Starting phenix.real_space_refine on Sat Jul 4 06:47:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvl_39606/07_2026/8yvl_39606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvl_39606/07_2026/8yvl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yvl_39606/07_2026/8yvl_39606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvl_39606/07_2026/8yvl_39606.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvl_39606/07_2026/8yvl_39606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvl_39606/07_2026/8yvl_39606.cif" } 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-dev-6108/lib/python3.11/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, 42 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 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, 42 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.32, per 1000 atoms: 0.23 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: 1.63 Conformation dependent library (CDL) restraints added in 954.2 milliseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.71 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: 4.64 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 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 3.250 nonbonded pdb=" O ASN B 344 " pdb="CA CA B 504 " model vdw 1.884 3.250 nonbonded pdb=" O ASN D 344 " pdb="CA CA D 504 " model vdw 1.952 3.250 nonbonded pdb=" O ASN C 344 " pdb="CA CA C 504 " model vdw 2.089 3.250 nonbonded pdb=" O ASN A 344 " pdb="CA CA A 504 " model vdw 2.091 3.250 ... (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: 2.910 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.590 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 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 are 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/Z covalent geometry : bond 0.00700 / 0.40 (19628) covalent geometry : angle 0.90233 / 0.54 (26640) SS BOND : bond 0.25103 / 13.02 ( 44) SS BOND : angle 8.52713 / 5.04 ( 88) hydrogen bonds : bond 0.13006 / 8.59 ( 708) hydrogen bonds : angle 7.29346 / 4.98 ( 1824) link_NAG-ASN : bond 0.05085 / 2.00 ( 12) link_NAG-ASN : angle 6.98146 / 4.57 ( 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 : 0.712 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: 0.8202 (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: 0.6123 time to fit residues: 200.2573 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 : 0.504 ------------------------------------------------------------------------------- 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... ** 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 = 0.3175 r_free = 0.3175 target = 0.108024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.085948 restraints weight = 19879.105| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.09 r_work: 0.2780 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 19684 Z= 0.191 Angle : 0.706 14.436 26764 Z= 0.374 Chirality : 0.049 0.267 2856 Planarity : 0.005 0.052 3444 Dihedral : 6.037 39.629 2934 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 are not related in a simple way. whole: 0.03 (0.16), residues: 2444 helix: -0.43 (0.78), residues: 52 sheet: 0.41 (0.17), residues: 904 loop : -0.14 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 107 TYR 0.014 0.002 TYR H 96 PHE 0.015 0.002 PHE B 406 TRP 0.013 0.002 TRP D 179 HIS 0.007 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (19628) covalent geometry : angle 0.66031 / 0.36 (26640) SS BOND : bond 0.01353 / 0.79 ( 44) SS BOND : angle 4.10036 / 2.59 ( 88) hydrogen bonds : bond 0.04326 / 2.90 ( 708) hydrogen bonds : angle 6.47090 / 4.45 ( 1824) link_NAG-ASN : bond 0.00858 / 0.50 ( 12) link_NAG-ASN : angle 2.54605 / 1.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 278 time to evaluate : 0.765 Fit side-chains REVERT: E 103 LYS cc_start: 0.8705 (tttm) cc_final: 0.8205 (tptt) REVERT: F 103 LYS cc_start: 0.8717 (tttm) cc_final: 0.8206 (tptt) REVERT: G 103 LYS cc_start: 0.8722 (tttm) cc_final: 0.8208 (tptt) REVERT: H 103 LYS cc_start: 0.8713 (tttm) cc_final: 0.8198 (tptt) outliers start: 11 outliers final: 9 residues processed: 282 average time/residue: 0.5974 time to fit residues: 189.1837 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 : 0.730 ------------------------------------------------------------------------------- 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: 7.9990 chunk 203 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 91 optimal weight: 0.4980 chunk 162 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3210 r_free = 0.3210 target = 0.110406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088202 restraints weight = 19695.350| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.10 r_work: 0.2813 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 19684 Z= 0.137 Angle : 0.604 9.953 26764 Z= 0.322 Chirality : 0.047 0.167 2856 Planarity : 0.005 0.051 3444 Dihedral : 5.459 33.170 2932 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.20 % Allowed : 6.03 % Favored : 92.77 % 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 are not related in a simple way. whole: 0.16 (0.17), residues: 2444 helix: -0.49 (0.76), residues: 52 sheet: 0.41 (0.17), residues: 924 loop : 0.01 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.008 0.001 TYR K 95 PHE 0.014 0.002 PHE D 406 TRP 0.011 0.001 TRP B 179 HIS 0.006 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (19628) covalent geometry : angle 0.57952 / 0.31 (26640) SS BOND : bond 0.00953 / 0.52 ( 44) SS BOND : angle 2.78919 / 1.75 ( 88) hydrogen bonds : bond 0.03642 / 2.46 ( 708) hydrogen bonds : angle 6.10868 / 4.21 ( 1824) link_NAG-ASN : bond 0.00400 / 0.24 ( 12) link_NAG-ASN : angle 2.00238 / 1.33 ( 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: 25 poor density : 275 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: E 103 LYS cc_start: 0.8668 (tttm) cc_final: 0.8148 (tptt) REVERT: F 103 LYS cc_start: 0.8686 (tttm) cc_final: 0.8158 (tptt) REVERT: G 103 LYS cc_start: 0.8673 (tttm) cc_final: 0.8141 (tptt) REVERT: H 103 LYS cc_start: 0.8678 (tttm) cc_final: 0.8418 (tmmt) outliers start: 25 outliers final: 14 residues processed: 287 average time/residue: 0.5963 time to fit residues: 191.8147 Evaluate side-chains 279 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 265 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 6.9990 chunk 228 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 176 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3233 r_free = 0.3233 target = 0.112198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.090270 restraints weight = 19443.007| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.07 r_work: 0.2841 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19684 Z= 0.113 Angle : 0.573 7.972 26764 Z= 0.304 Chirality : 0.046 0.217 2856 Planarity : 0.004 0.050 3444 Dihedral : 5.306 42.332 2932 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.96 % Allowed : 7.33 % Favored : 91.71 % 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 are not related in a simple way. whole: 0.22 (0.17), residues: 2444 helix: -0.48 (0.75), residues: 52 sheet: 0.43 (0.17), residues: 924 loop : 0.07 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 19 TYR 0.008 0.001 TYR I 95 PHE 0.014 0.002 PHE D 406 TRP 0.009 0.001 TRP C 179 HIS 0.005 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (19628) covalent geometry : angle 0.55240 / 0.30 (26640) SS BOND : bond 0.00815 / 0.46 ( 44) SS BOND : angle 2.45357 / 1.57 ( 88) hydrogen bonds : bond 0.03332 / 2.25 ( 708) hydrogen bonds : angle 5.93206 / 4.08 ( 1824) link_NAG-ASN : bond 0.00375 / 0.22 ( 12) link_NAG-ASN : angle 1.80333 / 1.19 ( 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 304 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.8011 (tp40) cc_final: 0.7724 (tp40) REVERT: E 103 LYS cc_start: 0.8567 (tttm) cc_final: 0.8366 (tmmt) REVERT: F 103 LYS cc_start: 0.8604 (tttm) cc_final: 0.8397 (tmmt) REVERT: G 103 LYS cc_start: 0.8656 (tttm) cc_final: 0.8415 (tmmt) REVERT: H 103 LYS cc_start: 0.8653 (tttm) cc_final: 0.8412 (tmmt) outliers start: 20 outliers final: 12 residues processed: 289 average time/residue: 0.6168 time to fit residues: 199.8813 Evaluate side-chains 290 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 278 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 K residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 128 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 0.0970 chunk 218 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3186 r_free = 0.3186 target = 0.108740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.086564 restraints weight = 19628.951| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.08 r_work: 0.2784 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 19684 Z= 0.190 Angle : 0.646 9.572 26764 Z= 0.346 Chirality : 0.049 0.216 2856 Planarity : 0.005 0.051 3444 Dihedral : 5.713 41.101 2932 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.72 % Allowed : 7.04 % Favored : 91.24 % 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 are not related in a simple way. whole: 0.12 (0.17), residues: 2444 helix: -0.80 (0.70), residues: 52 sheet: 0.34 (0.17), residues: 932 loop : 0.04 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 19 TYR 0.011 0.002 TYR K 95 PHE 0.016 0.002 PHE D 406 TRP 0.011 0.002 TRP A 97 HIS 0.009 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (19628) covalent geometry : angle 0.62002 / 0.34 (26640) SS BOND : bond 0.01062 / 0.59 ( 44) SS BOND : angle 2.93195 / 1.86 ( 88) hydrogen bonds : bond 0.03894 / 2.62 ( 708) hydrogen bonds : angle 6.23150 / 4.29 ( 1824) link_NAG-ASN : bond 0.00319 / 0.19 ( 12) link_NAG-ASN : angle 2.07128 / 1.36 ( 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 312 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 103 LYS cc_start: 0.8602 (tttm) cc_final: 0.8399 (tmmt) REVERT: G 103 LYS cc_start: 0.8602 (tttm) cc_final: 0.8400 (tmmt) REVERT: H 103 LYS cc_start: 0.8621 (tttm) cc_final: 0.8408 (tmmt) outliers start: 36 outliers final: 20 residues processed: 291 average time/residue: 0.5963 time to fit residues: 195.7032 Evaluate side-chains 291 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 271 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 234 VAL 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 83 MET 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 27 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 118 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 0.0980 chunk 184 optimal weight: 3.9990 chunk 155 optimal weight: 0.0370 chunk 176 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3237 r_free = 0.3237 target = 0.112484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.090474 restraints weight = 19274.639| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.07 r_work: 0.2839 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19684 Z= 0.105 Angle : 0.554 7.552 26764 Z= 0.296 Chirality : 0.046 0.213 2856 Planarity : 0.004 0.049 3444 Dihedral : 5.292 44.351 2932 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.86 % Allowed : 8.00 % Favored : 91.14 % 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 are not related in a simple way. whole: 0.19 (0.17), residues: 2444 helix: -0.49 (0.76), residues: 52 sheet: 0.39 (0.17), residues: 928 loop : 0.06 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.008 0.001 TYR K 95 PHE 0.014 0.001 PHE D 406 TRP 0.012 0.001 TRP B 179 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (19628) covalent geometry : angle 0.53735 / 0.29 (26640) SS BOND : bond 0.00733 / 0.43 ( 44) SS BOND : angle 2.17304 / 1.36 ( 88) hydrogen bonds : bond 0.03255 / 2.21 ( 708) hydrogen bonds : angle 5.89278 / 4.06 ( 1824) link_NAG-ASN : bond 0.00312 / 0.18 ( 12) link_NAG-ASN : angle 1.80091 / 1.18 ( 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 300 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 282 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.7964 (tp40) cc_final: 0.7718 (tp40) REVERT: B 250 GLN cc_start: 0.7932 (tp40) cc_final: 0.7674 (tp40) REVERT: C 250 GLN cc_start: 0.7943 (tp40) cc_final: 0.7683 (tp40) REVERT: D 250 GLN cc_start: 0.8010 (tp40) cc_final: 0.7752 (tp40) outliers start: 18 outliers final: 16 residues processed: 289 average time/residue: 0.6431 time to fit residues: 208.1912 Evaluate side-chains 293 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 234 VAL 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 83 MET 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 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 239 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3183 r_free = 0.3183 target = 0.108548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.086341 restraints weight = 19755.618| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.08 r_work: 0.2781 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19684 Z= 0.205 Angle : 0.654 8.969 26764 Z= 0.351 Chirality : 0.050 0.290 2856 Planarity : 0.005 0.050 3444 Dihedral : 5.803 46.466 2932 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.34 % Allowed : 8.05 % Favored : 90.61 % 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 are not related in a simple way. whole: 0.10 (0.17), residues: 2444 helix: -0.68 (0.72), residues: 52 sheet: 0.35 (0.17), residues: 904 loop : 0.00 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 327 TYR 0.011 0.002 TYR I 101 PHE 0.016 0.002 PHE A 406 TRP 0.011 0.002 TRP A 97 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (19628) covalent geometry : angle 0.62825 / 0.34 (26640) SS BOND : bond 0.01087 / 0.63 ( 44) SS BOND : angle 2.99579 / 1.96 ( 88) hydrogen bonds : bond 0.03930 / 2.64 ( 708) hydrogen bonds : angle 6.22445 / 4.29 ( 1824) link_NAG-ASN : bond 0.00260 / 0.15 ( 12) link_NAG-ASN : angle 2.06427 / 1.35 ( 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 302 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.7993 (tp40) cc_final: 0.7677 (tp40) REVERT: B 250 GLN cc_start: 0.7994 (tp40) cc_final: 0.7667 (tp40) REVERT: C 250 GLN cc_start: 0.8004 (tp40) cc_final: 0.7672 (tp40) REVERT: D 250 GLN cc_start: 0.7991 (tp40) cc_final: 0.7661 (tp40) outliers start: 28 outliers final: 21 residues processed: 282 average time/residue: 0.6466 time to fit residues: 204.7944 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 : 0.757 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 234 VAL 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 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 27 LEU Chi-restraints excluded: chain I residue 83 MET 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 L residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 105 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 232 optimal weight: 0.0040 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3191 r_free = 0.3191 target = 0.109094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.086858 restraints weight = 19580.083| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.08 r_work: 0.2789 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 19684 Z= 0.175 Angle : 0.631 8.449 26764 Z= 0.338 Chirality : 0.049 0.239 2856 Planarity : 0.005 0.051 3444 Dihedral : 5.786 46.489 2932 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.29 % Allowed : 8.48 % Favored : 90.23 % 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 are not related in a simple way. whole: 0.05 (0.17), residues: 2444 helix: -0.70 (0.71), residues: 52 sheet: 0.36 (0.17), residues: 900 loop : -0.06 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 19 TYR 0.011 0.002 TYR J 95 PHE 0.016 0.002 PHE A 406 TRP 0.011 0.002 TRP A 179 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (19628) covalent geometry : angle 0.60820 / 0.33 (26640) SS BOND : bond 0.01003 / 0.57 ( 44) SS BOND : angle 2.71867 / 1.76 ( 88) hydrogen bonds : bond 0.03786 / 2.54 ( 708) hydrogen bonds : angle 6.20282 / 4.28 ( 1824) link_NAG-ASN : bond 0.00293 / 0.17 ( 12) link_NAG-ASN : angle 2.05685 / 1.34 ( 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 298 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.7976 (tp40) cc_final: 0.7656 (tp40) REVERT: B 250 GLN cc_start: 0.7981 (tp40) cc_final: 0.7624 (tp40) REVERT: C 250 GLN cc_start: 0.7991 (tp40) cc_final: 0.7630 (tp40) REVERT: D 250 GLN cc_start: 0.7975 (tp40) cc_final: 0.7614 (tp40) outliers start: 27 outliers final: 22 residues processed: 280 average time/residue: 0.6498 time to fit residues: 204.4603 Evaluate side-chains 290 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 234 VAL 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: 4.9990 chunk 35 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3206 r_free = 0.3206 target = 0.110187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.088030 restraints weight = 19553.262| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.08 r_work: 0.2807 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19684 Z= 0.140 Angle : 0.599 7.628 26764 Z= 0.320 Chirality : 0.047 0.218 2856 Planarity : 0.005 0.050 3444 Dihedral : 5.642 45.036 2932 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.96 % Allowed : 9.29 % Favored : 89.75 % 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 are not related in a simple way. whole: 0.09 (0.17), residues: 2444 helix: -0.50 (0.74), residues: 52 sheet: 0.39 (0.17), residues: 900 loop : -0.05 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 19 TYR 0.010 0.001 TYR J 95 PHE 0.015 0.002 PHE A 406 TRP 0.012 0.001 TRP C 179 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (19628) covalent geometry : angle 0.57902 / 0.31 (26640) SS BOND : bond 0.00901 / 0.52 ( 44) SS BOND : angle 2.47448 / 1.59 ( 88) hydrogen bonds : bond 0.03531 / 2.38 ( 708) hydrogen bonds : angle 6.08543 / 4.20 ( 1824) link_NAG-ASN : bond 0.00259 / 0.15 ( 12) link_NAG-ASN : angle 1.95298 / 1.28 ( 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 292 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.7968 (tp40) cc_final: 0.7660 (tp40) REVERT: B 250 GLN cc_start: 0.7972 (tp40) cc_final: 0.7654 (tp40) REVERT: C 250 GLN cc_start: 0.7982 (tp40) cc_final: 0.7661 (tp40) REVERT: D 250 GLN cc_start: 0.7970 (tp40) cc_final: 0.7651 (tp40) outliers start: 20 outliers final: 20 residues processed: 281 average time/residue: 0.6780 time to fit residues: 213.6144 Evaluate side-chains 284 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 234 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 196 optimal weight: 0.7980 chunk 181 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3223 r_free = 0.3223 target = 0.111491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.089395 restraints weight = 19481.716| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.07 r_work: 0.2833 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1408 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= 0.118 Angle : 0.571 7.751 26764 Z= 0.305 Chirality : 0.046 0.204 2856 Planarity : 0.004 0.049 3444 Dihedral : 5.467 43.208 2932 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.01 % Allowed : 9.15 % 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 are not related in a simple way. whole: 0.14 (0.17), residues: 2444 helix: -0.30 (0.78), residues: 52 sheet: 0.39 (0.17), residues: 900 loop : 0.00 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 19 TYR 0.009 0.001 TYR L 95 PHE 0.014 0.002 PHE B 406 TRP 0.010 0.001 TRP D 179 HIS 0.002 0.001 HIS D 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (19628) covalent geometry : angle 0.55372 / 0.30 (26640) SS BOND : bond 0.00777 / 0.45 ( 44) SS BOND : angle 2.24592 / 1.44 ( 88) hydrogen bonds : bond 0.03344 / 2.26 ( 708) hydrogen bonds : angle 5.95862 / 4.11 ( 1824) link_NAG-ASN : bond 0.00240 / 0.14 ( 12) link_NAG-ASN : angle 1.83856 / 1.20 ( 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 293 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLN cc_start: 0.8060 (tp40) cc_final: 0.7777 (tp40) REVERT: B 250 GLN cc_start: 0.8066 (tp40) cc_final: 0.7778 (tp40) REVERT: C 250 GLN cc_start: 0.8073 (tp40) cc_final: 0.7780 (tp40) REVERT: D 250 GLN cc_start: 0.8065 (tp40) cc_final: 0.7775 (tp40) REVERT: J 77 GLN cc_start: 0.8358 (mt0) cc_final: 0.8135 (mt0) outliers start: 21 outliers final: 20 residues processed: 281 average time/residue: 0.6833 time to fit residues: 215.2395 Evaluate side-chains 284 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 309 ASN Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 234 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 114 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 188 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN B 313 GLN C 313 GLN D 313 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.084902 restraints weight = 19784.115| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.08 r_work: 0.2760 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 19684 Z= 0.258 Angle : 0.712 9.810 26764 Z= 0.383 Chirality : 0.052 0.266 2856 Planarity : 0.006 0.052 3444 Dihedral : 6.110 46.323 2932 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.10 % Allowed : 9.20 % Favored : 89.70 % 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 are not related in a simple way. whole: -0.07 (0.17), residues: 2444 helix: -0.65 (0.72), residues: 52 sheet: 0.27 (0.17), residues: 904 loop : -0.14 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 62 TYR 0.012 0.002 TYR L 101 PHE 0.020 0.003 PHE B 406 TRP 0.014 0.002 TRP A 97 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.26 (19628) covalent geometry : angle 0.68348 / 0.37 (26640) SS BOND : bond 0.01258 / 0.73 ( 44) SS BOND : angle 3.28870 / 2.12 ( 88) hydrogen bonds : bond 0.04283 / 2.86 ( 708) hydrogen bonds : angle 6.41272 / 4.42 ( 1824) link_NAG-ASN : bond 0.00300 / 0.19 ( 12) link_NAG-ASN : angle 2.22401 / 1.44 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.00 seconds wall clock time: 109 minutes 40.99 seconds (6580.99 seconds total)