Starting phenix.real_space_refine on Sun Aug 24 10:20:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvl_39606/08_2025/8yvl_39606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvl_39606/08_2025/8yvl_39606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yvl_39606/08_2025/8yvl_39606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvl_39606/08_2025/8yvl_39606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yvl_39606/08_2025/8yvl_39606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvl_39606/08_2025/8yvl_39606.map" } resolution = 2.47 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= -0.001 sd= 0.132 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 9 9.91 5 S 116 5.16 5 C 12012 2.51 5 N 3256 2.21 5 O 3768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19161 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2993 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "B" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2993 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "C" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2993 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "D" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2993 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "K" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' CA': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.23, per 1000 atoms: 0.22 Number of scatterers: 19161 At special positions: 0 Unit cell: (123.533, 123.533, 93.4554, 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 9 19.99 S 116 16.00 O 3768 8.00 N 3256 7.00 C 12012 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=2.04 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.11 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 233 " distance=2.84 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.08 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.07 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 233 " distance=2.88 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.08 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.07 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 233 " distance=2.88 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.08 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.07 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.04 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.04 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 233 " distance=2.85 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.08 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.07 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 88 " " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 235 " " NAG B 501 " - " ASN B 88 " " NAG B 502 " - " ASN B 146 " " NAG B 503 " - " ASN B 235 " " NAG C 501 " - " ASN C 88 " " NAG C 502 " - " ASN C 146 " " NAG C 503 " - " ASN C 235 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 146 " " NAG D 503 " - " ASN D 235 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 587.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 52 sheets defined 7.1% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.039A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.038A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.038A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'H' and resid 80 through 84 removed outlier: 4.038A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 32 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 25 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 25 through 32 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 25 through 32 Processing helix chain 'L' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.380A pdb=" N SER A 444 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.675A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 158 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.628A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA A 204 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 206 " --> pdb=" O THR A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.995A pdb=" N TYR A 253 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU A 268 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 255 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 266 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG A 257 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.579A pdb=" N GLU A 278 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG A 293 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 349 through 353 removed outlier: 4.682A pdb=" N PHE A 349 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 360 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY A 395 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.381A pdb=" N SER B 444 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.674A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 158 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 185 removed outlier: 3.628A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 204 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 215 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 206 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.996A pdb=" N TYR B 253 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU B 268 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 255 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER B 266 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG B 257 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.579A pdb=" N GLU B 278 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG B 293 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 349 through 353 removed outlier: 4.682A pdb=" N PHE B 349 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 360 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY B 395 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.381A pdb=" N SER C 444 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.674A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 158 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 185 removed outlier: 3.629A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA C 204 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 215 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 206 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 234 removed outlier: 6.996A pdb=" N TYR C 253 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU C 268 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 255 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER C 266 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 277 through 284 removed outlier: 5.579A pdb=" N GLU C 278 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG C 293 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 349 through 353 removed outlier: 4.681A pdb=" N PHE C 349 " --> pdb=" O GLY C 360 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY C 360 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLY C 395 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.380A pdb=" N SER D 444 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.675A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 158 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.629A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR D 215 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU D 206 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.995A pdb=" N TYR D 253 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU D 268 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE D 255 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D 266 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG D 257 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 277 through 284 removed outlier: 5.579A pdb=" N GLU D 278 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG D 293 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 349 through 353 removed outlier: 4.682A pdb=" N PHE D 349 " --> pdb=" O GLY D 360 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY D 360 " --> pdb=" O PHE D 349 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY D 395 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.724A pdb=" N LEU E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.725A pdb=" N LEU F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.724A pdb=" N LEU G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.725A pdb=" N LEU H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.395A pdb=" N GLY I 10 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET I 34 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.395A pdb=" N GLY I 10 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL I 112 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AE5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.395A pdb=" N GLY J 10 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET J 34 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.395A pdb=" N GLY J 10 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL J 112 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AE9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.396A pdb=" N GLY K 10 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET K 34 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.396A pdb=" N GLY K 10 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL K 112 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.395A pdb=" N GLY L 10 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET L 34 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.395A pdb=" N GLY L 10 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL L 112 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 101 through 102 744 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3163 1.30 - 1.44: 5688 1.44 - 1.57: 10629 1.57 - 1.71: 0 1.71 - 1.85: 148 Bond restraints: 19628 Sorted by residual: bond pdb=" C VAL A 234 " pdb=" N ASN A 235 " ideal model delta sigma weight residual 1.332 1.471 -0.138 1.38e-02 5.25e+03 1.01e+02 bond pdb=" C VAL L 5 " pdb=" O VAL L 5 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.09e-02 8.42e+03 3.36e+01 bond pdb=" C PHE B 239 " pdb=" O PHE B 239 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.28e-02 6.10e+03 3.17e+01 bond pdb=" C PHE D 239 " pdb=" O PHE D 239 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.28e-02 6.10e+03 3.12e+01 bond pdb=" C PHE A 239 " pdb=" O PHE A 239 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.28e-02 6.10e+03 3.06e+01 ... (remaining 19623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 25700 2.05 - 4.11: 731 4.11 - 6.16: 148 6.16 - 8.22: 39 8.22 - 10.27: 22 Bond angle restraints: 26640 Sorted by residual: angle pdb=" N PRO C 337 " pdb=" CA PRO C 337 " pdb=" CB PRO C 337 " ideal model delta sigma weight residual 103.27 96.16 7.11 9.00e-01 1.23e+00 6.24e+01 angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" CB PRO A 337 " ideal model delta sigma weight residual 103.27 96.21 7.06 9.00e-01 1.23e+00 6.16e+01 angle pdb=" N PRO D 337 " pdb=" CA PRO D 337 " pdb=" CB PRO D 337 " ideal model delta sigma weight residual 103.27 96.33 6.94 9.00e-01 1.23e+00 5.95e+01 angle pdb=" N PRO B 337 " pdb=" CA PRO B 337 " pdb=" CB PRO B 337 " ideal model delta sigma weight residual 103.27 96.39 6.88 9.00e-01 1.23e+00 5.85e+01 angle pdb=" CA ASN C 88 " pdb=" CB ASN C 88 " pdb=" CG ASN C 88 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.36e+01 ... (remaining 26635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10725 17.70 - 35.39: 853 35.39 - 53.08: 142 53.08 - 70.78: 20 70.78 - 88.47: 16 Dihedral angle restraints: 11756 sinusoidal: 4780 harmonic: 6976 Sorted by residual: dihedral pdb=" CA ASN D 325 " pdb=" C ASN D 325 " pdb=" N PRO D 326 " pdb=" CA PRO D 326 " ideal model delta harmonic sigma weight residual 0.00 -29.79 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ASN B 325 " pdb=" C ASN B 325 " pdb=" N PRO B 326 " pdb=" CA PRO B 326 " ideal model delta harmonic sigma weight residual 0.00 -29.76 29.76 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ASN A 325 " pdb=" C ASN A 325 " pdb=" N PRO A 326 " pdb=" CA PRO A 326 " ideal model delta harmonic sigma weight residual 0.00 -29.75 29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 11753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2744 0.124 - 0.248: 76 0.248 - 0.372: 35 0.372 - 0.496: 0 0.496 - 0.620: 1 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 235 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.62e+00 chirality pdb=" CB VAL D 338 " pdb=" CA VAL D 338 " pdb=" CG1 VAL D 338 " pdb=" CG2 VAL D 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CB VAL B 338 " pdb=" CA VAL B 338 " pdb=" CG1 VAL B 338 " pdb=" CG2 VAL B 338 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 2853 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.208 2.00e-02 2.50e+03 1.74e-01 3.77e+02 pdb=" C7 NAG D 501 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.287 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.208 2.00e-02 2.50e+03 1.74e-01 3.76e+02 pdb=" C7 NAG A 501 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.287 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " 0.199 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" C7 NAG B 501 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " 0.142 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " -0.275 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " -0.013 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 73 2.46 - 3.07: 12111 3.07 - 3.68: 29223 3.68 - 4.29: 48742 4.29 - 4.90: 80155 Nonbonded interactions: 170304 Sorted by model distance: nonbonded pdb=" O ASP A 294 " pdb="CA CA A 504 " model vdw 1.852 2.510 nonbonded pdb=" O ASN B 344 " pdb="CA CA B 504 " model vdw 1.884 2.510 nonbonded pdb=" O ASN D 344 " pdb="CA CA D 504 " model vdw 1.952 2.510 nonbonded pdb=" O ASN C 344 " pdb="CA CA C 504 " model vdw 2.089 2.510 nonbonded pdb=" O ASN A 344 " pdb="CA CA A 504 " model vdw 2.091 2.510 ... (remaining 170299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 83 through 505) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.700 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:5.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 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 : 0.014 0.847 19684 Z= 0.718 Angle : 1.056 34.851 26764 Z= 0.595 Chirality : 0.065 0.620 2856 Planarity : 0.009 0.174 3444 Dihedral : 13.073 88.475 7208 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.53 % Allowed : 0.10 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2444 helix: -0.70 (0.73), residues: 52 sheet: 0.40 (0.17), residues: 900 loop : -0.23 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 107 TYR 0.031 0.002 TYR F 96 PHE 0.014 0.002 PHE D 406 TRP 0.017 0.002 TRP C 455 HIS 0.011 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00700 (19628) covalent geometry : angle 0.90233 (26640) SS BOND : bond 0.25103 ( 44) SS BOND : angle 8.52713 ( 88) hydrogen bonds : bond 0.13006 ( 708) hydrogen bonds : angle 7.29346 ( 1824) link_NAG-ASN : bond 0.05085 ( 12) link_NAG-ASN : angle 6.98146 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 287 time to evaluate : 0.564 Fit side-chains REVERT: E 103 LYS cc_start: 0.8497 (tttm) cc_final: 0.8228 (tptt) REVERT: F 103 LYS cc_start: 0.8491 (tttm) cc_final: 0.8203 (tptt) REVERT: G 103 LYS cc_start: 0.8511 (tttm) cc_final: 0.8206 (tptt) REVERT: H 103 LYS cc_start: 0.8517 (tttm) cc_final: 0.8195 (tptt) outliers start: 11 outliers final: 2 residues processed: 293 average time/residue: 0.6031 time to fit residues: 196.6811 Evaluate side-chains 255 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain D residue 339 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.085599 restraints weight = 19816.800| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.08 r_work: 0.2759 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 19684 Z= 0.188 Angle : 0.704 14.616 26764 Z= 0.372 Chirality : 0.049 0.268 2856 Planarity : 0.005 0.052 3444 Dihedral : 6.035 39.894 2934 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.53 % Allowed : 5.41 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.06 (0.17), residues: 2444 helix: -0.46 (0.77), residues: 52 sheet: 0.45 (0.17), residues: 924 loop : -0.14 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 107 TYR 0.015 0.002 TYR H 96 PHE 0.015 0.002 PHE B 406 TRP 0.012 0.002 TRP C 179 HIS 0.008 0.002 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00434 (19628) covalent geometry : angle 0.65762 (26640) SS BOND : bond 0.01475 ( 44) SS BOND : angle 4.12390 ( 88) hydrogen bonds : bond 0.04317 ( 708) hydrogen bonds : angle 6.46572 ( 1824) link_NAG-ASN : bond 0.00883 ( 12) link_NAG-ASN : angle 2.55691 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 276 time to evaluate : 0.631 Fit side-chains REVERT: E 103 LYS cc_start: 0.8702 (tttm) cc_final: 0.8182 (tptt) REVERT: F 103 LYS cc_start: 0.8719 (tttm) cc_final: 0.8191 (tptt) REVERT: G 103 LYS cc_start: 0.8721 (tttm) cc_final: 0.8187 (tptt) REVERT: H 103 LYS cc_start: 0.8722 (tttm) cc_final: 0.8190 (tptt) outliers start: 11 outliers final: 9 residues processed: 280 average time/residue: 0.5747 time to fit residues: 180.1128 Evaluate side-chains 272 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 263 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN B 250 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN C 250 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN D 250 GLN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.086559 restraints weight = 19776.238| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.09 r_work: 0.2774 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 19684 Z= 0.153 Angle : 0.624 10.579 26764 Z= 0.332 Chirality : 0.047 0.162 2856 Planarity : 0.005 0.053 3444 Dihedral : 5.587 33.740 2932 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.39 % Allowed : 5.89 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.16 (0.17), residues: 2444 helix: -0.58 (0.75), residues: 52 sheet: 0.42 (0.17), residues: 924 loop : 0.01 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.009 0.001 TYR K 95 PHE 0.015 0.002 PHE B 406 TRP 0.011 0.001 TRP B 179 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00352 (19628) covalent geometry : angle 0.59610 (26640) SS BOND : bond 0.01037 ( 44) SS BOND : angle 2.99620 ( 88) hydrogen bonds : bond 0.03797 ( 708) hydrogen bonds : angle 6.19353 ( 1824) link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 2.09727 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 0.499 Fit side-chains REVERT: E 103 LYS cc_start: 0.8705 (tttm) cc_final: 0.8193 (tptt) REVERT: F 103 LYS cc_start: 0.8714 (tttm) cc_final: 0.8195 (tptt) REVERT: G 103 LYS cc_start: 0.8707 (tttm) cc_final: 0.8185 (tptt) REVERT: H 103 LYS cc_start: 0.8710 (tttm) cc_final: 0.8456 (tmmt) outliers start: 29 outliers final: 14 residues processed: 283 average time/residue: 0.5828 time to fit residues: 184.0479 Evaluate side-chains 277 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 263 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 176 optimal weight: 0.0010 chunk 54 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN B 250 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN C 250 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN D 250 GLN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.086659 restraints weight = 19642.125| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.08 r_work: 0.2777 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 19684 Z= 0.158 Angle : 0.626 9.699 26764 Z= 0.334 Chirality : 0.048 0.240 2856 Planarity : 0.005 0.052 3444 Dihedral : 5.654 44.408 2932 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.29 % Allowed : 6.66 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.14 (0.17), residues: 2444 helix: -0.80 (0.70), residues: 52 sheet: 0.37 (0.17), residues: 928 loop : 0.03 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.010 0.001 TYR K 95 PHE 0.015 0.002 PHE D 406 TRP 0.011 0.001 TRP A 179 HIS 0.008 0.002 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00361 (19628) covalent geometry : angle 0.60109 (26640) SS BOND : bond 0.01022 ( 44) SS BOND : angle 2.88079 ( 88) hydrogen bonds : bond 0.03739 ( 708) hydrogen bonds : angle 6.16828 ( 1824) link_NAG-ASN : bond 0.00390 ( 12) link_NAG-ASN : angle 2.02898 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 LYS cc_start: 0.8646 (tttm) cc_final: 0.8433 (tmmt) REVERT: F 103 LYS cc_start: 0.8646 (tttm) cc_final: 0.8439 (tmmt) REVERT: H 103 LYS cc_start: 0.8644 (tttm) cc_final: 0.8433 (tmmt) outliers start: 27 outliers final: 16 residues processed: 288 average time/residue: 0.5602 time to fit residues: 180.6981 Evaluate side-chains 285 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 128 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 181 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 313 GLN C 313 GLN D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.085222 restraints weight = 19819.393| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.08 r_work: 0.2763 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 19684 Z= 0.198 Angle : 0.663 10.207 26764 Z= 0.355 Chirality : 0.049 0.216 2856 Planarity : 0.005 0.055 3444 Dihedral : 5.807 41.714 2932 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.58 % Allowed : 6.94 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.04 (0.17), residues: 2444 helix: -0.84 (0.69), residues: 52 sheet: 0.30 (0.17), residues: 932 loop : -0.03 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 107 TYR 0.011 0.002 TYR J 95 PHE 0.017 0.002 PHE D 406 TRP 0.011 0.002 TRP A 457 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00457 (19628) covalent geometry : angle 0.63400 (26640) SS BOND : bond 0.01120 ( 44) SS BOND : angle 3.17000 ( 88) hydrogen bonds : bond 0.03967 ( 708) hydrogen bonds : angle 6.29567 ( 1824) link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 2.15828 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.593 Fit side-chains REVERT: E 103 LYS cc_start: 0.8621 (tttm) cc_final: 0.8414 (tmmt) REVERT: H 103 LYS cc_start: 0.8640 (tttm) cc_final: 0.8428 (tmmt) outliers start: 33 outliers final: 20 residues processed: 284 average time/residue: 0.5899 time to fit residues: 187.5507 Evaluate side-chains 290 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 176 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 313 GLN B 250 GLN B 313 GLN C 313 GLN D 250 GLN D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088278 restraints weight = 19775.091| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.07 r_work: 0.2812 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 19684 Z= 0.120 Angle : 0.580 7.727 26764 Z= 0.309 Chirality : 0.046 0.231 2856 Planarity : 0.004 0.051 3444 Dihedral : 5.475 45.656 2932 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.20 % Allowed : 7.71 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.16 (0.17), residues: 2444 helix: -0.56 (0.74), residues: 52 sheet: 0.40 (0.17), residues: 904 loop : 0.03 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 19 TYR 0.009 0.001 TYR J 95 PHE 0.014 0.002 PHE A 406 TRP 0.013 0.001 TRP A 179 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00270 (19628) covalent geometry : angle 0.55946 (26640) SS BOND : bond 0.00819 ( 44) SS BOND : angle 2.45171 ( 88) hydrogen bonds : bond 0.03399 ( 708) hydrogen bonds : angle 6.02134 ( 1824) link_NAG-ASN : bond 0.00332 ( 12) link_NAG-ASN : angle 1.91051 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 278 time to evaluate : 0.548 Fit side-chains REVERT: C 250 GLN cc_start: 0.8026 (tp40) cc_final: 0.7744 (tp40) REVERT: G 103 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8482 (ttmt) REVERT: H 103 LYS cc_start: 0.8623 (tttm) cc_final: 0.8418 (tmmt) outliers start: 25 outliers final: 15 residues processed: 286 average time/residue: 0.6032 time to fit residues: 192.2933 Evaluate side-chains 291 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 250 GLN B 313 GLN C 313 GLN D 250 GLN D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.086851 restraints weight = 19826.413| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.08 r_work: 0.2791 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19684 Z= 0.150 Angle : 0.601 7.945 26764 Z= 0.322 Chirality : 0.047 0.218 2856 Planarity : 0.005 0.049 3444 Dihedral : 5.575 44.225 2932 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.20 % Allowed : 8.52 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.14 (0.17), residues: 2444 helix: -0.54 (0.74), residues: 52 sheet: 0.39 (0.17), residues: 900 loop : 0.01 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.010 0.001 TYR K 95 PHE 0.015 0.002 PHE D 406 TRP 0.009 0.001 TRP C 179 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00343 (19628) covalent geometry : angle 0.58028 (26640) SS BOND : bond 0.00874 ( 44) SS BOND : angle 2.53551 ( 88) hydrogen bonds : bond 0.03600 ( 708) hydrogen bonds : angle 6.09790 ( 1824) link_NAG-ASN : bond 0.00276 ( 12) link_NAG-ASN : angle 1.94320 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 0.679 Fit side-chains REVERT: A 250 GLN cc_start: 0.7966 (tp40) cc_final: 0.7670 (tp40) REVERT: C 250 GLN cc_start: 0.8031 (tp40) cc_final: 0.7745 (tp40) REVERT: G 103 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8474 (ttmt) REVERT: H 103 LYS cc_start: 0.8609 (tttm) cc_final: 0.8408 (tmmt) outliers start: 25 outliers final: 18 residues processed: 288 average time/residue: 0.5969 time to fit residues: 191.8449 Evaluate side-chains 293 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 274 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 105 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 232 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 250 GLN B 313 GLN C 313 GLN D 250 GLN D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.085761 restraints weight = 19672.697| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.07 r_work: 0.2770 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19684 Z= 0.185 Angle : 0.637 8.730 26764 Z= 0.342 Chirality : 0.049 0.222 2856 Planarity : 0.005 0.050 3444 Dihedral : 5.784 44.653 2932 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.20 % Allowed : 8.91 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.04 (0.17), residues: 2444 helix: -0.60 (0.73), residues: 52 sheet: 0.30 (0.17), residues: 904 loop : -0.05 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 327 TYR 0.011 0.002 TYR K 95 PHE 0.017 0.002 PHE C 406 TRP 0.010 0.002 TRP A 97 HIS 0.003 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00423 (19628) covalent geometry : angle 0.61451 (26640) SS BOND : bond 0.00973 ( 44) SS BOND : angle 2.73907 ( 88) hydrogen bonds : bond 0.03869 ( 708) hydrogen bonds : angle 6.24950 ( 1824) link_NAG-ASN : bond 0.00264 ( 12) link_NAG-ASN : angle 2.08742 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 277 time to evaluate : 0.641 Fit side-chains REVERT: H 103 LYS cc_start: 0.8609 (tttm) cc_final: 0.8408 (tmmt) outliers start: 25 outliers final: 19 residues processed: 286 average time/residue: 0.6004 time to fit residues: 191.6516 Evaluate side-chains 286 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 267 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 158 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 313 GLN B 250 GLN B 313 GLN C 250 GLN C 313 GLN D 250 GLN D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.086596 restraints weight = 19680.936| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.08 r_work: 0.2784 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19684 Z= 0.154 Angle : 0.608 7.861 26764 Z= 0.326 Chirality : 0.048 0.204 2856 Planarity : 0.005 0.050 3444 Dihedral : 5.667 42.977 2932 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.10 % Allowed : 9.00 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.07 (0.17), residues: 2444 helix: -0.49 (0.75), residues: 52 sheet: 0.36 (0.17), residues: 900 loop : -0.05 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 38 TYR 0.011 0.001 TYR K 95 PHE 0.016 0.002 PHE C 406 TRP 0.012 0.002 TRP A 179 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00349 (19628) covalent geometry : angle 0.58766 (26640) SS BOND : bond 0.00861 ( 44) SS BOND : angle 2.50486 ( 88) hydrogen bonds : bond 0.03648 ( 708) hydrogen bonds : angle 6.15339 ( 1824) link_NAG-ASN : bond 0.00271 ( 12) link_NAG-ASN : angle 1.99366 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 276 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8458 (ttmt) REVERT: H 103 LYS cc_start: 0.8591 (tttm) cc_final: 0.8385 (tmmt) outliers start: 23 outliers final: 20 residues processed: 286 average time/residue: 0.5802 time to fit residues: 185.5121 Evaluate side-chains 290 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 196 optimal weight: 0.0040 chunk 181 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 169 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 313 GLN C 250 GLN C 313 GLN D 313 GLN E 43 GLN F 43 GLN G 43 GLN H 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.087922 restraints weight = 19712.088| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.07 r_work: 0.2803 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19684 Z= 0.126 Angle : 0.583 7.224 26764 Z= 0.312 Chirality : 0.046 0.191 2856 Planarity : 0.004 0.049 3444 Dihedral : 5.500 41.080 2932 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.15 % Allowed : 9.00 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.10 (0.17), residues: 2444 helix: -0.30 (0.78), residues: 52 sheet: 0.38 (0.17), residues: 900 loop : -0.04 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.010 0.001 TYR K 95 PHE 0.015 0.002 PHE D 406 TRP 0.012 0.001 TRP A 179 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00285 (19628) covalent geometry : angle 0.56415 (26640) SS BOND : bond 0.00736 ( 44) SS BOND : angle 2.39114 ( 88) hydrogen bonds : bond 0.03442 ( 708) hydrogen bonds : angle 6.03905 ( 1824) link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 1.89991 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.720 Fit side-chains REVERT: A 250 GLN cc_start: 0.7970 (tp40) cc_final: 0.7694 (tp40) REVERT: C 250 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7723 (tp40) REVERT: G 103 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8468 (ttmt) outliers start: 24 outliers final: 19 residues processed: 280 average time/residue: 0.5661 time to fit residues: 177.9046 Evaluate side-chains 291 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 114 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 313 GLN C 250 GLN C 313 GLN D 313 GLN E 43 GLN F 43 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.087833 restraints weight = 19835.208| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.08 r_work: 0.2802 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 19684 Z= 0.192 Angle : 0.768 59.144 26764 Z= 0.437 Chirality : 0.047 0.187 2856 Planarity : 0.005 0.049 3444 Dihedral : 5.506 41.017 2932 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 1.05 % Allowed : 9.29 % Favored : 89.66 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: 0.10 (0.17), residues: 2444 helix: -0.29 (0.78), residues: 52 sheet: 0.38 (0.17), residues: 900 loop : -0.04 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.010 0.001 TYR K 95 PHE 0.014 0.002 PHE D 406 TRP 0.011 0.002 TRP A 179 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00409 (19628) covalent geometry : angle 0.75132 (26640) SS BOND : bond 0.00758 ( 44) SS BOND : angle 2.65981 ( 88) hydrogen bonds : bond 0.03458 ( 708) hydrogen bonds : angle 6.03869 ( 1824) link_NAG-ASN : bond 0.00266 ( 12) link_NAG-ASN : angle 1.89312 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5724.02 seconds wall clock time: 98 minutes 26.95 seconds (5906.95 seconds total)