / 1.15 ( 24) link_NAG-ASN : bond 0.00444 / 0.28 ( 12) link_NAG-ASN : angle 2.10170 / 1.37 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7839 (tt0) cc_final: 0.7539 (tp30) REVERT: A 150 HIS cc_start: 0.7779 (m-70) cc_final: 0.6571 (p-80) REVERT: H 70 THR cc_start: 0.8587 (m) cc_final: 0.8312 (p) REVERT: B 83 GLU cc_start: 0.7857 (tt0) cc_final: 0.7530 (tp30) REVERT: B 150 HIS cc_start: 0.7780 (m-70) cc_final: 0.6568 (p-80) REVERT: E 70 THR cc_start: 0.8542 (m) cc_final: 0.8273 (p) REVERT: C 83 GLU cc_start: 0.7871 (tt0) cc_final: 0.7571 (tp30) REVERT: C 150 HIS cc_start: 0.7774 (m-70) cc_final: 0.6572 (p-80) REVERT: F 70 THR cc_start: 0.8558 (m) cc_final: 0.8301 (p) REVERT: D 83 GLU cc_start: 0.7852 (tt0) cc_final: 0.7531 (tp30) REVERT: D 150 HIS cc_start: 0.7775 (m-70) cc_final: 0.6572 (p-80) REVERT: G 70 THR cc_start: 0.8550 (m) cc_final: 0.8284 (p) outliers start: 50 outliers final: 42 residues processed: 290 average time/residue: 0.5452 time to fit residues: 180.0922 Evaluate side-chains 302 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 22 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN F 105 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.112956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.091322 restraints weight = 22570.266| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.41 r_work: 0.2812 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20048 Z= 0.252 Angle : 0.664 5.519 27288 Z= 0.359 Chirality : 0.049 0.178 3020 Planarity : 0.004 0.043 3448 Dihedral : 8.242 61.321 3324 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 2.25 % Allowed : 13.37 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2444 helix: -1.92 (0.86), residues: 24 sheet: -0.15 (0.16), residues: 1016 loop : -0.75 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 85 TYR 0.017 0.002 TYR B 121 PHE 0.015 0.002 PHE C 354 TRP 0.017 0.002 TRP H 103 HIS 0.004 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (19972) covalent geometry : angle 0.65297 / 0.36 (27104) SS BOND : bond 0.00448 / 0.27 ( 44) SS BOND : angle 0.95924 / 0.68 ( 88) hydrogen bonds : bond 0.04932 / 3.22 ( 580) hydrogen bonds : angle 6.30275 / 4.34 ( 1563) link_ALPHA1-3 : bond 0.00921 / 0.56 ( 4) link_ALPHA1-3 : angle 1.63508 / 0.82 ( 12) link_ALPHA1-6 : bond 0.00811 / 0.49 ( 4) link_ALPHA1-6 : angle 1.42202 / 0.71 ( 12) link_BETA1-2 : bond 0.00779 / 0.47 ( 4) link_BETA1-2 : angle 1.35834 / 0.69 ( 12) link_BETA1-4 : bond 0.00454 / 0.34 ( 8) link_BETA1-4 : angle 2.19792 / 1.30 ( 24) link_NAG-ASN : bond 0.00576 / 0.37 ( 12) link_NAG-ASN : angle 2.28289 / 1.49 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6337.04 seconds wall clock time: 109 minutes 19.74 seconds (6559.74 seconds total)