Starting phenix.real_space_refine on Sat Jul 4 10:27:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md4_48167/07_2026/9md4_48167.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md4_48167/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9md4_48167/07_2026/9md4_48167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md4_48167/07_2026/9md4_48167.map" model { file = "/net/cci-nas-00/data/ceres_data/9md4_48167/07_2026/9md4_48167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md4_48167/07_2026/9md4_48167.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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-dev-6108/lib/python3.11/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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 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, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.76, per 1000 atoms: 0.24 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: 2.14 Conformation dependent library (CDL) restraints added in 786.1 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: 0.77 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: 4.28 Time building geometry restraints manager: 2.75 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.670 Find NCS groups from input model: 0.200 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 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/Z covalent geometry : bond 0.00282 / 0.14 (20132) covalent geometry : angle 0.61870 / 0.34 (27304) SS BOND : bond 0.00328 / 0.22 ( 44) SS BOND : angle 1.65100 / 1.24 ( 88) hydrogen bonds : bond 0.23996 / 16.75 ( 580) hydrogen bonds : angle 10.36622 / 7.28 ( 1608) link_ALPHA1-3 : bond 0.01289 / 0.76 ( 4) link_ALPHA1-3 : angle 1.54158 / 0.75 ( 12) link_ALPHA1-6 : bond 0.00729 / 0.44 ( 4) link_ALPHA1-6 : angle 1.24578 / 0.64 ( 12) link_BETA1-2 : bond 0.00503 / 0.30 ( 4) link_BETA1-2 : angle 1.45736 / 0.70 ( 12) link_BETA1-4 : bond 0.00492 / 0.35 ( 8) link_BETA1-4 : angle 1.79848 / 1.08 ( 24) link_NAG-ASN : bond 0.00199 / 0.13 ( 16) link_NAG-ASN : angle 2.69080 / 1.88 ( 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 : 0.734 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: 0.4719 time to fit residues: 130.7288 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 : 0.711 ------------------------------------------------------------------------------- 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... 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 = 0.3559 r_free = 0.3559 target = 0.143338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100509 restraints weight = 19738.554| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.32 r_work: 0.2922 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0922 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= 0.176 Angle : 0.627 5.147 27500 Z= 0.339 Chirality : 0.046 0.194 3056 Planarity : 0.005 0.040 3440 Dihedral : 7.707 55.387 3428 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.43 % Favored : 96.24 % Rotamer: Outliers : 0.75 % Allowed : 5.25 % Favored : 94.00 % 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: -1.00 (0.17), residues: 2448 helix: -3.09 (0.64), residues: 24 sheet: -0.37 (0.16), residues: 1004 loop : -0.79 (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 C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (20132) covalent geometry : angle 0.61297 / 0.34 (27304) SS BOND : bond 0.00352 / 0.23 ( 44) SS BOND : angle 1.04254 / 0.77 ( 88) hydrogen bonds : bond 0.05362 / 3.80 ( 580) hydrogen bonds : angle 7.72561 / 5.47 ( 1608) link_ALPHA1-3 : bond 0.01178 / 0.71 ( 4) link_ALPHA1-3 : angle 1.45860 / 0.71 ( 12) link_ALPHA1-6 : bond 0.00664 / 0.40 ( 4) link_ALPHA1-6 : angle 1.30037 / 0.67 ( 12) link_BETA1-2 : bond 0.00537 / 0.32 ( 4) link_BETA1-2 : angle 1.61119 / 0.76 ( 12) link_BETA1-4 : bond 0.00410 / 0.30 ( 8) link_BETA1-4 : angle 1.92095 / 1.13 ( 24) link_NAG-ASN : bond 0.00367 / 0.22 ( 16) link_NAG-ASN : angle 2.46495 / 1.69 ( 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 253 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.811 Fit side-chains REVERT: A 308 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8083 (mmmm) REVERT: A 330 ASP cc_start: 0.8421 (m-30) cc_final: 0.8099 (m-30) REVERT: A 417 CYS cc_start: 0.7884 (p) cc_final: 0.7248 (p) REVERT: L 63 THR cc_start: 0.7617 (m) cc_final: 0.7337 (t) REVERT: B 308 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8075 (mmmm) REVERT: B 330 ASP cc_start: 0.8506 (m-30) cc_final: 0.8279 (m-30) REVERT: B 417 CYS cc_start: 0.7906 (p) cc_final: 0.7275 (p) REVERT: I 63 THR cc_start: 0.7615 (m) cc_final: 0.7332 (t) REVERT: C 330 ASP cc_start: 0.8411 (m-30) cc_final: 0.8086 (m-30) REVERT: C 417 CYS cc_start: 0.7897 (p) cc_final: 0.7263 (p) REVERT: J 63 THR cc_start: 0.7614 (m) cc_final: 0.7328 (t) REVERT: D 308 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8080 (mmmm) REVERT: D 330 ASP cc_start: 0.8412 (m-30) cc_final: 0.8090 (m-30) REVERT: D 417 CYS cc_start: 0.7888 (p) cc_final: 0.7252 (p) REVERT: K 63 THR cc_start: 0.7615 (m) cc_final: 0.7334 (t) outliers start: 16 outliers final: 4 residues processed: 245 average time/residue: 0.3994 time to fit residues: 118.9076 Evaluate side-chains 236 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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: 3.9990 chunk 179 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 GLN A 274 HIS L 27 GLN B 131 GLN I 27 GLN C 131 GLN J 27 GLN D 131 GLN D 274 HIS K 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.144507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107981 restraints weight = 19324.375| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.05 r_work: 0.2958 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1178 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 : 0.563 4.560 27500 Z= 0.304 Chirality : 0.045 0.191 3056 Planarity : 0.004 0.037 3440 Dihedral : 7.278 51.256 3428 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.45 % Favored : 97.22 % Rotamer: Outliers : 1.31 % Allowed : 7.36 % Favored : 91.32 % 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: -0.77 (0.17), residues: 2448 helix: -2.21 (0.92), residues: 24 sheet: -0.15 (0.17), residues: 996 loop : -0.70 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 71 TYR 0.013 0.002 TYR C 374 PHE 0.013 0.002 PHE C 354 TRP 0.014 0.001 TRP C 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20132) covalent geometry : angle 0.55241 / 0.30 (27304) SS BOND : bond 0.00240 / 0.15 ( 44) SS BOND : angle 0.73136 / 0.54 ( 88) hydrogen bonds : bond 0.04449 / 3.12 ( 580) hydrogen bonds : angle 7.03397 / 4.98 ( 1608) link_ALPHA1-3 : bond 0.01309 / 0.79 ( 4) link_ALPHA1-3 : angle 1.36210 / 0.66 ( 12) link_ALPHA1-6 : bond 0.00756 / 0.45 ( 4) link_ALPHA1-6 : angle 1.30223 / 0.67 ( 12) link_BETA1-2 : bond 0.00502 / 0.30 ( 4) link_BETA1-2 : angle 1.48991 / 0.71 ( 12) link_BETA1-4 : bond 0.00445 / 0.32 ( 8) link_BETA1-4 : angle 1.69219 / 1.02 ( 24) link_NAG-ASN : bond 0.00251 / 0.15 ( 16) link_NAG-ASN : angle 2.03565 / 1.38 ( 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 283 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.790 Fit side-chains REVERT: A 308 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8180 (mmmm) REVERT: A 330 ASP cc_start: 0.8323 (m-30) cc_final: 0.8067 (m-30) REVERT: A 359 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: B 308 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8175 (mmmm) REVERT: B 359 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: C 330 ASP cc_start: 0.8324 (m-30) cc_final: 0.8007 (m-30) REVERT: C 359 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: D 308 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8180 (mmmm) REVERT: D 330 ASP cc_start: 0.8325 (m-30) cc_final: 0.8015 (m-30) REVERT: D 359 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.7974 (m-30) outliers start: 28 outliers final: 8 residues processed: 267 average time/residue: 0.4001 time to fit residues: 129.3270 Evaluate side-chains 250 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 56 optimal weight: 0.0050 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 chunk 76 optimal weight: 0.0040 chunk 153 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN I 27 GLN C 221 ASN J 27 GLN K 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.147250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110617 restraints weight = 19365.316| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.20 r_work: 0.3012 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20212 Z= 0.107 Angle : 0.522 4.150 27500 Z= 0.281 Chirality : 0.044 0.188 3056 Planarity : 0.003 0.036 3440 Dihedral : 6.673 44.768 3428 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.61 % Rotamer: Outliers : 1.31 % Allowed : 9.01 % Favored : 89.68 % 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: -0.55 (0.17), residues: 2448 helix: -1.61 (1.08), residues: 24 sheet: 0.01 (0.17), residues: 996 loop : -0.57 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 71 TYR 0.011 0.001 TYR A 374 PHE 0.012 0.002 PHE B 354 TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (20132) covalent geometry : angle 0.51390 / 0.28 (27304) SS BOND : bond 0.00200 / 0.13 ( 44) SS BOND : angle 0.54328 / 0.40 ( 88) hydrogen bonds : bond 0.03831 / 2.68 ( 580) hydrogen bonds : angle 6.57402 / 4.65 ( 1608) link_ALPHA1-3 : bond 0.01392 / 0.83 ( 4) link_ALPHA1-3 : angle 1.15692 / 0.56 ( 12) link_ALPHA1-6 : bond 0.00864 / 0.52 ( 4) link_ALPHA1-6 : angle 1.28533 / 0.66 ( 12) link_BETA1-2 : bond 0.00452 / 0.27 ( 4) link_BETA1-2 : angle 1.45977 / 0.70 ( 12) link_BETA1-4 : bond 0.00523 / 0.37 ( 8) link_BETA1-4 : angle 1.49658 / 0.90 ( 24) link_NAG-ASN : bond 0.00187 / 0.11 ( 16) link_NAG-ASN : angle 1.73603 / 1.16 ( 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 314 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8450 (t) cc_final: 0.8042 (p) REVERT: A 330 ASP cc_start: 0.8303 (m-30) cc_final: 0.7916 (m-30) REVERT: A 417 CYS cc_start: 0.7741 (p) cc_final: 0.7137 (p) REVERT: B 417 CYS cc_start: 0.7762 (p) cc_final: 0.7158 (p) REVERT: C 329 SER cc_start: 0.8455 (t) cc_final: 0.8042 (p) REVERT: C 330 ASP cc_start: 0.8314 (m-30) cc_final: 0.7917 (m-30) REVERT: C 417 CYS cc_start: 0.7748 (p) cc_final: 0.7140 (p) REVERT: D 329 SER cc_start: 0.8453 (t) cc_final: 0.8041 (p) REVERT: D 330 ASP cc_start: 0.8307 (m-30) cc_final: 0.7908 (m-30) REVERT: D 417 CYS cc_start: 0.7754 (p) cc_final: 0.7147 (p) outliers start: 28 outliers final: 20 residues processed: 298 average time/residue: 0.3453 time to fit residues: 125.1195 Evaluate side-chains 282 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094572 restraints weight = 20292.404| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.16 r_work: 0.2838 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.069 20212 Z= 0.431 Angle : 0.774 6.473 27500 Z= 0.411 Chirality : 0.056 0.235 3056 Planarity : 0.006 0.056 3440 Dihedral : 8.945 65.458 3428 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 1.69 % Allowed : 9.76 % Favored : 88.56 % 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: -0.93 (0.17), residues: 2448 helix: -2.41 (0.70), residues: 24 sheet: -0.28 (0.16), residues: 1004 loop : -0.79 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 364 TYR 0.027 0.004 TYR G 97 PHE 0.023 0.003 PHE F 100F TRP 0.021 0.002 TRP B 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.01000 / 0.43 (20132) covalent geometry : angle 0.75891 / 0.41 (27304) SS BOND : bond 0.00628 / 0.40 ( 44) SS BOND : angle 1.14628 / 0.82 ( 88) hydrogen bonds : bond 0.05685 / 4.04 ( 580) hydrogen bonds : angle 7.06547 / 4.99 ( 1608) link_ALPHA1-3 : bond 0.00703 / 0.42 ( 4) link_ALPHA1-3 : angle 1.99796 / 0.98 ( 12) link_ALPHA1-6 : bond 0.00312 / 0.19 ( 4) link_ALPHA1-6 : angle 1.30490 / 0.67 ( 12) link_BETA1-2 : bond 0.00759 / 0.45 ( 4) link_BETA1-2 : angle 2.10698 / 0.99 ( 12) link_BETA1-4 : bond 0.00228 / 0.14 ( 8) link_BETA1-4 : angle 2.55137 / 1.42 ( 24) link_NAG-ASN : bond 0.00842 / 0.56 ( 16) link_NAG-ASN : angle 2.74276 / 1.77 ( 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 262 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8439 (t) cc_final: 0.8037 (p) REVERT: A 330 ASP cc_start: 0.8433 (m-30) cc_final: 0.8206 (m-30) REVERT: A 359 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8270 (m-30) REVERT: B 359 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: C 329 SER cc_start: 0.8435 (t) cc_final: 0.8031 (p) REVERT: C 330 ASP cc_start: 0.8443 (m-30) cc_final: 0.8204 (m-30) REVERT: C 359 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: D 329 SER cc_start: 0.8432 (t) cc_final: 0.8030 (p) REVERT: D 330 ASP cc_start: 0.8423 (m-30) cc_final: 0.8197 (m-30) REVERT: D 359 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8267 (m-30) outliers start: 36 outliers final: 16 residues processed: 242 average time/residue: 0.4091 time to fit residues: 119.1062 Evaluate side-chains 227 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 236 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 205 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.142521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.107931 restraints weight = 19056.909| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.14 r_work: 0.2910 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1657 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= 0.138 Angle : 0.571 5.780 27500 Z= 0.307 Chirality : 0.045 0.168 3056 Planarity : 0.004 0.036 3440 Dihedral : 7.835 56.814 3428 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % 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: -0.68 (0.17), residues: 2448 helix: -1.66 (0.93), residues: 24 sheet: -0.16 (0.16), residues: 996 loop : -0.59 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.015 0.002 TYR B 121 PHE 0.012 0.002 PHE A 354 TRP 0.017 0.001 TRP D 178 HIS 0.003 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (20132) covalent geometry : angle 0.56167 / 0.31 (27304) SS BOND : bond 0.00280 / 0.18 ( 44) SS BOND : angle 0.63311 / 0.46 ( 88) hydrogen bonds : bond 0.03984 / 2.79 ( 580) hydrogen bonds : angle 6.48667 / 4.59 ( 1608) link_ALPHA1-3 : bond 0.01186 / 0.71 ( 4) link_ALPHA1-3 : angle 1.55934 / 0.76 ( 12) link_ALPHA1-6 : bond 0.00701 / 0.42 ( 4) link_ALPHA1-6 : angle 1.30226 / 0.67 ( 12) link_BETA1-2 : bond 0.00443 / 0.27 ( 4) link_BETA1-2 : angle 1.46711 / 0.71 ( 12) link_BETA1-4 : bond 0.00458 / 0.33 ( 8) link_BETA1-4 : angle 1.78119 / 1.09 ( 24) link_NAG-ASN : bond 0.00267 / 0.16 ( 16) link_NAG-ASN : angle 1.92277 / 1.27 ( 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 280 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8539 (t) cc_final: 0.8204 (p) REVERT: A 330 ASP cc_start: 0.8442 (m-30) cc_final: 0.8185 (m-30) REVERT: A 359 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: A 417 CYS cc_start: 0.8169 (p) cc_final: 0.7601 (p) REVERT: B 359 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: B 417 CYS cc_start: 0.8181 (p) cc_final: 0.7614 (p) REVERT: C 308 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8354 (mmmm) REVERT: C 329 SER cc_start: 0.8532 (t) cc_final: 0.8194 (p) REVERT: C 330 ASP cc_start: 0.8450 (m-30) cc_final: 0.8093 (m-30) REVERT: C 417 CYS cc_start: 0.8182 (p) cc_final: 0.7617 (p) REVERT: D 329 SER cc_start: 0.8533 (t) cc_final: 0.8193 (p) REVERT: D 330 ASP cc_start: 0.8432 (m-30) cc_final: 0.8073 (m-30) REVERT: D 359 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8381 (m-30) REVERT: D 417 CYS cc_start: 0.8177 (p) cc_final: 0.7610 (p) outliers start: 30 outliers final: 14 residues processed: 256 average time/residue: 0.4217 time to fit residues: 129.9366 Evaluate side-chains 251 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.5980 chunk 86 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 231 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.144538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.105286 restraints weight = 18876.428| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.32 r_work: 0.2905 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 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 : 0.003 0.033 20212 Z= 0.152 Angle : 0.563 5.135 27500 Z= 0.302 Chirality : 0.045 0.191 3056 Planarity : 0.004 0.034 3440 Dihedral : 7.497 53.819 3428 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 1.59 % Allowed : 10.08 % Favored : 88.32 % 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: -0.54 (0.17), residues: 2448 helix: -1.38 (0.99), residues: 24 sheet: 0.06 (0.17), residues: 956 loop : -0.59 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.016 0.002 TYR B 121 PHE 0.013 0.002 PHE B 354 TRP 0.016 0.001 TRP B 178 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (20132) covalent geometry : angle 0.55369 / 0.30 (27304) SS BOND : bond 0.00269 / 0.17 ( 44) SS BOND : angle 0.61613 / 0.45 ( 88) hydrogen bonds : bond 0.03944 / 2.77 ( 580) hydrogen bonds : angle 6.38965 / 4.53 ( 1608) link_ALPHA1-3 : bond 0.01228 / 0.74 ( 4) link_ALPHA1-3 : angle 1.50202 / 0.73 ( 12) link_ALPHA1-6 : bond 0.00698 / 0.42 ( 4) link_ALPHA1-6 : angle 1.29976 / 0.67 ( 12) link_BETA1-2 : bond 0.00510 / 0.31 ( 4) link_BETA1-2 : angle 1.44192 / 0.69 ( 12) link_BETA1-4 : bond 0.00399 / 0.29 ( 8) link_BETA1-4 : angle 1.81769 / 1.09 ( 24) link_NAG-ASN : bond 0.00310 / 0.19 ( 16) link_NAG-ASN : angle 1.87557 / 1.23 ( 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 285 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8502 (t) cc_final: 0.8133 (p) REVERT: A 330 ASP cc_start: 0.8404 (m-30) cc_final: 0.8164 (m-30) REVERT: A 359 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: A 417 CYS cc_start: 0.7981 (p) cc_final: 0.7350 (p) REVERT: A 431 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8321 (mttt) REVERT: B 359 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: B 417 CYS cc_start: 0.7993 (p) cc_final: 0.7365 (p) REVERT: B 431 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8286 (mttt) REVERT: C 308 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8302 (mmmm) REVERT: C 329 SER cc_start: 0.8495 (t) cc_final: 0.8121 (p) REVERT: C 330 ASP cc_start: 0.8406 (m-30) cc_final: 0.8049 (m-30) REVERT: C 417 CYS cc_start: 0.7990 (p) cc_final: 0.7359 (p) REVERT: C 431 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8326 (mttt) REVERT: D 329 SER cc_start: 0.8494 (t) cc_final: 0.8122 (p) REVERT: D 330 ASP cc_start: 0.8401 (m-30) cc_final: 0.8049 (m-30) REVERT: D 359 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: D 417 CYS cc_start: 0.7998 (p) cc_final: 0.7369 (p) REVERT: D 431 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8331 (mttt) outliers start: 34 outliers final: 24 residues processed: 259 average time/residue: 0.3990 time to fit residues: 125.1174 Evaluate side-chains 264 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 142 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 170 optimal weight: 0.2980 chunk 156 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.106450 restraints weight = 19268.713| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.15 r_work: 0.2911 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20212 Z= 0.132 Angle : 0.540 5.181 27500 Z= 0.290 Chirality : 0.045 0.192 3056 Planarity : 0.003 0.035 3440 Dihedral : 7.121 49.764 3428 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.86 % Favored : 96.98 % Rotamer: Outliers : 1.74 % Allowed : 10.51 % Favored : 87.76 % 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: -0.46 (0.17), residues: 2448 helix: -1.22 (1.06), residues: 24 sheet: 0.17 (0.17), residues: 956 loop : -0.58 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 85 TYR 0.014 0.002 TYR B 121 PHE 0.012 0.002 PHE A 354 TRP 0.014 0.001 TRP C 178 HIS 0.002 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (20132) covalent geometry : angle 0.53167 / 0.29 (27304) SS BOND : bond 0.00252 / 0.16 ( 44) SS BOND : angle 0.57516 / 0.43 ( 88) hydrogen bonds : bond 0.03710 / 2.59 ( 580) hydrogen bonds : angle 6.29102 / 4.47 ( 1608) link_ALPHA1-3 : bond 0.01223 / 0.74 ( 4) link_ALPHA1-3 : angle 1.36874 / 0.66 ( 12) link_ALPHA1-6 : bond 0.00753 / 0.45 ( 4) link_ALPHA1-6 : angle 1.29820 / 0.67 ( 12) link_BETA1-2 : bond 0.00449 / 0.27 ( 4) link_BETA1-2 : angle 1.40972 / 0.67 ( 12) link_BETA1-4 : bond 0.00428 / 0.31 ( 8) link_BETA1-4 : angle 1.65751 / 1.00 ( 24) link_NAG-ASN : bond 0.00224 / 0.14 ( 16) link_NAG-ASN : angle 1.74441 / 1.14 ( 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 286 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8534 (t) cc_final: 0.8191 (p) REVERT: A 330 ASP cc_start: 0.8384 (m-30) cc_final: 0.8145 (m-30) REVERT: C 308 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8292 (mmmm) REVERT: C 329 SER cc_start: 0.8520 (t) cc_final: 0.8172 (p) REVERT: C 330 ASP cc_start: 0.8395 (m-30) cc_final: 0.8032 (m-30) REVERT: D 329 SER cc_start: 0.8528 (t) cc_final: 0.8181 (p) REVERT: D 330 ASP cc_start: 0.8380 (m-30) cc_final: 0.8023 (m-30) outliers start: 37 outliers final: 24 residues processed: 261 average time/residue: 0.4022 time to fit residues: 126.9514 Evaluate side-chains 267 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.140409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103348 restraints weight = 19171.370| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.07 r_work: 0.2886 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1785 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= 0.188 Angle : 0.581 4.843 27500 Z= 0.310 Chirality : 0.046 0.209 3056 Planarity : 0.004 0.035 3440 Dihedral : 7.404 52.305 3428 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 1.88 % Allowed : 10.51 % Favored : 87.62 % 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: -0.54 (0.17), residues: 2448 helix: -1.36 (1.00), residues: 24 sheet: 0.10 (0.17), residues: 956 loop : -0.62 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 85 TYR 0.018 0.002 TYR B 121 PHE 0.014 0.002 PHE D 354 TRP 0.016 0.001 TRP C 178 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (20132) covalent geometry : angle 0.57072 / 0.31 (27304) SS BOND : bond 0.00391 / 0.24 ( 44) SS BOND : angle 0.76869 / 0.55 ( 88) hydrogen bonds : bond 0.04078 / 2.88 ( 580) hydrogen bonds : angle 6.41414 / 4.56 ( 1608) link_ALPHA1-3 : bond 0.01150 / 0.69 ( 4) link_ALPHA1-3 : angle 1.57663 / 0.77 ( 12) link_ALPHA1-6 : bond 0.00629 / 0.38 ( 4) link_ALPHA1-6 : angle 1.31581 / 0.68 ( 12) link_BETA1-2 : bond 0.00510 / 0.31 ( 4) link_BETA1-2 : angle 1.48693 / 0.71 ( 12) link_BETA1-4 : bond 0.00320 / 0.24 ( 8) link_BETA1-4 : angle 1.88363 / 1.10 ( 24) link_NAG-ASN : bond 0.00370 / 0.24 ( 16) link_NAG-ASN : angle 1.93927 / 1.26 ( 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 275 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8515 (t) cc_final: 0.8151 (p) REVERT: A 330 ASP cc_start: 0.8384 (m-30) cc_final: 0.8147 (m-30) REVERT: A 359 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: A 417 CYS cc_start: 0.7934 (p) cc_final: 0.7307 (p) REVERT: B 359 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: B 417 CYS cc_start: 0.7959 (p) cc_final: 0.7333 (p) REVERT: C 308 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8316 (mmmm) REVERT: C 329 SER cc_start: 0.8504 (t) cc_final: 0.8140 (p) REVERT: C 330 ASP cc_start: 0.8392 (m-30) cc_final: 0.8035 (m-30) REVERT: C 359 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: C 417 CYS cc_start: 0.7955 (p) cc_final: 0.7330 (p) REVERT: D 329 SER cc_start: 0.8507 (t) cc_final: 0.8144 (p) REVERT: D 330 ASP cc_start: 0.8387 (m-30) cc_final: 0.8036 (m-30) REVERT: D 359 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: D 417 CYS cc_start: 0.7960 (p) cc_final: 0.7336 (p) outliers start: 40 outliers final: 33 residues processed: 248 average time/residue: 0.4082 time to fit residues: 121.7675 Evaluate side-chains 276 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS 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 H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 CYS 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 E residue 107 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 314 SER 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 F residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 183 CYS 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 G residue 107 THR 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: 1.9990 chunk 79 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 211 optimal weight: 0.3980 chunk 169 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.140194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.104539 restraints weight = 19312.193| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.10 r_work: 0.2879 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1806 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= 0.177 Angle : 0.576 5.346 27500 Z= 0.308 Chirality : 0.046 0.201 3056 Planarity : 0.004 0.035 3440 Dihedral : 7.452 52.847 3428 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 1.55 % Allowed : 10.55 % Favored : 87.90 % 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: -0.55 (0.17), residues: 2448 helix: -1.38 (1.00), residues: 24 sheet: 0.09 (0.17), residues: 956 loop : -0.63 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.017 0.002 TYR B 121 PHE 0.013 0.002 PHE B 354 TRP 0.015 0.001 TRP C 178 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (20132) covalent geometry : angle 0.56623 / 0.31 (27304) SS BOND : bond 0.00341 / 0.21 ( 44) SS BOND : angle 0.71412 / 0.51 ( 88) hydrogen bonds : bond 0.04004 / 2.84 ( 580) hydrogen bonds : angle 6.39816 / 4.54 ( 1608) link_ALPHA1-3 : bond 0.01144 / 0.69 ( 4) link_ALPHA1-3 : angle 1.57231 / 0.76 ( 12) link_ALPHA1-6 : bond 0.00625 / 0.37 ( 4) link_ALPHA1-6 : angle 1.30777 / 0.67 ( 12) link_BETA1-2 : bond 0.00491 / 0.29 ( 4) link_BETA1-2 : angle 1.45201 / 0.69 ( 12) link_BETA1-4 : bond 0.00319 / 0.24 ( 8) link_BETA1-4 : angle 1.82693 / 1.08 ( 24) link_NAG-ASN : bond 0.00326 / 0.21 ( 16) link_NAG-ASN : angle 1.88629 / 1.22 ( 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 262 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 SER cc_start: 0.8514 (t) cc_final: 0.8150 (p) REVERT: A 330 ASP cc_start: 0.8397 (m-30) cc_final: 0.8149 (m-30) REVERT: A 359 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: A 417 CYS cc_start: 0.7983 (p) cc_final: 0.7347 (p) REVERT: B 359 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: B 417 CYS cc_start: 0.7998 (p) cc_final: 0.7364 (p) REVERT: C 308 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8325 (mmmm) REVERT: C 329 SER cc_start: 0.8507 (t) cc_final: 0.8140 (p) REVERT: C 330 ASP cc_start: 0.8403 (m-30) cc_final: 0.8046 (m-30) REVERT: C 359 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8344 (m-30) REVERT: C 417 CYS cc_start: 0.7997 (p) cc_final: 0.7365 (p) REVERT: D 329 SER cc_start: 0.8505 (t) cc_final: 0.8139 (p) REVERT: D 330 ASP cc_start: 0.8394 (m-30) cc_final: 0.8039 (m-30) REVERT: D 359 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: D 417 CYS cc_start: 0.8008 (p) cc_final: 0.7376 (p) outliers start: 33 outliers final: 29 residues processed: 242 average time/residue: 0.4178 time to fit residues: 121.4666 Evaluate side-chains 264 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS 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 H residue 107 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 CYS 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 E residue 107 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 314 SER 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 F residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 183 CYS 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 G residue 107 THR 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: 1.9990 chunk 174 optimal weight: 0.0870 chunk 143 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.104475 restraints weight = 19303.557| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.15 r_work: 0.2862 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1817 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= 0.172 Angle : 0.574 5.760 27500 Z= 0.307 Chirality : 0.046 0.198 3056 Planarity : 0.004 0.035 3440 Dihedral : 7.442 52.809 3428 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer: Outliers : 1.74 % Allowed : 10.46 % Favored : 87.80 % 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: -0.55 (0.17), residues: 2448 helix: -1.38 (1.00), residues: 24 sheet: 0.09 (0.17), residues: 956 loop : -0.63 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.017 0.002 TYR B 121 PHE 0.013 0.002 PHE C 354 TRP 0.016 0.001 TRP C 178 HIS 0.002 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (20132) covalent geometry : angle 0.56451 / 0.31 (27304) SS BOND : bond 0.00327 / 0.20 ( 44) SS BOND : angle 0.68427 / 0.50 ( 88) hydrogen bonds : bond 0.03970 / 2.80 ( 580) hydrogen bonds : angle 6.39273 / 4.54 ( 1608) link_ALPHA1-3 : bond 0.01149 / 0.69 ( 4) link_ALPHA1-3 : angle 1.57321 / 0.76 ( 12) link_ALPHA1-6 : bond 0.00636 / 0.38 ( 4) link_ALPHA1-6 : angle 1.31294 / 0.68 ( 12) link_BETA1-2 : bond 0.00478 / 0.29 ( 4) link_BETA1-2 : angle 1.42248 / 0.68 ( 12) link_BETA1-4 : bond 0.00334 / 0.25 ( 8) link_BETA1-4 : angle 1.83237 / 1.09 ( 24) link_NAG-ASN : bond 0.00319 / 0.21 ( 16) link_NAG-ASN : angle 1.88936 / 1.22 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6510.82 seconds wall clock time: 112 minutes 27.89 seconds (6747.89 seconds total)