Starting phenix.real_space_refine on Thu Feb 5 20:22:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md4_48167/02_2026/9md4_48167.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md4_48167/02_2026/9md4_48167.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/9md4_48167/02_2026/9md4_48167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md4_48167/02_2026/9md4_48167.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9md4_48167/02_2026/9md4_48167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md4_48167/02_2026/9md4_48167.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= 0.032 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 128 5.16 5 C 12304 2.51 5 N 3308 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 19684 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: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 975 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} 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: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 975 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "I" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} 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: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 975 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} 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: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 975 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.11, per 1000 atoms: 0.21 Number of scatterers: 19684 At special positions: 0 Unit cell: (151.525, 151.525, 79.025, 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 128 16.00 O 3940 8.00 N 3308 7.00 C 12304 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=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 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=2.02 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 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 A 504 " - " ASN A 309 " " NAG B 501 " - " ASN B 146 " " NAG B 502 " - " ASN B 367 " " NAG B 504 " - " ASN B 309 " " NAG C 501 " - " ASN C 146 " " NAG C 502 " - " ASN C 367 " " NAG C 504 " - " ASN C 309 " " NAG D 501 " - " ASN D 146 " " NAG D 502 " - " ASN D 367 " " NAG D 504 " - " ASN D 309 " " NAG M 1 " - " ASN A 200 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN C 200 " " NAG P 1 " - " ASN D 200 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 732.4 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4472 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 56 sheets defined 3.6% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.747A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.575A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.841A pdb=" N ASP H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.728A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.747A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.575A pdb=" N SER B 145 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.841A pdb=" N ASP E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.728A pdb=" N LEU I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.747A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.575A pdb=" N SER C 145 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 146 " --> pdb=" O GLY C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.841A pdb=" N ASP F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.728A pdb=" N LEU J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.747A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.575A pdb=" N SER D 145 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN D 146 " --> pdb=" O GLY D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.841A pdb=" N ASP G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.728A pdb=" N LEU K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 5.435A pdb=" N PHE A 97 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR A 449 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N CYS A 447 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 408 " --> pdb=" O TYR A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.781A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.322A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.512A pdb=" N HIS A 264 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.474A 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: 5.293A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 355 removed outlier: 4.476A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU A 372 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS A 400 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 376 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL A 396 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS A 378 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG A 394 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.665A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.133A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.657A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.524A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.915A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.435A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 408 " --> pdb=" O TYR B 423 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.781A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.322A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.512A pdb=" N HIS B 264 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.293A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 352 through 355 removed outlier: 4.476A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B 372 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS B 400 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR B 376 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL B 396 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS B 378 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG B 394 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.665A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.133A pdb=" N VAL E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.657A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.524A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.915A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 96 through 102 removed outlier: 5.435A pdb=" N PHE C 97 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR C 449 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N CYS C 447 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 408 " --> pdb=" O TYR C 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.781A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.322A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AD6, first strand: chain 'C' and resid 224 through 225 removed outlier: 3.512A pdb=" N HIS C 264 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.294A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 352 through 355 removed outlier: 4.476A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU C 372 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS C 400 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 376 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL C 396 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS C 378 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG C 394 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.665A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.133A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.657A pdb=" N LEU F 80 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.524A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.915A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 96 through 102 removed outlier: 5.435A pdb=" N PHE D 97 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR D 449 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N CYS D 447 " --> pdb=" O PRO D 99 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 408 " --> pdb=" O TYR D 423 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.781A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.322A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AF2, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.512A pdb=" N HIS D 264 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.293A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 352 through 355 removed outlier: 4.476A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU D 372 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS D 400 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR D 376 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL D 396 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS D 378 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 394 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.665A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.133A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.657A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.524A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.915A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1608 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: 3.06 Time building geometry restraints manager: 2.18 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: 6259 1.34 - 1.47: 5441 1.47 - 1.59: 8264 1.59 - 1.72: 0 1.72 - 1.84: 168 Bond restraints: 20132 Sorted by residual: bond pdb=" CA GLU C 119 " pdb=" CB GLU C 119 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 9.54e-01 bond pdb=" CA GLU D 119 " pdb=" CB GLU D 119 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 9.54e-01 bond pdb=" CA GLU A 119 " pdb=" CB GLU A 119 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 9.54e-01 bond pdb=" CA GLU B 119 " pdb=" CB GLU B 119 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 9.54e-01 bond pdb=" CG ARG A 118 " pdb=" CD ARG A 118 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.22e-01 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 26104 1.33 - 2.65: 952 2.65 - 3.98: 192 3.98 - 5.30: 44 5.30 - 6.63: 12 Bond angle restraints: 27304 Sorted by residual: angle pdb=" C TYR E 99 " pdb=" N GLY E 100 " pdb=" CA GLY E 100 " ideal model delta sigma weight residual 123.30 120.35 2.95 1.06e+00 8.90e-01 7.75e+00 angle pdb=" C TYR H 99 " pdb=" N GLY H 100 " pdb=" CA GLY H 100 " ideal model delta sigma weight residual 123.30 120.35 2.95 1.06e+00 8.90e-01 7.75e+00 angle pdb=" C TYR F 99 " pdb=" N GLY F 100 " pdb=" CA GLY F 100 " ideal model delta sigma weight residual 123.30 120.35 2.95 1.06e+00 8.90e-01 7.75e+00 angle pdb=" C TYR G 99 " pdb=" N GLY G 100 " pdb=" CA GLY G 100 " ideal model delta sigma weight residual 123.30 120.35 2.95 1.06e+00 8.90e-01 7.75e+00 angle pdb=" CA CYS B 230 " pdb=" CB CYS B 230 " pdb=" SG CYS B 230 " ideal model delta sigma weight residual 114.40 120.73 -6.33 2.30e+00 1.89e-01 7.57e+00 ... (remaining 27299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 11124 17.37 - 34.73: 952 34.73 - 52.10: 200 52.10 - 69.46: 28 69.46 - 86.83: 24 Dihedral angle restraints: 12328 sinusoidal: 5280 harmonic: 7048 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 45.04 47.96 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 45.04 47.96 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 45.04 47.96 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 12325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2026 0.035 - 0.070: 674 0.070 - 0.106: 267 0.106 - 0.141: 81 0.141 - 0.176: 8 Chirality restraints: 3056 Sorted by residual: chirality pdb=" C3 BMA P 3 " pdb=" C2 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" O3 BMA P 3 " both_signs ideal model delta sigma weight residual False 2.41 2.23 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" C3 BMA N 3 " pdb=" C2 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" O3 BMA N 3 " both_signs ideal model delta sigma weight residual False 2.41 2.23 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" C3 BMA O 3 " pdb=" C2 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" O3 BMA O 3 " both_signs ideal model delta sigma weight residual False 2.41 2.23 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 3053 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS I 39 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO I 40 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 40 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 40 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO L 40 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 39 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO K 40 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO K 40 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 40 " 0.023 5.00e-02 4.00e+02 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1077 2.72 - 3.26: 18769 3.26 - 3.81: 35543 3.81 - 4.35: 46855 4.35 - 4.90: 77946 Nonbonded interactions: 180190 Sorted by model distance: nonbonded pdb=" OG SER C 269 " pdb=" O ILE C 312 " model vdw 2.174 3.040 nonbonded pdb=" OG SER B 219 " pdb=" OD2 ASP B 251 " model vdw 2.199 3.040 nonbonded pdb=" OG SER C 219 " pdb=" OD2 ASP C 251 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A 219 " pdb=" OD2 ASP A 251 " model vdw 2.200 3.040 nonbonded pdb=" OG SER D 219 " pdb=" OD2 ASP D 251 " model vdw 2.200 3.040 ... (remaining 180185 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: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.003 0.036 20212 Z= 0.137 Angle : 0.638 6.629 27500 Z= 0.340 Chirality : 0.043 0.176 3056 Planarity : 0.005 0.044 3440 Dihedral : 13.498 86.829 7724 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.47 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.38 (0.16), residues: 2448 helix: -4.09 (0.33), residues: 24 sheet: -0.44 (0.17), residues: 960 loop : -1.20 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 428 TYR 0.011 0.002 TYR D 374 PHE 0.012 0.002 PHE J 71 TRP 0.012 0.001 TRP A 115 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00282 (20132) covalent geometry : angle 0.61870 (27304) SS BOND : bond 0.00328 ( 44) SS BOND : angle 1.65100 ( 88) hydrogen bonds : bond 0.23996 ( 580) hydrogen bonds : angle 10.36622 ( 1608) link_ALPHA1-3 : bond 0.01289 ( 4) link_ALPHA1-3 : angle 1.54158 ( 12) link_ALPHA1-6 : bond 0.00729 ( 4) link_ALPHA1-6 : angle 1.24578 ( 12) link_BETA1-2 : bond 0.00503 ( 4) link_BETA1-2 : angle 1.45736 ( 12) link_BETA1-4 : bond 0.00492 ( 8) link_BETA1-4 : angle 1.79848 ( 24) link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 2.69080 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.730 Fit side-chains REVERT: A 330 ASP cc_start: 0.8176 (m-30) cc_final: 0.7881 (m-30) REVERT: A 417 CYS cc_start: 0.6926 (p) cc_final: 0.6266 (p) REVERT: B 417 CYS cc_start: 0.7013 (p) cc_final: 0.6365 (p) REVERT: C 330 ASP cc_start: 0.8249 (m-30) cc_final: 0.7897 (m-30) REVERT: C 417 CYS cc_start: 0.7017 (p) cc_final: 0.6370 (p) REVERT: D 330 ASP cc_start: 0.8197 (m-30) cc_final: 0.7932 (m-30) REVERT: D 417 CYS cc_start: 0.7198 (p) cc_final: 0.6558 (p) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.4332 time to fit residues: 119.5654 Evaluate side-chains 203 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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: 0.9980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN L 27 GLN B 142 ASN I 27 GLN C 142 ASN J 27 GLN D 142 ASN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.144003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100891 restraints weight = 19589.912| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.36 r_work: 0.2924 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20212 Z= 0.178 Angle : 0.626 5.145 27500 Z= 0.338 Chirality : 0.046 0.193 3056 Planarity : 0.005 0.040 3440 Dihedral : 7.710 55.396 3428 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.43 % Favored : 96.24 % Rotamer: Outliers : 0.75 % Allowed : 5.07 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -0.99 (0.17), residues: 2448 helix: -3.08 (0.65), residues: 24 sheet: -0.36 (0.16), residues: 1004 loop : -0.78 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 71 TYR 0.015 0.002 TYR A 121 PHE 0.015 0.002 PHE B 354 TRP 0.016 0.001 TRP B 178 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00392 (20132) covalent geometry : angle 0.61214 (27304) SS BOND : bond 0.00349 ( 44) SS BOND : angle 1.04026 ( 88) hydrogen bonds : bond 0.05245 ( 580) hydrogen bonds : angle 7.69858 ( 1608) link_ALPHA1-3 : bond 0.01169 ( 4) link_ALPHA1-3 : angle 1.46476 ( 12) link_ALPHA1-6 : bond 0.00662 ( 4) link_ALPHA1-6 : angle 1.30253 ( 12) link_BETA1-2 : bond 0.00533 ( 4) link_BETA1-2 : angle 1.62094 ( 12) link_BETA1-4 : bond 0.00379 ( 8) link_BETA1-4 : angle 1.91335 ( 24) link_NAG-ASN : bond 0.00368 ( 16) link_NAG-ASN : angle 2.46470 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.843 Fit side-chains REVERT: A 308 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8186 (mmmm) REVERT: A 330 ASP cc_start: 0.8447 (m-30) cc_final: 0.8130 (m-30) REVERT: A 417 CYS cc_start: 0.7976 (p) cc_final: 0.7361 (p) REVERT: L 63 THR cc_start: 0.7769 (m) cc_final: 0.7499 (t) REVERT: B 308 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8183 (mmmm) REVERT: B 330 ASP cc_start: 0.8522 (m-30) cc_final: 0.8308 (m-30) REVERT: B 417 CYS cc_start: 0.8005 (p) cc_final: 0.7398 (p) REVERT: I 63 THR cc_start: 0.7769 (m) cc_final: 0.7494 (t) REVERT: C 330 ASP cc_start: 0.8434 (m-30) cc_final: 0.8118 (m-30) REVERT: C 417 CYS cc_start: 0.8000 (p) cc_final: 0.7393 (p) REVERT: J 63 THR cc_start: 0.7761 (m) cc_final: 0.7486 (t) REVERT: D 308 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8184 (mmmm) REVERT: D 330 ASP cc_start: 0.8440 (m-30) cc_final: 0.8122 (m-30) REVERT: D 417 CYS cc_start: 0.7994 (p) cc_final: 0.7384 (p) REVERT: K 63 THR cc_start: 0.7765 (m) cc_final: 0.7493 (t) outliers start: 16 outliers final: 4 residues processed: 246 average time/residue: 0.3551 time to fit residues: 105.8362 Evaluate side-chains 229 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain D residue 415 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN L 27 GLN B 131 GLN I 27 GLN C 131 GLN J 27 GLN D 131 GLN K 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.144827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.107421 restraints weight = 19196.706| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.29 r_work: 0.2953 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20212 Z= 0.133 Angle : 0.561 4.526 27500 Z= 0.302 Chirality : 0.045 0.191 3056 Planarity : 0.004 0.037 3440 Dihedral : 7.252 50.820 3428 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.61 % Favored : 97.06 % Rotamer: Outliers : 1.31 % Allowed : 7.74 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -0.74 (0.17), residues: 2448 helix: -2.20 (0.93), residues: 24 sheet: -0.14 (0.17), residues: 996 loop : -0.67 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 71 TYR 0.013 0.002 TYR B 374 PHE 0.013 0.002 PHE C 354 TRP 0.014 0.001 TRP B 178 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00286 (20132) covalent geometry : angle 0.55059 (27304) SS BOND : bond 0.00221 ( 44) SS BOND : angle 0.70600 ( 88) hydrogen bonds : bond 0.04475 ( 580) hydrogen bonds : angle 6.97797 ( 1608) link_ALPHA1-3 : bond 0.01321 ( 4) link_ALPHA1-3 : angle 1.36028 ( 12) link_ALPHA1-6 : bond 0.00768 ( 4) link_ALPHA1-6 : angle 1.30320 ( 12) link_BETA1-2 : bond 0.00500 ( 4) link_BETA1-2 : angle 1.47911 ( 12) link_BETA1-4 : bond 0.00426 ( 8) link_BETA1-4 : angle 1.66829 ( 24) link_NAG-ASN : bond 0.00253 ( 16) link_NAG-ASN : angle 1.99062 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.647 Fit side-chains REVERT: A 308 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8195 (mmmm) REVERT: A 329 SER cc_start: 0.8447 (t) cc_final: 0.8033 (p) REVERT: A 330 ASP cc_start: 0.8325 (m-30) cc_final: 0.8056 (m-30) REVERT: A 359 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: B 308 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8185 (mmmm) REVERT: B 359 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: C 329 SER cc_start: 0.8454 (t) cc_final: 0.8039 (p) REVERT: C 330 ASP cc_start: 0.8325 (m-30) cc_final: 0.8052 (m-30) REVERT: C 359 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: D 308 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8194 (mmmm) REVERT: D 329 SER cc_start: 0.8444 (t) cc_final: 0.8031 (p) REVERT: D 330 ASP cc_start: 0.8329 (m-30) cc_final: 0.8059 (m-30) REVERT: D 359 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8030 (m-30) outliers start: 28 outliers final: 8 residues processed: 268 average time/residue: 0.3911 time to fit residues: 126.7359 Evaluate side-chains 254 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 115 optimal weight: 0.1980 chunk 211 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN I 27 GLN J 27 GLN D 274 HIS K 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.146469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108347 restraints weight = 19248.016| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.13 r_work: 0.2967 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20212 Z= 0.116 Angle : 0.531 4.307 27500 Z= 0.285 Chirality : 0.044 0.189 3056 Planarity : 0.003 0.035 3440 Dihedral : 6.821 46.320 3428 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 1.31 % Allowed : 9.05 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 2448 helix: -1.55 (1.11), residues: 24 sheet: -0.05 (0.17), residues: 1000 loop : -0.55 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.011 0.001 TYR C 374 PHE 0.012 0.002 PHE C 354 TRP 0.013 0.001 TRP C 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00247 (20132) covalent geometry : angle 0.52211 (27304) SS BOND : bond 0.00221 ( 44) SS BOND : angle 0.57152 ( 88) hydrogen bonds : bond 0.03938 ( 580) hydrogen bonds : angle 6.65042 ( 1608) link_ALPHA1-3 : bond 0.01406 ( 4) link_ALPHA1-3 : angle 1.25030 ( 12) link_ALPHA1-6 : bond 0.00819 ( 4) link_ALPHA1-6 : angle 1.29141 ( 12) link_BETA1-2 : bond 0.00485 ( 4) link_BETA1-2 : angle 1.45730 ( 12) link_BETA1-4 : bond 0.00501 ( 8) link_BETA1-4 : angle 1.56718 ( 24) link_NAG-ASN : bond 0.00217 ( 16) link_NAG-ASN : angle 1.81127 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8443 (t) cc_final: 0.8011 (p) REVERT: A 330 ASP cc_start: 0.8326 (m-30) cc_final: 0.7957 (m-30) REVERT: A 417 CYS cc_start: 0.7836 (p) cc_final: 0.7246 (p) REVERT: B 417 CYS cc_start: 0.7844 (p) cc_final: 0.7256 (p) REVERT: C 329 SER cc_start: 0.8449 (t) cc_final: 0.8015 (p) REVERT: C 330 ASP cc_start: 0.8332 (m-30) cc_final: 0.7958 (m-30) REVERT: C 417 CYS cc_start: 0.7836 (p) cc_final: 0.7247 (p) REVERT: D 329 SER cc_start: 0.8440 (t) cc_final: 0.8007 (p) REVERT: D 330 ASP cc_start: 0.8324 (m-30) cc_final: 0.7951 (m-30) REVERT: D 417 CYS cc_start: 0.7847 (p) cc_final: 0.7261 (p) outliers start: 28 outliers final: 20 residues processed: 284 average time/residue: 0.3926 time to fit residues: 134.2115 Evaluate side-chains 275 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 136 optimal weight: 0.0370 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.143085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102788 restraints weight = 19050.744| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.12 r_work: 0.2901 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20212 Z= 0.189 Angle : 0.585 4.925 27500 Z= 0.313 Chirality : 0.046 0.215 3056 Planarity : 0.004 0.034 3440 Dihedral : 7.283 50.559 3428 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.06 % Favored : 96.77 % Rotamer: Outliers : 1.31 % Allowed : 9.85 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -0.58 (0.17), residues: 2448 helix: -1.55 (0.97), residues: 24 sheet: -0.07 (0.17), residues: 1000 loop : -0.53 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 85 TYR 0.018 0.002 TYR D 121 PHE 0.014 0.002 PHE B 354 TRP 0.014 0.001 TRP C 178 HIS 0.002 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00423 (20132) covalent geometry : angle 0.57398 (27304) SS BOND : bond 0.00305 ( 44) SS BOND : angle 0.71592 ( 88) hydrogen bonds : bond 0.04373 ( 580) hydrogen bonds : angle 6.65931 ( 1608) link_ALPHA1-3 : bond 0.01133 ( 4) link_ALPHA1-3 : angle 1.44803 ( 12) link_ALPHA1-6 : bond 0.00665 ( 4) link_ALPHA1-6 : angle 1.29758 ( 12) link_BETA1-2 : bond 0.00539 ( 4) link_BETA1-2 : angle 1.56064 ( 12) link_BETA1-4 : bond 0.00333 ( 8) link_BETA1-4 : angle 1.85395 ( 24) link_NAG-ASN : bond 0.00408 ( 16) link_NAG-ASN : angle 2.03285 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8451 (t) cc_final: 0.8015 (p) REVERT: A 330 ASP cc_start: 0.8341 (m-30) cc_final: 0.7947 (m-30) REVERT: A 359 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: A 417 CYS cc_start: 0.7921 (p) cc_final: 0.7260 (p) REVERT: B 359 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: B 417 CYS cc_start: 0.7937 (p) cc_final: 0.7281 (p) REVERT: C 329 SER cc_start: 0.8451 (t) cc_final: 0.8015 (p) REVERT: C 330 ASP cc_start: 0.8345 (m-30) cc_final: 0.7947 (m-30) REVERT: C 359 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: C 417 CYS cc_start: 0.7932 (p) cc_final: 0.7275 (p) REVERT: D 329 SER cc_start: 0.8452 (t) cc_final: 0.8019 (p) REVERT: D 330 ASP cc_start: 0.8341 (m-30) cc_final: 0.7943 (m-30) REVERT: D 359 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: D 417 CYS cc_start: 0.7929 (p) cc_final: 0.7269 (p) outliers start: 28 outliers final: 20 residues processed: 267 average time/residue: 0.4241 time to fit residues: 134.5462 Evaluate side-chains 274 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN L 27 GLN B 273 GLN I 27 GLN D 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098650 restraints weight = 18919.155| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.15 r_work: 0.2847 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20212 Z= 0.292 Angle : 0.669 5.707 27500 Z= 0.356 Chirality : 0.050 0.216 3056 Planarity : 0.005 0.038 3440 Dihedral : 8.298 60.296 3428 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.19 % Favored : 96.65 % Rotamer: Outliers : 1.69 % Allowed : 10.37 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2448 helix: -1.52 (0.92), residues: 24 sheet: -0.20 (0.17), residues: 956 loop : -0.71 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 85 TYR 0.021 0.003 TYR D 121 PHE 0.018 0.003 PHE F 100F TRP 0.018 0.002 TRP B 178 HIS 0.003 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00673 (20132) covalent geometry : angle 0.65641 (27304) SS BOND : bond 0.00418 ( 44) SS BOND : angle 0.86411 ( 88) hydrogen bonds : bond 0.04939 ( 580) hydrogen bonds : angle 6.83881 ( 1608) link_ALPHA1-3 : bond 0.00975 ( 4) link_ALPHA1-3 : angle 1.84571 ( 12) link_ALPHA1-6 : bond 0.00426 ( 4) link_ALPHA1-6 : angle 1.28422 ( 12) link_BETA1-2 : bond 0.00565 ( 4) link_BETA1-2 : angle 1.77108 ( 12) link_BETA1-4 : bond 0.00224 ( 8) link_BETA1-4 : angle 2.15485 ( 24) link_NAG-ASN : bond 0.00581 ( 16) link_NAG-ASN : angle 2.33041 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8478 (t) cc_final: 0.8078 (p) REVERT: A 330 ASP cc_start: 0.8407 (m-30) cc_final: 0.8134 (m-30) REVERT: A 359 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: A 417 CYS cc_start: 0.8031 (p) cc_final: 0.7336 (p) REVERT: B 359 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: B 417 CYS cc_start: 0.8027 (p) cc_final: 0.7332 (p) REVERT: C 329 SER cc_start: 0.8482 (t) cc_final: 0.8080 (p) REVERT: C 330 ASP cc_start: 0.8416 (m-30) cc_final: 0.8141 (m-30) REVERT: C 359 ASP cc_start: 0.8858 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: C 417 CYS cc_start: 0.8046 (p) cc_final: 0.7356 (p) REVERT: D 329 SER cc_start: 0.8484 (t) cc_final: 0.8086 (p) REVERT: D 330 ASP cc_start: 0.8406 (m-30) cc_final: 0.8134 (m-30) REVERT: D 359 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: D 417 CYS cc_start: 0.8034 (p) cc_final: 0.7340 (p) outliers start: 36 outliers final: 16 residues processed: 242 average time/residue: 0.4288 time to fit residues: 122.4916 Evaluate side-chains 230 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.142392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102445 restraints weight = 19028.117| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.11 r_work: 0.2897 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20212 Z= 0.169 Angle : 0.577 5.838 27500 Z= 0.309 Chirality : 0.046 0.184 3056 Planarity : 0.004 0.036 3440 Dihedral : 7.750 56.072 3428 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 1.45 % Allowed : 10.60 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2448 helix: -1.43 (0.98), residues: 24 sheet: -0.14 (0.16), residues: 1024 loop : -0.61 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 85 TYR 0.016 0.002 TYR C 121 PHE 0.013 0.002 PHE B 354 TRP 0.017 0.001 TRP C 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00379 (20132) covalent geometry : angle 0.56770 (27304) SS BOND : bond 0.00303 ( 44) SS BOND : angle 0.62168 ( 88) hydrogen bonds : bond 0.04095 ( 580) hydrogen bonds : angle 6.54637 ( 1608) link_ALPHA1-3 : bond 0.01127 ( 4) link_ALPHA1-3 : angle 1.57814 ( 12) link_ALPHA1-6 : bond 0.00644 ( 4) link_ALPHA1-6 : angle 1.30092 ( 12) link_BETA1-2 : bond 0.00475 ( 4) link_BETA1-2 : angle 1.47212 ( 12) link_BETA1-4 : bond 0.00364 ( 8) link_BETA1-4 : angle 1.85295 ( 24) link_NAG-ASN : bond 0.00290 ( 16) link_NAG-ASN : angle 1.91528 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8473 (t) cc_final: 0.8087 (p) REVERT: A 330 ASP cc_start: 0.8387 (m-30) cc_final: 0.8008 (m-30) REVERT: A 359 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: A 417 CYS cc_start: 0.7954 (p) cc_final: 0.7318 (p) REVERT: B 359 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: B 417 CYS cc_start: 0.7961 (p) cc_final: 0.7322 (p) REVERT: C 329 SER cc_start: 0.8472 (t) cc_final: 0.8089 (p) REVERT: C 330 ASP cc_start: 0.8400 (m-30) cc_final: 0.8047 (m-30) REVERT: C 359 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: C 417 CYS cc_start: 0.7969 (p) cc_final: 0.7332 (p) REVERT: D 329 SER cc_start: 0.8474 (t) cc_final: 0.8090 (p) REVERT: D 330 ASP cc_start: 0.8384 (m-30) cc_final: 0.8002 (m-30) REVERT: D 359 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: D 417 CYS cc_start: 0.7970 (p) cc_final: 0.7336 (p) outliers start: 31 outliers final: 20 residues processed: 241 average time/residue: 0.4167 time to fit residues: 121.1422 Evaluate side-chains 254 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 273 GLN D 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.140820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.100765 restraints weight = 19112.867| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.10 r_work: 0.2888 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20212 Z= 0.192 Angle : 0.591 6.081 27500 Z= 0.315 Chirality : 0.046 0.197 3056 Planarity : 0.004 0.036 3440 Dihedral : 7.788 56.467 3428 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.24 % Rotamer: Outliers : 1.78 % Allowed : 10.27 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 2448 helix: -1.44 (0.96), residues: 24 sheet: -0.01 (0.17), residues: 968 loop : -0.65 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.018 0.002 TYR B 121 PHE 0.014 0.002 PHE B 354 TRP 0.017 0.001 TRP C 178 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00435 (20132) covalent geometry : angle 0.58066 (27304) SS BOND : bond 0.00323 ( 44) SS BOND : angle 0.65266 ( 88) hydrogen bonds : bond 0.04219 ( 580) hydrogen bonds : angle 6.57870 ( 1608) link_ALPHA1-3 : bond 0.01101 ( 4) link_ALPHA1-3 : angle 1.60867 ( 12) link_ALPHA1-6 : bond 0.00616 ( 4) link_ALPHA1-6 : angle 1.29516 ( 12) link_BETA1-2 : bond 0.00514 ( 4) link_BETA1-2 : angle 1.51295 ( 12) link_BETA1-4 : bond 0.00321 ( 8) link_BETA1-4 : angle 1.93014 ( 24) link_NAG-ASN : bond 0.00376 ( 16) link_NAG-ASN : angle 1.98132 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8510 (t) cc_final: 0.8146 (p) REVERT: A 330 ASP cc_start: 0.8387 (m-30) cc_final: 0.8009 (m-30) REVERT: A 359 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: A 417 CYS cc_start: 0.8016 (p) cc_final: 0.7352 (p) REVERT: B 359 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: B 417 CYS cc_start: 0.8021 (p) cc_final: 0.7356 (p) REVERT: C 329 SER cc_start: 0.8509 (t) cc_final: 0.8150 (p) REVERT: C 330 ASP cc_start: 0.8394 (m-30) cc_final: 0.8145 (m-30) REVERT: C 359 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: C 417 CYS cc_start: 0.8037 (p) cc_final: 0.7377 (p) REVERT: D 329 SER cc_start: 0.8508 (t) cc_final: 0.8145 (p) REVERT: D 330 ASP cc_start: 0.8382 (m-30) cc_final: 0.7997 (m-30) REVERT: D 359 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: D 417 CYS cc_start: 0.8042 (p) cc_final: 0.7381 (p) outliers start: 38 outliers final: 24 residues processed: 243 average time/residue: 0.3965 time to fit residues: 115.3668 Evaluate side-chains 255 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 273 GLN D 273 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.139971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099603 restraints weight = 19102.618| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.12 r_work: 0.2885 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20212 Z= 0.197 Angle : 0.593 6.329 27500 Z= 0.316 Chirality : 0.046 0.198 3056 Planarity : 0.004 0.036 3440 Dihedral : 7.842 57.020 3428 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.61 % Rotamer: Outliers : 1.64 % Allowed : 10.32 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -0.64 (0.17), residues: 2448 helix: -1.44 (0.96), residues: 24 sheet: -0.02 (0.17), residues: 968 loop : -0.65 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.018 0.002 TYR B 121 PHE 0.014 0.002 PHE D 354 TRP 0.017 0.001 TRP B 178 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00447 (20132) covalent geometry : angle 0.58280 (27304) SS BOND : bond 0.00343 ( 44) SS BOND : angle 0.65191 ( 88) hydrogen bonds : bond 0.04237 ( 580) hydrogen bonds : angle 6.59638 ( 1608) link_ALPHA1-3 : bond 0.01082 ( 4) link_ALPHA1-3 : angle 1.64556 ( 12) link_ALPHA1-6 : bond 0.00596 ( 4) link_ALPHA1-6 : angle 1.29376 ( 12) link_BETA1-2 : bond 0.00500 ( 4) link_BETA1-2 : angle 1.49913 ( 12) link_BETA1-4 : bond 0.00285 ( 8) link_BETA1-4 : angle 1.93758 ( 24) link_NAG-ASN : bond 0.00375 ( 16) link_NAG-ASN : angle 1.96974 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8497 (t) cc_final: 0.8134 (p) REVERT: A 330 ASP cc_start: 0.8391 (m-30) cc_final: 0.8012 (m-30) REVERT: A 359 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: A 381 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: A 417 CYS cc_start: 0.8033 (p) cc_final: 0.7365 (p) REVERT: B 359 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: B 417 CYS cc_start: 0.8027 (p) cc_final: 0.7358 (p) REVERT: C 329 SER cc_start: 0.8496 (t) cc_final: 0.8140 (p) REVERT: C 330 ASP cc_start: 0.8397 (m-30) cc_final: 0.8149 (m-30) REVERT: C 359 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: C 381 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: C 417 CYS cc_start: 0.8053 (p) cc_final: 0.7388 (p) REVERT: D 329 SER cc_start: 0.8499 (t) cc_final: 0.8137 (p) REVERT: D 330 ASP cc_start: 0.8387 (m-30) cc_final: 0.8013 (m-30) REVERT: D 359 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: D 381 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: D 417 CYS cc_start: 0.8049 (p) cc_final: 0.7384 (p) outliers start: 35 outliers final: 24 residues processed: 239 average time/residue: 0.4335 time to fit residues: 123.6487 Evaluate side-chains 256 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.141475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104806 restraints weight = 19193.060| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.04 r_work: 0.2908 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20212 Z= 0.152 Angle : 0.563 6.486 27500 Z= 0.301 Chirality : 0.045 0.187 3056 Planarity : 0.003 0.036 3440 Dihedral : 7.524 54.063 3428 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.98 % Favored : 96.85 % Rotamer: Outliers : 1.55 % Allowed : 10.60 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2448 helix: -1.39 (1.00), residues: 24 sheet: 0.00 (0.17), residues: 976 loop : -0.61 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.015 0.002 TYR J 86 PHE 0.012 0.002 PHE D 354 TRP 0.016 0.001 TRP C 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00341 (20132) covalent geometry : angle 0.55446 (27304) SS BOND : bond 0.00288 ( 44) SS BOND : angle 0.57319 ( 88) hydrogen bonds : bond 0.03876 ( 580) hydrogen bonds : angle 6.39645 ( 1608) link_ALPHA1-3 : bond 0.01189 ( 4) link_ALPHA1-3 : angle 1.52819 ( 12) link_ALPHA1-6 : bond 0.00673 ( 4) link_ALPHA1-6 : angle 1.30556 ( 12) link_BETA1-2 : bond 0.00469 ( 4) link_BETA1-2 : angle 1.39704 ( 12) link_BETA1-4 : bond 0.00377 ( 8) link_BETA1-4 : angle 1.79292 ( 24) link_NAG-ASN : bond 0.00262 ( 16) link_NAG-ASN : angle 1.82001 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8485 (t) cc_final: 0.8118 (p) REVERT: A 330 ASP cc_start: 0.8384 (m-30) cc_final: 0.8012 (m-30) REVERT: A 417 CYS cc_start: 0.7947 (p) cc_final: 0.7291 (p) REVERT: B 359 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: B 417 CYS cc_start: 0.7949 (p) cc_final: 0.7293 (p) REVERT: C 329 SER cc_start: 0.8482 (t) cc_final: 0.8116 (p) REVERT: C 330 ASP cc_start: 0.8390 (m-30) cc_final: 0.8012 (m-30) REVERT: C 381 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8278 (mt-10) REVERT: C 417 CYS cc_start: 0.7956 (p) cc_final: 0.7301 (p) REVERT: D 329 SER cc_start: 0.8483 (t) cc_final: 0.8119 (p) REVERT: D 330 ASP cc_start: 0.8380 (m-30) cc_final: 0.8007 (m-30) REVERT: D 381 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: D 417 CYS cc_start: 0.7959 (p) cc_final: 0.7304 (p) outliers start: 33 outliers final: 25 residues processed: 242 average time/residue: 0.4151 time to fit residues: 120.5255 Evaluate side-chains 251 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 164 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 37 GLN J 37 GLN K 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.140185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100343 restraints weight = 19126.233| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.08 r_work: 0.2881 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20212 Z= 0.206 Angle : 0.598 6.483 27500 Z= 0.318 Chirality : 0.047 0.205 3056 Planarity : 0.004 0.036 3440 Dihedral : 7.777 56.216 3428 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 1.41 % Allowed : 10.60 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -0.66 (0.17), residues: 2448 helix: -1.40 (0.97), residues: 24 sheet: -0.07 (0.17), residues: 976 loop : -0.64 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.019 0.002 TYR B 121 PHE 0.014 0.002 PHE C 354 TRP 0.017 0.001 TRP A 178 HIS 0.002 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00472 (20132) covalent geometry : angle 0.58832 (27304) SS BOND : bond 0.00346 ( 44) SS BOND : angle 0.66662 ( 88) hydrogen bonds : bond 0.04198 ( 580) hydrogen bonds : angle 6.50621 ( 1608) link_ALPHA1-3 : bond 0.01061 ( 4) link_ALPHA1-3 : angle 1.65673 ( 12) link_ALPHA1-6 : bond 0.00582 ( 4) link_ALPHA1-6 : angle 1.30407 ( 12) link_BETA1-2 : bond 0.00501 ( 4) link_BETA1-2 : angle 1.46463 ( 12) link_BETA1-4 : bond 0.00277 ( 8) link_BETA1-4 : angle 1.93446 ( 24) link_NAG-ASN : bond 0.00400 ( 16) link_NAG-ASN : angle 1.98771 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6405.47 seconds wall clock time: 110 minutes 32.12 seconds (6632.12 seconds total)