Starting phenix.real_space_refine on Thu Feb 5 19:51:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md6_48169/02_2026/9md6_48169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md6_48169/02_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_48169/02_2026/9md6_48169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md6_48169/02_2026/9md6_48169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9md6_48169/02_2026/9md6_48169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md6_48169/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.70, per 1000 atoms: 0.24 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: 2.02 Conformation dependent library (CDL) restraints added in 912.4 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: 1.05 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: 3.94 Time building geometry restraints manager: 2.53 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: 0.03 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: 5.790 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: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 covalent geometry : bond 0.00224 (19972) covalent geometry : angle 0.56099 (27104) SS BOND : bond 0.00242 ( 44) SS BOND : angle 0.86001 ( 88) hydrogen bonds : bond 0.24485 ( 580) hydrogen bonds : angle 9.91830 ( 1563) link_ALPHA1-3 : bond 0.01345 ( 4) link_ALPHA1-3 : angle 1.15375 ( 12) link_ALPHA1-6 : bond 0.01072 ( 4) link_ALPHA1-6 : angle 1.32187 ( 12) link_BETA1-2 : bond 0.00517 ( 4) link_BETA1-2 : angle 1.09068 ( 12) link_BETA1-4 : bond 0.00725 ( 8) link_BETA1-4 : angle 1.63278 ( 24) link_NAG-ASN : bond 0.00227 ( 12) link_NAG-ASN : angle 3.29900 ( 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 : 0.938 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: 0.5626 time to fit residues: 195.8433 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 : 0.862 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3236 r_free = 0.3236 target = 0.115354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.094151 restraints weight = 22679.348| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.39 r_work: 0.2826 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20048 Z= 0.260 Angle : 0.706 5.392 27288 Z= 0.382 Chirality : 0.050 0.207 3020 Planarity : 0.005 0.041 3448 Dihedral : 7.846 54.337 3324 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.42 % Favored : 95.25 % 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 (0.31), residues: 24 sheet: -0.22 (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 L 54 TYR 0.018 0.003 TYR D 121 PHE 0.016 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 covalent geometry : bond 0.00594 (19972) covalent geometry : angle 0.69502 (27104) SS BOND : bond 0.00498 ( 44) SS BOND : angle 1.11353 ( 88) hydrogen bonds : bond 0.05911 ( 580) hydrogen bonds : angle 7.17687 ( 1563) link_ALPHA1-3 : bond 0.01030 ( 4) link_ALPHA1-3 : angle 1.56535 ( 12) link_ALPHA1-6 : bond 0.00892 ( 4) link_ALPHA1-6 : angle 1.33975 ( 12) link_BETA1-2 : bond 0.00819 ( 4) link_BETA1-2 : angle 1.40433 ( 12) link_BETA1-4 : bond 0.00471 ( 8) link_BETA1-4 : angle 2.06923 ( 24) link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 2.54776 ( 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 : 0.824 Fit side-chains REVERT: A 150 HIS cc_start: 0.7803 (m-70) cc_final: 0.6726 (p-80) REVERT: A 434 THR cc_start: 0.9151 (m) cc_final: 0.8904 (p) REVERT: H 70 THR cc_start: 0.8683 (m) cc_final: 0.8441 (p) REVERT: B 150 HIS cc_start: 0.7810 (m-70) cc_final: 0.6732 (p-80) REVERT: B 434 THR cc_start: 0.9152 (m) cc_final: 0.8906 (p) REVERT: E 70 THR cc_start: 0.8674 (m) cc_final: 0.8439 (p) REVERT: C 150 HIS cc_start: 0.7785 (m-70) cc_final: 0.6710 (p-80) REVERT: C 434 THR cc_start: 0.9147 (m) cc_final: 0.8891 (p) REVERT: F 70 THR cc_start: 0.8679 (m) cc_final: 0.8445 (p) REVERT: D 150 HIS cc_start: 0.7793 (m-70) cc_final: 0.6732 (p-80) REVERT: D 434 THR cc_start: 0.9141 (m) cc_final: 0.8891 (p) REVERT: G 70 THR cc_start: 0.8680 (m) cc_final: 0.8444 (p) outliers start: 40 outliers final: 28 residues processed: 289 average time/residue: 0.5846 time to fit residues: 193.2590 Evaluate side-chains 289 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 L residue 70 ASP 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 I residue 70 ASP 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 J residue 3 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 70 ASP 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 Chi-restraints excluded: chain K residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 165 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3233 r_free = 0.3233 target = 0.116380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.094178 restraints weight = 22937.333| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.55 r_work: 0.2852 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1440 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= 0.127 Angle : 0.567 4.499 27288 Z= 0.309 Chirality : 0.045 0.183 3020 Planarity : 0.004 0.037 3448 Dihedral : 7.043 47.727 3324 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.50 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 9.19 % Favored : 88.74 % 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: -0.76 (0.17), residues: 2444 helix: -2.43 (0.69), residues: 24 sheet: -0.15 (0.16), residues: 1016 loop : -0.70 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 54 TYR 0.012 0.001 TYR D 121 PHE 0.015 0.002 PHE B 410 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00267 (19972) covalent geometry : angle 0.56040 (27104) SS BOND : bond 0.00280 ( 44) SS BOND : angle 0.60112 ( 88) hydrogen bonds : bond 0.04645 ( 580) hydrogen bonds : angle 6.45256 ( 1563) link_ALPHA1-3 : bond 0.01339 ( 4) link_ALPHA1-3 : angle 1.29338 ( 12) link_ALPHA1-6 : bond 0.00940 ( 4) link_ALPHA1-6 : angle 1.34724 ( 12) link_BETA1-2 : bond 0.00650 ( 4) link_BETA1-2 : angle 1.22589 ( 12) link_BETA1-4 : bond 0.00595 ( 8) link_BETA1-4 : angle 1.66294 ( 24) link_NAG-ASN : bond 0.00175 ( 12) link_NAG-ASN : angle 1.79930 ( 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 321 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 HIS cc_start: 0.7765 (m-70) cc_final: 0.6510 (p90) REVERT: A 434 THR cc_start: 0.9101 (m) cc_final: 0.8879 (p) REVERT: H 70 THR cc_start: 0.8631 (m) cc_final: 0.8313 (p) REVERT: L 3 VAL cc_start: 0.8835 (m) cc_final: 0.8553 (t) REVERT: B 150 HIS cc_start: 0.7756 (m-70) cc_final: 0.6494 (p90) REVERT: B 434 THR cc_start: 0.9093 (m) cc_final: 0.8863 (p) REVERT: E 70 THR cc_start: 0.8632 (m) cc_final: 0.8314 (p) REVERT: I 3 VAL cc_start: 0.8835 (m) cc_final: 0.8557 (t) REVERT: C 150 HIS cc_start: 0.7755 (m-70) cc_final: 0.6507 (p90) REVERT: C 434 THR cc_start: 0.9099 (m) cc_final: 0.8878 (p) REVERT: F 70 THR cc_start: 0.8632 (m) cc_final: 0.8317 (p) REVERT: J 3 VAL cc_start: 0.8839 (m) cc_final: 0.8566 (t) REVERT: D 150 HIS cc_start: 0.7760 (m-70) cc_final: 0.6521 (p90) REVERT: D 434 THR cc_start: 0.9097 (m) cc_final: 0.8874 (p) REVERT: G 70 THR cc_start: 0.8632 (m) cc_final: 0.8321 (p) REVERT: K 3 VAL cc_start: 0.8837 (m) cc_final: 0.8558 (t) outliers start: 44 outliers final: 24 residues processed: 297 average time/residue: 0.6171 time to fit residues: 207.1202 Evaluate side-chains 289 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 1.9990 chunk 190 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 239 optimal weight: 0.5980 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: 0.0670 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN H 105 GLN E 39 GLN E 105 GLN F 105 GLN G 39 GLN G 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.112805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.090244 restraints weight = 23053.868| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.59 r_work: 0.2802 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20048 Z= 0.188 Angle : 0.613 4.924 27288 Z= 0.332 Chirality : 0.047 0.190 3020 Planarity : 0.004 0.040 3448 Dihedral : 7.514 52.792 3324 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.89 % Favored : 95.95 % Rotamer: Outliers : 2.25 % Allowed : 10.32 % Favored : 87.43 % 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: -0.82 (0.17), residues: 2444 helix: -2.14 (0.82), residues: 24 sheet: -0.22 (0.16), residues: 1016 loop : -0.71 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 54 TYR 0.016 0.002 TYR C 121 PHE 0.014 0.002 PHE B 354 TRP 0.013 0.002 TRP C 178 HIS 0.003 0.001 HIS I 89 Details of bonding type rmsd covalent geometry : bond 0.00426 (19972) covalent geometry : angle 0.60427 (27104) SS BOND : bond 0.00345 ( 44) SS BOND : angle 0.79334 ( 88) hydrogen bonds : bond 0.04784 ( 580) hydrogen bonds : angle 6.31679 ( 1563) link_ALPHA1-3 : bond 0.01140 ( 4) link_ALPHA1-3 : angle 1.45026 ( 12) link_ALPHA1-6 : bond 0.00875 ( 4) link_ALPHA1-6 : angle 1.34096 ( 12) link_BETA1-2 : bond 0.00765 ( 4) link_BETA1-2 : angle 1.24901 ( 12) link_BETA1-4 : bond 0.00539 ( 8) link_BETA1-4 : angle 1.92561 ( 24) link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 2.11465 ( 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: 48 poor density : 276 time to evaluate : 0.790 Fit side-chains REVERT: A 83 GLU cc_start: 0.7865 (tt0) cc_final: 0.7507 (tp30) REVERT: A 150 HIS cc_start: 0.7789 (m-70) cc_final: 0.6582 (p-80) REVERT: H 70 THR cc_start: 0.8638 (m) cc_final: 0.8303 (p) REVERT: L 61 ARG cc_start: 0.8286 (ttm170) cc_final: 0.8037 (ttm170) REVERT: B 83 GLU cc_start: 0.7855 (tt0) cc_final: 0.7497 (tp30) REVERT: B 150 HIS cc_start: 0.7781 (m-70) cc_final: 0.6563 (p-80) REVERT: E 70 THR cc_start: 0.8632 (m) cc_final: 0.8298 (p) REVERT: I 61 ARG cc_start: 0.8289 (ttm170) cc_final: 0.8039 (ttm170) REVERT: C 83 GLU cc_start: 0.7860 (tt0) cc_final: 0.7508 (tp30) REVERT: C 150 HIS cc_start: 0.7779 (m-70) cc_final: 0.6573 (p-80) REVERT: F 70 THR cc_start: 0.8629 (m) cc_final: 0.8305 (p) REVERT: J 61 ARG cc_start: 0.8283 (ttm170) cc_final: 0.8030 (ttm170) REVERT: D 83 GLU cc_start: 0.7849 (tt0) cc_final: 0.7501 (tp30) REVERT: D 150 HIS cc_start: 0.7783 (m-70) cc_final: 0.6578 (p-80) REVERT: G 70 THR cc_start: 0.8636 (m) cc_final: 0.8308 (p) REVERT: K 61 ARG cc_start: 0.8281 (ttm170) cc_final: 0.8035 (ttm170) outliers start: 48 outliers final: 28 residues processed: 296 average time/residue: 0.5894 time to fit residues: 198.5334 Evaluate side-chains 296 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 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 D residue 88 SER 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: 5.9990 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 187 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3210 r_free = 0.3210 target = 0.114807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.092559 restraints weight = 22855.528| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.54 r_work: 0.2839 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20048 Z= 0.141 Angle : 0.564 4.562 27288 Z= 0.306 Chirality : 0.045 0.181 3020 Planarity : 0.004 0.038 3448 Dihedral : 7.127 49.136 3324 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.62 % Favored : 97.22 % Rotamer: Outliers : 1.88 % Allowed : 11.07 % Favored : 87.05 % 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: -0.73 (0.17), residues: 2444 helix: -1.87 (0.94), residues: 24 sheet: -0.16 (0.16), residues: 1016 loop : -0.65 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 85 TYR 0.014 0.002 TYR D 121 PHE 0.013 0.002 PHE B 354 TRP 0.014 0.001 TRP D 178 HIS 0.002 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00307 (19972) covalent geometry : angle 0.55632 (27104) SS BOND : bond 0.00281 ( 44) SS BOND : angle 0.59244 ( 88) hydrogen bonds : bond 0.04285 ( 580) hydrogen bonds : angle 6.09042 ( 1563) link_ALPHA1-3 : bond 0.01241 ( 4) link_ALPHA1-3 : angle 1.30981 ( 12) link_ALPHA1-6 : bond 0.00917 ( 4) link_ALPHA1-6 : angle 1.34012 ( 12) link_BETA1-2 : bond 0.00627 ( 4) link_BETA1-2 : angle 1.20454 ( 12) link_BETA1-4 : bond 0.00553 ( 8) link_BETA1-4 : angle 1.70900 ( 24) link_NAG-ASN : bond 0.00253 ( 12) link_NAG-ASN : angle 1.82344 ( 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 316 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7858 (tt0) cc_final: 0.7516 (tp30) REVERT: A 150 HIS cc_start: 0.7762 (m-70) cc_final: 0.6504 (p90) REVERT: H 70 THR cc_start: 0.8614 (m) cc_final: 0.8308 (p) REVERT: B 83 GLU cc_start: 0.7856 (tt0) cc_final: 0.7514 (tp30) REVERT: B 150 HIS cc_start: 0.7754 (m-70) cc_final: 0.6493 (p90) REVERT: E 70 THR cc_start: 0.8605 (m) cc_final: 0.8297 (p) REVERT: C 83 GLU cc_start: 0.7860 (tt0) cc_final: 0.7530 (tp30) REVERT: C 150 HIS cc_start: 0.7745 (m-70) cc_final: 0.6499 (p90) REVERT: F 70 THR cc_start: 0.8594 (m) cc_final: 0.8302 (p) REVERT: D 83 GLU cc_start: 0.7846 (tt0) cc_final: 0.7520 (tp30) REVERT: D 150 HIS cc_start: 0.7755 (m-70) cc_final: 0.6515 (p90) REVERT: G 70 THR cc_start: 0.8619 (m) cc_final: 0.8319 (p) outliers start: 40 outliers final: 28 residues processed: 296 average time/residue: 0.6020 time to fit residues: 202.6996 Evaluate side-chains 286 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 0.0060 chunk 8 optimal weight: 0.7980 chunk 223 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3237 r_free = 0.3237 target = 0.116648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.094297 restraints weight = 22614.879| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.58 r_work: 0.2857 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20048 Z= 0.119 Angle : 0.540 4.414 27288 Z= 0.292 Chirality : 0.045 0.184 3020 Planarity : 0.004 0.038 3448 Dihedral : 6.717 45.065 3324 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.56 % Favored : 96.28 % Rotamer: Outliers : 1.88 % Allowed : 12.10 % Favored : 86.02 % 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: -0.62 (0.17), residues: 2444 helix: -1.64 (1.03), residues: 24 sheet: -0.05 (0.16), residues: 1016 loop : -0.61 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 54 TYR 0.013 0.001 TYR D 121 PHE 0.012 0.001 PHE D 354 TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00255 (19972) covalent geometry : angle 0.53361 (27104) SS BOND : bond 0.00246 ( 44) SS BOND : angle 0.52375 ( 88) hydrogen bonds : bond 0.03911 ( 580) hydrogen bonds : angle 5.87313 ( 1563) link_ALPHA1-3 : bond 0.01336 ( 4) link_ALPHA1-3 : angle 1.19300 ( 12) link_ALPHA1-6 : bond 0.00982 ( 4) link_ALPHA1-6 : angle 1.32609 ( 12) link_BETA1-2 : bond 0.00597 ( 4) link_BETA1-2 : angle 1.16957 ( 12) link_BETA1-4 : bond 0.00601 ( 8) link_BETA1-4 : angle 1.58665 ( 24) link_NAG-ASN : bond 0.00199 ( 12) link_NAG-ASN : angle 1.74171 ( 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 306 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7848 (tt0) cc_final: 0.7503 (tp30) REVERT: A 150 HIS cc_start: 0.7747 (m-70) cc_final: 0.6486 (p90) REVERT: A 197 ASN cc_start: 0.8183 (p0) cc_final: 0.7479 (m110) REVERT: H 70 THR cc_start: 0.8597 (m) cc_final: 0.8306 (p) REVERT: L 3 VAL cc_start: 0.8795 (m) cc_final: 0.8486 (t) REVERT: B 83 GLU cc_start: 0.7863 (tt0) cc_final: 0.7515 (tp30) REVERT: B 150 HIS cc_start: 0.7755 (m-70) cc_final: 0.6493 (p90) REVERT: E 70 THR cc_start: 0.8591 (m) cc_final: 0.8300 (p) REVERT: I 3 VAL cc_start: 0.8794 (m) cc_final: 0.8487 (t) REVERT: C 83 GLU cc_start: 0.7854 (tt0) cc_final: 0.7519 (tp30) REVERT: C 150 HIS cc_start: 0.7748 (m-70) cc_final: 0.6496 (p90) REVERT: F 70 THR cc_start: 0.8592 (m) cc_final: 0.8312 (p) REVERT: J 3 VAL cc_start: 0.8792 (m) cc_final: 0.8498 (t) REVERT: D 83 GLU cc_start: 0.7856 (tt0) cc_final: 0.7522 (tp30) REVERT: D 150 HIS cc_start: 0.7749 (m-70) cc_final: 0.6516 (p90) REVERT: G 70 THR cc_start: 0.8598 (m) cc_final: 0.8315 (p) REVERT: K 3 VAL cc_start: 0.8792 (m) cc_final: 0.8494 (t) outliers start: 40 outliers final: 36 residues processed: 282 average time/residue: 0.6019 time to fit residues: 193.4211 Evaluate side-chains 293 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 20 SER 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 20 SER 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 20 SER 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 20 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 160 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3255 r_free = 0.3255 target = 0.117836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.095503 restraints weight = 22686.469| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.58 r_work: 0.2865 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20048 Z= 0.114 Angle : 0.532 4.298 27288 Z= 0.287 Chirality : 0.045 0.184 3020 Planarity : 0.004 0.037 3448 Dihedral : 6.493 42.613 3324 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.01 % Rotamer: Outliers : 1.92 % Allowed : 12.01 % Favored : 86.07 % 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: -0.50 (0.17), residues: 2444 helix: -1.64 (1.01), residues: 24 sheet: 0.03 (0.16), residues: 1016 loop : -0.52 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 54 TYR 0.013 0.001 TYR D 121 PHE 0.012 0.001 PHE B 354 TRP 0.012 0.001 TRP C 178 HIS 0.002 0.001 HIS L 89 Details of bonding type rmsd covalent geometry : bond 0.00245 (19972) covalent geometry : angle 0.52546 (27104) SS BOND : bond 0.00249 ( 44) SS BOND : angle 0.50156 ( 88) hydrogen bonds : bond 0.03811 ( 580) hydrogen bonds : angle 5.75579 ( 1563) link_ALPHA1-3 : bond 0.01381 ( 4) link_ALPHA1-3 : angle 1.18091 ( 12) link_ALPHA1-6 : bond 0.00992 ( 4) link_ALPHA1-6 : angle 1.30748 ( 12) link_BETA1-2 : bond 0.00588 ( 4) link_BETA1-2 : angle 1.18869 ( 12) link_BETA1-4 : bond 0.00579 ( 8) link_BETA1-4 : angle 1.52790 ( 24) link_NAG-ASN : bond 0.00200 ( 12) link_NAG-ASN : angle 1.71737 ( 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 320 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7852 (tt0) cc_final: 0.7531 (tp30) REVERT: A 150 HIS cc_start: 0.7764 (m-70) cc_final: 0.6502 (p90) REVERT: A 197 ASN cc_start: 0.8143 (p0) cc_final: 0.7491 (m110) REVERT: H 70 THR cc_start: 0.8575 (m) cc_final: 0.8297 (p) REVERT: L 3 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8480 (t) REVERT: B 83 GLU cc_start: 0.7859 (tt0) cc_final: 0.7532 (tp30) REVERT: B 150 HIS cc_start: 0.7765 (m-70) cc_final: 0.6498 (p90) REVERT: E 70 THR cc_start: 0.8573 (m) cc_final: 0.8297 (p) REVERT: I 3 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8470 (t) REVERT: C 83 GLU cc_start: 0.7865 (tt0) cc_final: 0.7553 (tp30) REVERT: C 150 HIS cc_start: 0.7756 (m-70) cc_final: 0.6503 (p90) REVERT: F 70 THR cc_start: 0.8573 (m) cc_final: 0.8304 (p) REVERT: J 3 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8482 (t) REVERT: D 83 GLU cc_start: 0.7868 (tt0) cc_final: 0.7555 (tp30) REVERT: D 150 HIS cc_start: 0.7760 (m-70) cc_final: 0.6517 (p90) REVERT: G 70 THR cc_start: 0.8576 (m) cc_final: 0.8308 (p) REVERT: K 3 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8484 (t) outliers start: 41 outliers final: 32 residues processed: 295 average time/residue: 0.6046 time to fit residues: 203.1683 Evaluate side-chains 307 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 174 optimal weight: 0.0670 chunk 155 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3173 r_free = 0.3173 target = 0.112066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.089467 restraints weight = 23003.090| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.58 r_work: 0.2783 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20048 Z= 0.223 Angle : 0.630 5.384 27288 Z= 0.340 Chirality : 0.048 0.196 3020 Planarity : 0.004 0.042 3448 Dihedral : 7.538 53.348 3324 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 2.44 % Allowed : 11.87 % Favored : 85.69 % 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: -1.70 (0.99), residues: 24 sheet: -0.04 (0.16), residues: 1016 loop : -0.63 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.017 0.002 TYR C 121 PHE 0.015 0.002 PHE B 354 TRP 0.015 0.002 TRP F 103 HIS 0.004 0.001 HIS J 89 Details of bonding type rmsd covalent geometry : bond 0.00510 (19972) covalent geometry : angle 0.62041 (27104) SS BOND : bond 0.00403 ( 44) SS BOND : angle 0.84133 ( 88) hydrogen bonds : bond 0.04704 ( 580) hydrogen bonds : angle 6.13299 ( 1563) link_ALPHA1-3 : bond 0.01058 ( 4) link_ALPHA1-3 : angle 1.53471 ( 12) link_ALPHA1-6 : bond 0.00834 ( 4) link_ALPHA1-6 : angle 1.38289 ( 12) link_BETA1-2 : bond 0.00746 ( 4) link_BETA1-2 : angle 1.28138 ( 12) link_BETA1-4 : bond 0.00480 ( 8) link_BETA1-4 : angle 1.99805 ( 24) link_NAG-ASN : bond 0.00515 ( 12) link_NAG-ASN : angle 2.20608 ( 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 324 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7847 (tt0) cc_final: 0.7498 (tp30) REVERT: A 150 HIS cc_start: 0.7788 (m-70) cc_final: 0.6567 (p-80) REVERT: H 70 THR cc_start: 0.8535 (m) cc_final: 0.8237 (p) REVERT: L 61 ARG cc_start: 0.8320 (ttm170) cc_final: 0.8090 (ttm170) REVERT: B 83 GLU cc_start: 0.7865 (tt0) cc_final: 0.7513 (tp30) REVERT: B 150 HIS cc_start: 0.7807 (m-70) cc_final: 0.6560 (p-80) REVERT: E 70 THR cc_start: 0.8534 (m) cc_final: 0.8240 (p) REVERT: I 61 ARG cc_start: 0.8328 (ttm170) cc_final: 0.8099 (ttm170) REVERT: C 83 GLU cc_start: 0.7867 (tt0) cc_final: 0.7522 (tp30) REVERT: C 150 HIS cc_start: 0.7798 (m-70) cc_final: 0.6557 (p-80) REVERT: F 70 THR cc_start: 0.8541 (m) cc_final: 0.8253 (p) REVERT: J 61 ARG cc_start: 0.8330 (ttm170) cc_final: 0.8048 (ttm170) REVERT: D 83 GLU cc_start: 0.7847 (tt0) cc_final: 0.7504 (tp30) REVERT: D 150 HIS cc_start: 0.7792 (m-70) cc_final: 0.6557 (p-80) REVERT: G 70 THR cc_start: 0.8543 (m) cc_final: 0.8251 (p) REVERT: K 61 ARG cc_start: 0.8334 (ttm170) cc_final: 0.8102 (ttm170) outliers start: 52 outliers final: 44 residues processed: 292 average time/residue: 0.5709 time to fit residues: 189.7582 Evaluate side-chains 321 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 L residue 20 SER Chi-restraints excluded: chain L residue 87 LEU 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 I residue 20 SER Chi-restraints excluded: chain I residue 87 LEU 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 J residue 20 SER Chi-restraints excluded: chain J residue 87 LEU 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 Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 87 LEU 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: 2.9990 chunk 108 optimal weight: 0.4980 chunk 188 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3214 r_free = 0.3214 target = 0.115055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.092864 restraints weight = 22798.228| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.54 r_work: 0.2844 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20048 Z= 0.131 Angle : 0.553 4.500 27288 Z= 0.300 Chirality : 0.045 0.182 3020 Planarity : 0.004 0.039 3448 Dihedral : 6.951 47.529 3324 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 12.80 % Favored : 85.32 % 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: -0.53 (0.17), residues: 2444 helix: -1.57 (0.98), residues: 24 sheet: 0.02 (0.16), residues: 1016 loop : -0.56 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 85 TYR 0.013 0.001 TYR C 121 PHE 0.013 0.001 PHE A 354 TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS J 89 Details of bonding type rmsd covalent geometry : bond 0.00287 (19972) covalent geometry : angle 0.54614 (27104) SS BOND : bond 0.00266 ( 44) SS BOND : angle 0.53620 ( 88) hydrogen bonds : bond 0.04004 ( 580) hydrogen bonds : angle 5.90735 ( 1563) link_ALPHA1-3 : bond 0.01239 ( 4) link_ALPHA1-3 : angle 1.30467 ( 12) link_ALPHA1-6 : bond 0.00936 ( 4) link_ALPHA1-6 : angle 1.34506 ( 12) link_BETA1-2 : bond 0.00590 ( 4) link_BETA1-2 : angle 1.22407 ( 12) link_BETA1-4 : bond 0.00559 ( 8) link_BETA1-4 : angle 1.63260 ( 24) link_NAG-ASN : bond 0.00230 ( 12) link_NAG-ASN : angle 1.79637 ( 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 318 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7837 (tt0) cc_final: 0.7535 (tp30) REVERT: A 150 HIS cc_start: 0.7741 (m-70) cc_final: 0.6484 (p90) REVERT: H 70 THR cc_start: 0.8588 (m) cc_final: 0.8312 (p) REVERT: B 83 GLU cc_start: 0.7871 (tt0) cc_final: 0.7555 (tp30) REVERT: B 150 HIS cc_start: 0.7744 (m-70) cc_final: 0.6481 (p90) REVERT: E 70 THR cc_start: 0.8583 (m) cc_final: 0.8310 (p) REVERT: C 83 GLU cc_start: 0.7876 (tt0) cc_final: 0.7572 (tp30) REVERT: C 150 HIS cc_start: 0.7730 (m-70) cc_final: 0.6481 (p90) REVERT: F 70 THR cc_start: 0.8590 (m) cc_final: 0.8325 (p) REVERT: D 83 GLU cc_start: 0.7862 (tt0) cc_final: 0.7560 (tp30) REVERT: D 150 HIS cc_start: 0.7740 (m-70) cc_final: 0.6497 (p90) REVERT: G 70 THR cc_start: 0.8592 (m) cc_final: 0.8324 (p) outliers start: 40 outliers final: 36 residues processed: 294 average time/residue: 0.6100 time to fit residues: 204.0241 Evaluate side-chains 302 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 158 optimal weight: 0.0370 chunk 162 optimal weight: 0.3980 chunk 237 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3206 r_free = 0.3206 target = 0.114475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.092224 restraints weight = 22870.293| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.55 r_work: 0.2833 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20048 Z= 0.146 Angle : 0.564 4.706 27288 Z= 0.305 Chirality : 0.046 0.185 3020 Planarity : 0.004 0.040 3448 Dihedral : 6.975 47.889 3324 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.97 % Favored : 95.87 % Rotamer: Outliers : 1.88 % Allowed : 12.95 % Favored : 85.18 % 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: -0.52 (0.17), residues: 2444 helix: -1.54 (1.02), residues: 24 sheet: 0.03 (0.16), residues: 1016 loop : -0.55 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 54 TYR 0.014 0.002 TYR C 121 PHE 0.013 0.002 PHE A 354 TRP 0.013 0.001 TRP B 178 HIS 0.002 0.001 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00326 (19972) covalent geometry : angle 0.55675 (27104) SS BOND : bond 0.00292 ( 44) SS BOND : angle 0.59582 ( 88) hydrogen bonds : bond 0.04085 ( 580) hydrogen bonds : angle 5.90891 ( 1563) link_ALPHA1-3 : bond 0.01227 ( 4) link_ALPHA1-3 : angle 1.33103 ( 12) link_ALPHA1-6 : bond 0.00926 ( 4) link_ALPHA1-6 : angle 1.34135 ( 12) link_BETA1-2 : bond 0.00639 ( 4) link_BETA1-2 : angle 1.19577 ( 12) link_BETA1-4 : bond 0.00556 ( 8) link_BETA1-4 : angle 1.71184 ( 24) link_NAG-ASN : bond 0.00282 ( 12) link_NAG-ASN : angle 1.90260 ( 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 309 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 269 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7851 (tt0) cc_final: 0.7520 (tp30) REVERT: A 150 HIS cc_start: 0.7748 (m-70) cc_final: 0.6468 (p90) REVERT: H 70 THR cc_start: 0.8543 (m) cc_final: 0.8268 (p) REVERT: B 83 GLU cc_start: 0.7876 (tt0) cc_final: 0.7537 (tp30) REVERT: B 150 HIS cc_start: 0.7753 (m-70) cc_final: 0.6473 (p90) REVERT: E 70 THR cc_start: 0.8536 (m) cc_final: 0.8265 (p) REVERT: C 83 GLU cc_start: 0.7879 (tt0) cc_final: 0.7552 (tp30) REVERT: C 150 HIS cc_start: 0.7738 (m-70) cc_final: 0.6466 (p90) REVERT: F 70 THR cc_start: 0.8542 (m) cc_final: 0.8281 (p) REVERT: D 83 GLU cc_start: 0.7848 (tt0) cc_final: 0.7522 (tp30) REVERT: D 150 HIS cc_start: 0.7751 (m-70) cc_final: 0.6491 (p90) REVERT: G 70 THR cc_start: 0.8545 (m) cc_final: 0.8282 (p) outliers start: 40 outliers final: 36 residues processed: 285 average time/residue: 0.5781 time to fit residues: 187.1421 Evaluate side-chains 301 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 22 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3193 r_free = 0.3193 target = 0.113473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.091144 restraints weight = 22856.870| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.54 r_work: 0.2811 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20048 Z= 0.174 Angle : 0.588 4.748 27288 Z= 0.318 Chirality : 0.047 0.190 3020 Planarity : 0.004 0.040 3448 Dihedral : 7.211 50.317 3324 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 1.88 % Allowed : 13.23 % Favored : 84.90 % 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: -0.57 (0.17), residues: 2444 helix: -1.56 (1.02), residues: 24 sheet: 0.01 (0.16), residues: 1016 loop : -0.60 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 61 TYR 0.015 0.002 TYR C 121 PHE 0.014 0.002 PHE B 354 TRP 0.013 0.001 TRP E 103 HIS 0.003 0.001 HIS J 89 Details of bonding type rmsd covalent geometry : bond 0.00393 (19972) covalent geometry : angle 0.57997 (27104) SS BOND : bond 0.00334 ( 44) SS BOND : angle 0.68979 ( 88) hydrogen bonds : bond 0.04297 ( 580) hydrogen bonds : angle 5.99168 ( 1563) link_ALPHA1-3 : bond 0.01166 ( 4) link_ALPHA1-3 : angle 1.43123 ( 12) link_ALPHA1-6 : bond 0.00893 ( 4) link_ALPHA1-6 : angle 1.36215 ( 12) link_BETA1-2 : bond 0.00679 ( 4) link_BETA1-2 : angle 1.23864 ( 12) link_BETA1-4 : bond 0.00519 ( 8) link_BETA1-4 : angle 1.80896 ( 24) link_NAG-ASN : bond 0.00366 ( 12) link_NAG-ASN : angle 1.99399 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6454.74 seconds wall clock time: 111 minutes 24.97 seconds (6684.97 seconds total)