Starting phenix.real_space_refine on Mon May 26 04:27:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhp_60111/05_2025/8zhp_60111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhp_60111/05_2025/8zhp_60111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zhp_60111/05_2025/8zhp_60111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhp_60111/05_2025/8zhp_60111.map" model { file = "/net/cci-nas-00/data/ceres_data/8zhp_60111/05_2025/8zhp_60111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhp_60111/05_2025/8zhp_60111.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6132 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 14468 2.51 5 N 3802 2.21 5 O 4500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22856 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4932 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 31, 'TRANS': 590} Chain breaks: 2 Chain: "D" Number of atoms: 1663 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1694 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4932 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 31, 'TRANS': 590} Chain breaks: 2 Chain: "B" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1593 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 15, 'TRANS': 197} Chain breaks: 1 Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.96, per 1000 atoms: 0.61 Number of scatterers: 22856 At special positions: 0 Unit cell: (157.635, 199.485, 104.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 4500 8.00 N 3802 7.00 C 14468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 145 " - pdb=" SG CYS L 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 145 " - pdb=" SG CYS I 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 343 " " NAG C 701 " - " ASN C 343 " Time building additional restraints: 5.94 Conformation dependent library (CDL) restraints added in 3.2 seconds 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5518 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 70 sheets defined 4.2% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.703A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.816A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.836A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.522A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'E' and resid 186 through 191 removed outlier: 4.104A pdb=" N LYS E 191 " --> pdb=" O PRO E 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 Processing helix chain 'L' and resid 192 through 199 removed outlier: 3.512A pdb=" N HIS L 199 " --> pdb=" O GLN L 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.951A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.709A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.773A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.653A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'F' and resid 186 through 191 removed outlier: 4.082A pdb=" N LYS F 191 " --> pdb=" O PRO F 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 192 through 199 Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.840A pdb=" N LYS G 66 " --> pdb=" O PRO G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.897A pdb=" N THR G 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.139A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR C 279 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 67 removed outlier: 4.366A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.571A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 160 removed outlier: 6.523A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.910A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.654A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.051A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.006A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 466 through 467 Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.436A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.513A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.697A pdb=" N THR D 121 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 52 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 57 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.697A pdb=" N THR D 121 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 113 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN D 100 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE D 111 " --> pdb=" O ASN D 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 131 through 135 removed outlier: 3.587A pdb=" N SER D 191 " --> pdb=" O CYS D 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 153 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 189 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 155 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR D 187 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 163 through 165 removed outlier: 4.622A pdb=" N TYR D 205 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 220 " --> pdb=" O CYS D 207 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL D 209 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 218 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.530A pdb=" N VAL E 10 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 108 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 86 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.530A pdb=" N VAL E 10 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 108 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 86 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E 99 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 18 through 23 removed outlier: 3.628A pdb=" N VAL E 18 " --> pdb=" O ILE E 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 119 through 123 removed outlier: 4.181A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP E 143 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR E 177 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.281A pdb=" N TRP E 153 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N CYS E 198 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS E 209 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL E 200 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 207 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.697A pdb=" N THR L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.697A pdb=" N THR L 108 " --> pdb=" O VAL L 10 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.588A pdb=" N SER L 125 " --> pdb=" O SER L 148 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 148 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL L 144 " --> pdb=" O PHE L 129 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR L 183 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 129 removed outlier: 3.588A pdb=" N SER L 125 " --> pdb=" O SER L 148 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 148 " --> pdb=" O SER L 125 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL L 144 " --> pdb=" O PHE L 129 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR L 183 " --> pdb=" O ASP L 149 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 165 through 166 removed outlier: 4.134A pdb=" N TRP L 159 " --> pdb=" O VAL L 166 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR L 156 " --> pdb=" O THR L 207 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS L 204 " --> pdb=" O LYS L 215 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS L 215 " --> pdb=" O CYS L 204 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL L 206 " --> pdb=" O VAL L 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.614A pdb=" N SER H 72 " --> pdb=" O SER H 81 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.568A pdb=" N THR H 114 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP H 36 " --> pdb=" O CYS H 52 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N CYS H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.568A pdb=" N THR H 114 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR H 109 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.939A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 187 " --> pdb=" O CYS H 147 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N SER H 184 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA H 175 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER H 186 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.252A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.139A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 279 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 63 through 67 removed outlier: 4.282A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.572A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 152 through 160 removed outlier: 6.520A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 245 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.914A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.669A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.081A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.807A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AE8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.510A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.425A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.681A pdb=" N VAL B 20 " --> pdb=" O MET B 81 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B 81 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.730A pdb=" N THR B 121 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 52 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE B 57 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.730A pdb=" N THR B 121 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 113 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN B 100 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N PHE B 111 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.600A pdb=" N SER B 191 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 153 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 189 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 155 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR B 187 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 163 through 165 removed outlier: 4.626A pdb=" N TYR B 205 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 222 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 207 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS B 220 " --> pdb=" O CYS B 207 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 209 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 218 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 9 through 11 removed outlier: 3.503A pdb=" N TYR F 88 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 108 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA F 86 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP F 37 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 9 through 11 removed outlier: 3.503A pdb=" N TYR F 88 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 108 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA F 86 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY F 99 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AF9, first strand: chain 'F' and resid 119 through 123 removed outlier: 4.212A pdb=" N PHE F 123 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL F 138 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP F 143 " --> pdb=" O TYR F 177 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR F 177 " --> pdb=" O ASP F 143 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 159 through 160 removed outlier: 4.294A pdb=" N TRP F 153 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N CYS F 198 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS F 209 " --> pdb=" O CYS F 198 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL F 200 " --> pdb=" O VAL F 207 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 207 " --> pdb=" O VAL F 200 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.867A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN I 38 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 18 through 20 Processing sheet with id=AG5, first strand: chain 'I' and resid 67 through 68 Processing sheet with id=AG6, first strand: chain 'I' and resid 93 through 95 Processing sheet with id=AG7, first strand: chain 'I' and resid 125 through 129 removed outlier: 3.691A pdb=" N VAL I 144 " --> pdb=" O PHE I 129 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR I 183 " --> pdb=" O ASP I 149 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 125 through 129 removed outlier: 3.691A pdb=" N VAL I 144 " --> pdb=" O PHE I 129 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR I 183 " --> pdb=" O ASP I 149 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 165 through 166 removed outlier: 4.032A pdb=" N TRP I 159 " --> pdb=" O VAL I 166 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR I 156 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS I 215 " --> pdb=" O CYS I 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL I 206 " --> pdb=" O VAL I 213 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.560A pdb=" N THR G 114 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL G 116 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP G 36 " --> pdb=" O CYS G 52 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N CYS G 52 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TRP G 38 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.560A pdb=" N THR G 114 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL G 116 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR G 109 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 17 through 18 Processing sheet with id=AH5, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.801A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 145 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS G 147 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER G 187 " --> pdb=" O CYS G 147 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR G 183 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 127 through 131 removed outlier: 3.801A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 145 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS G 147 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER G 187 " --> pdb=" O CYS G 147 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR G 183 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.283A pdb=" N TYR G 201 " --> pdb=" O VAL G 218 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 1755 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: 9.85 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7286 1.34 - 1.47: 6036 1.47 - 1.59: 10009 1.59 - 1.72: 0 1.72 - 1.85: 97 Bond restraints: 23428 Sorted by residual: bond pdb=" N VAL F 101 " pdb=" CA VAL F 101 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 1.02e+01 bond pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.17e-02 7.31e+03 9.25e+00 bond pdb=" N VAL A 341 " pdb=" CA VAL A 341 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.89e+00 bond pdb=" N LYS A 529 " pdb=" CA LYS A 529 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.22e-02 6.72e+03 7.74e+00 bond pdb=" N ASN A 343 " pdb=" CA ASN A 343 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.10e-02 8.26e+03 7.58e+00 ... (remaining 23423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 31216 1.62 - 3.23: 637 3.23 - 4.85: 55 4.85 - 6.46: 20 6.46 - 8.08: 9 Bond angle restraints: 31937 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 113.43 109.16 4.27 1.09e+00 8.42e-01 1.53e+01 angle pdb=" CA ARG E 194 " pdb=" CB ARG E 194 " pdb=" CG ARG E 194 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ARG F 194 " pdb=" CB ARG F 194 " pdb=" CG ARG F 194 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" N ILE A 410 " pdb=" CA ILE A 410 " pdb=" C ILE A 410 " ideal model delta sigma weight residual 111.91 108.82 3.09 8.90e-01 1.26e+00 1.21e+01 angle pdb=" N VAL C 367 " pdb=" CA VAL C 367 " pdb=" C VAL C 367 " ideal model delta sigma weight residual 112.29 109.04 3.25 9.40e-01 1.13e+00 1.20e+01 ... (remaining 31932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12189 17.97 - 35.95: 1295 35.95 - 53.92: 356 53.92 - 71.90: 66 71.90 - 89.87: 31 Dihedral angle restraints: 13937 sinusoidal: 5287 harmonic: 8650 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -175.37 89.37 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 -179.14 -87.86 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 43.91 49.09 1 1.00e+01 1.00e-02 3.31e+01 ... (remaining 13934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2460 0.036 - 0.072: 715 0.072 - 0.108: 302 0.108 - 0.144: 112 0.144 - 0.180: 6 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CB ILE B 52 " pdb=" CA ILE B 52 " pdb=" CG1 ILE B 52 " pdb=" CG2 ILE B 52 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA VAL A 341 " pdb=" N VAL A 341 " pdb=" C VAL A 341 " pdb=" CB VAL A 341 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CG LEU A 441 " pdb=" CB LEU A 441 " pdb=" CD1 LEU A 441 " pdb=" CD2 LEU A 441 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 3592 not shown) Planarity restraints: 4107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 153 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO G 154 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 154 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 154 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.017 2.00e-02 2.50e+03 1.55e-02 4.81e+00 pdb=" CG TYR A 453 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 385 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C THR A 385 " -0.038 2.00e-02 2.50e+03 pdb=" O THR A 385 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 386 " 0.013 2.00e-02 2.50e+03 ... (remaining 4104 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3981 2.77 - 3.31: 19490 3.31 - 3.84: 38406 3.84 - 4.37: 41541 4.37 - 4.90: 73778 Nonbonded interactions: 177196 Sorted by model distance: nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.294 3.040 nonbonded pdb=" O THR G 70 " pdb=" OG1 THR G 70 " model vdw 2.298 3.040 ... (remaining 177191 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' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 2 through 206 or resid 208 through 228)) selection = (chain 'D' and (resid 2 through 206 or resid 208 through 228)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 54.790 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23464 Z= 0.153 Angle : 0.543 8.077 32012 Z= 0.307 Chirality : 0.044 0.180 3595 Planarity : 0.004 0.055 4105 Dihedral : 16.340 89.872 8315 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.47 % Allowed : 24.44 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2967 helix: -2.76 (0.44), residues: 86 sheet: 0.71 (0.17), residues: 973 loop : -0.78 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 102 HIS 0.001 0.000 HIS I 208 PHE 0.016 0.001 PHE C 338 TYR 0.039 0.001 TYR A 453 ARG 0.005 0.000 ARG F 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 2) link_NAG-ASN : angle 1.77536 ( 6) hydrogen bonds : bond 0.28635 ( 666) hydrogen bonds : angle 10.41909 ( 1755) SS BOND : bond 0.00361 ( 34) SS BOND : angle 0.83446 ( 69) covalent geometry : bond 0.00252 (23428) covalent geometry : angle 0.54167 (31937) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.2049 (ptm) cc_final: -0.2667 (ptp) REVERT: C 386 LYS cc_start: 0.5748 (mmmt) cc_final: 0.5131 (ptmt) REVERT: C 458 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7928 (mttm) REVERT: C 473 TYR cc_start: 0.3012 (t80) cc_final: 0.2690 (t80) REVERT: D 3 GLN cc_start: 0.6603 (tp-100) cc_final: 0.6324 (tm-30) REVERT: D 102 TYR cc_start: 0.5591 (p90) cc_final: 0.4630 (p90) REVERT: D 182 GLN cc_start: 0.5076 (mt0) cc_final: 0.4672 (mt0) REVERT: D 221 LYS cc_start: 0.6953 (mmtm) cc_final: 0.6420 (ttpt) REVERT: L 151 TYR cc_start: 0.6696 (t80) cc_final: 0.6378 (t80) REVERT: B 221 LYS cc_start: 0.7028 (mmtm) cc_final: 0.6331 (ttpt) REVERT: G 3 GLN cc_start: 0.7725 (pp30) cc_final: 0.7196 (pt0) outliers start: 12 outliers final: 1 residues processed: 183 average time/residue: 0.3509 time to fit residues: 99.8836 Evaluate side-chains 91 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 3.9990 chunk 224 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 76 optimal weight: 8.9990 chunk 151 optimal weight: 0.0270 chunk 119 optimal weight: 5.9990 chunk 232 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 172 optimal weight: 40.0000 chunk 268 optimal weight: 20.0000 overall best weight: 3.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 641 ASN C 658 ASN E 6 GLN E 133 ASN E 202 HIS L 39 GLN H 41 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 641 ASN A 658 ASN F 133 ASN F 202 HIS I 39 GLN G 41 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.226515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.204690 restraints weight = 356121.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.205581 restraints weight = 183534.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.204662 restraints weight = 161043.038| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4485 r_free = 0.4485 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4485 r_free = 0.4485 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 23464 Z= 0.288 Angle : 0.690 11.639 32012 Z= 0.370 Chirality : 0.049 0.215 3595 Planarity : 0.005 0.047 4105 Dihedral : 4.560 45.430 3261 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.63 % Allowed : 23.82 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2967 helix: -2.17 (0.53), residues: 74 sheet: 0.41 (0.17), residues: 1019 loop : -0.75 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 47 HIS 0.007 0.001 HIS I 199 PHE 0.036 0.002 PHE C 338 TYR 0.030 0.003 TYR L 37 ARG 0.014 0.001 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 1.39499 ( 6) hydrogen bonds : bond 0.05116 ( 666) hydrogen bonds : angle 7.55549 ( 1755) SS BOND : bond 0.00448 ( 34) SS BOND : angle 1.36170 ( 69) covalent geometry : bond 0.00667 (23428) covalent geometry : angle 0.68775 (31937) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 88 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 VAL cc_start: 0.6329 (OUTLIER) cc_final: 0.5268 (m) REVERT: E 92 SER cc_start: 0.5884 (OUTLIER) cc_final: 0.5670 (m) REVERT: E 207 VAL cc_start: -0.3588 (OUTLIER) cc_final: -0.3950 (t) REVERT: L 95 ASP cc_start: 0.7007 (t0) cc_final: 0.6695 (t0) REVERT: L 164 SER cc_start: 0.6256 (p) cc_final: 0.5881 (t) REVERT: H 49 TRP cc_start: 0.8123 (t60) cc_final: 0.7889 (t60) REVERT: A 450 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.6360 (m-40) REVERT: B 113 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7262 (mm) REVERT: F 207 VAL cc_start: -0.3793 (OUTLIER) cc_final: -0.4173 (t) REVERT: I 164 SER cc_start: 0.6154 (p) cc_final: 0.5793 (t) outliers start: 93 outliers final: 59 residues processed: 168 average time/residue: 0.2885 time to fit residues: 80.7551 Evaluate side-chains 127 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 62 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.0270 chunk 83 optimal weight: 40.0000 chunk 223 optimal weight: 20.0000 chunk 183 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 269 optimal weight: 30.0000 chunk 290 optimal weight: 0.0070 chunk 239 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN F 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.228937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.207097 restraints weight = 359065.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.207615 restraints weight = 185616.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.207128 restraints weight = 166670.280| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4511 r_free = 0.4511 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4511 r_free = 0.4511 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23464 Z= 0.155 Angle : 0.538 6.804 32012 Z= 0.286 Chirality : 0.045 0.186 3595 Planarity : 0.004 0.048 4105 Dihedral : 4.167 40.443 3260 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.12 % Allowed : 23.94 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2967 helix: -2.42 (0.49), residues: 86 sheet: 0.39 (0.16), residues: 1055 loop : -0.78 (0.15), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 47 HIS 0.005 0.001 HIS I 199 PHE 0.017 0.001 PHE H 80 TYR 0.022 0.001 TYR L 151 ARG 0.003 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 2) link_NAG-ASN : angle 1.00749 ( 6) hydrogen bonds : bond 0.03955 ( 666) hydrogen bonds : angle 6.62187 ( 1755) SS BOND : bond 0.00359 ( 34) SS BOND : angle 0.87798 ( 69) covalent geometry : bond 0.00359 (23428) covalent geometry : angle 0.53678 (31937) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 71 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: -0.0158 (OUTLIER) cc_final: -0.0486 (mt) REVERT: C 177 MET cc_start: -0.1796 (ptp) cc_final: -0.2394 (pmm) REVERT: C 355 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7337 (ptm160) REVERT: E 207 VAL cc_start: -0.3725 (OUTLIER) cc_final: -0.4106 (t) REVERT: L 95 ASP cc_start: 0.6972 (t0) cc_final: 0.6716 (t0) REVERT: L 164 SER cc_start: 0.6172 (p) cc_final: 0.5808 (t) REVERT: H 49 TRP cc_start: 0.7999 (t60) cc_final: 0.7586 (t60) REVERT: H 115 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7060 (mt) REVERT: A 355 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7421 (ptm-80) REVERT: A 450 ASN cc_start: 0.6239 (OUTLIER) cc_final: 0.5752 (m-40) REVERT: F 207 VAL cc_start: -0.3799 (OUTLIER) cc_final: -0.4169 (t) REVERT: I 164 SER cc_start: 0.6045 (p) cc_final: 0.5687 (t) outliers start: 80 outliers final: 53 residues processed: 140 average time/residue: 0.3091 time to fit residues: 72.4152 Evaluate side-chains 121 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 61 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 270 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN B 62 GLN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.227174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.203941 restraints weight = 354158.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.204435 restraints weight = 178620.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.203423 restraints weight = 159831.997| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4435 r_free = 0.4435 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4435 r_free = 0.4435 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23464 Z= 0.183 Angle : 0.558 8.063 32012 Z= 0.296 Chirality : 0.045 0.197 3595 Planarity : 0.004 0.047 4105 Dihedral : 4.307 42.842 3260 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.78 % Allowed : 23.12 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2967 helix: -1.97 (0.55), residues: 74 sheet: 0.21 (0.16), residues: 1071 loop : -0.81 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 47 HIS 0.003 0.001 HIS I 199 PHE 0.023 0.001 PHE C 338 TYR 0.022 0.002 TYR A 495 ARG 0.004 0.000 ARG H 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 2) link_NAG-ASN : angle 1.06834 ( 6) hydrogen bonds : bond 0.03614 ( 666) hydrogen bonds : angle 6.33127 ( 1755) SS BOND : bond 0.00442 ( 34) SS BOND : angle 0.99814 ( 69) covalent geometry : bond 0.00427 (23428) covalent geometry : angle 0.55665 (31937) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 66 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: -0.0138 (OUTLIER) cc_final: -0.0506 (mt) REVERT: C 177 MET cc_start: -0.1445 (ptp) cc_final: -0.1866 (pmm) REVERT: C 355 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7754 (ptm160) REVERT: H 49 TRP cc_start: 0.7960 (t60) cc_final: 0.7558 (t60) REVERT: H 115 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7057 (mt) REVERT: A 177 MET cc_start: -0.2785 (OUTLIER) cc_final: -0.4222 (mmm) REVERT: A 355 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7444 (ptm160) REVERT: A 450 ASN cc_start: 0.6339 (OUTLIER) cc_final: 0.5810 (m-40) REVERT: B 34 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7113 (tp) REVERT: F 207 VAL cc_start: -0.3887 (OUTLIER) cc_final: -0.4294 (t) REVERT: I 199 HIS cc_start: -0.0713 (OUTLIER) cc_final: -0.0927 (m-70) outliers start: 97 outliers final: 69 residues processed: 153 average time/residue: 0.3111 time to fit residues: 79.0510 Evaluate side-chains 135 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 57 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 199 HIS Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 55 TYR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 10.0000 chunk 162 optimal weight: 50.0000 chunk 4 optimal weight: 0.0370 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 146 optimal weight: 30.0000 chunk 256 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN E 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.224599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.202966 restraints weight = 358574.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.203482 restraints weight = 184628.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.202798 restraints weight = 166753.079| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4468 r_free = 0.4468 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4468 r_free = 0.4468 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23464 Z= 0.211 Angle : 0.587 8.978 32012 Z= 0.312 Chirality : 0.046 0.198 3595 Planarity : 0.004 0.048 4105 Dihedral : 4.608 43.811 3260 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.60 % Allowed : 23.24 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2967 helix: -1.95 (0.56), residues: 74 sheet: 0.09 (0.17), residues: 1029 loop : -0.89 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 47 HIS 0.004 0.001 HIS E 193 PHE 0.041 0.002 PHE C 338 TYR 0.030 0.002 TYR A 495 ARG 0.005 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 2) link_NAG-ASN : angle 0.93321 ( 6) hydrogen bonds : bond 0.03639 ( 666) hydrogen bonds : angle 6.20420 ( 1755) SS BOND : bond 0.00408 ( 34) SS BOND : angle 1.08597 ( 69) covalent geometry : bond 0.00499 (23428) covalent geometry : angle 0.58509 (31937) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 63 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 ILE cc_start: -0.0094 (OUTLIER) cc_final: -0.0306 (mt) REVERT: C 177 MET cc_start: -0.1082 (ptp) cc_final: -0.1294 (pmm) REVERT: C 355 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7703 (ptm160) REVERT: E 96 SER cc_start: 0.6455 (OUTLIER) cc_final: 0.5816 (m) REVERT: H 49 TRP cc_start: 0.7851 (t60) cc_final: 0.7601 (t60) REVERT: A 355 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7802 (ptm160) REVERT: A 450 ASN cc_start: 0.7138 (OUTLIER) cc_final: 0.6705 (m-40) REVERT: F 207 VAL cc_start: -0.3896 (OUTLIER) cc_final: -0.4282 (t) outliers start: 118 outliers final: 86 residues processed: 168 average time/residue: 0.3161 time to fit residues: 86.6725 Evaluate side-chains 148 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 56 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 55 TYR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.0070 chunk 257 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 286 optimal weight: 40.0000 chunk 237 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 150 optimal weight: 20.0000 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN F 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.229538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.209740 restraints weight = 357841.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.210059 restraints weight = 186842.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.209479 restraints weight = 165915.577| |-----------------------------------------------------------------------------| r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4572 r_free = 0.4572 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4572 r_free = 0.4572 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23464 Z= 0.098 Angle : 0.501 7.543 32012 Z= 0.261 Chirality : 0.044 0.308 3595 Planarity : 0.004 0.047 4105 Dihedral : 4.080 39.045 3260 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.85 % Allowed : 25.19 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2967 helix: -2.21 (0.50), residues: 86 sheet: 0.32 (0.17), residues: 1031 loop : -0.74 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.003 0.000 HIS I 199 PHE 0.017 0.001 PHE A 377 TYR 0.020 0.001 TYR D 95 ARG 0.005 0.000 ARG F 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 2) link_NAG-ASN : angle 1.10326 ( 6) hydrogen bonds : bond 0.02815 ( 666) hydrogen bonds : angle 5.75142 ( 1755) SS BOND : bond 0.00369 ( 34) SS BOND : angle 0.74015 ( 69) covalent geometry : bond 0.00223 (23428) covalent geometry : angle 0.50019 (31937) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 80 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 355 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7398 (ptm160) REVERT: E 96 SER cc_start: 0.5941 (OUTLIER) cc_final: 0.5394 (m) REVERT: L 100 VAL cc_start: 0.7733 (m) cc_final: 0.7517 (m) REVERT: L 164 SER cc_start: 0.6015 (p) cc_final: 0.5603 (t) REVERT: H 204 ASN cc_start: 0.2770 (OUTLIER) cc_final: 0.1672 (t0) REVERT: A 355 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7408 (ptm160) REVERT: A 450 ASN cc_start: 0.6677 (OUTLIER) cc_final: 0.6268 (m-40) REVERT: F 207 VAL cc_start: -0.3915 (OUTLIER) cc_final: -0.4283 (t) REVERT: I 164 SER cc_start: 0.5860 (p) cc_final: 0.5562 (t) outliers start: 73 outliers final: 54 residues processed: 144 average time/residue: 0.3124 time to fit residues: 74.8167 Evaluate side-chains 130 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 70 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 52 CYS Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 55 TYR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 163 optimal weight: 30.0000 chunk 209 optimal weight: 40.0000 chunk 162 optimal weight: 8.9990 chunk 241 optimal weight: 0.9990 chunk 159 optimal weight: 40.0000 chunk 285 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN F 6 GLN F 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.224369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.202940 restraints weight = 356140.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.203377 restraints weight = 185481.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.202597 restraints weight = 166220.962| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4473 r_free = 0.4473 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4473 r_free = 0.4473 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23464 Z= 0.233 Angle : 0.599 9.306 32012 Z= 0.319 Chirality : 0.047 0.308 3595 Planarity : 0.004 0.047 4105 Dihedral : 4.561 44.847 3260 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.82 % Allowed : 24.56 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2967 helix: -1.92 (0.55), residues: 74 sheet: 0.03 (0.16), residues: 1048 loop : -0.89 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 47 HIS 0.005 0.001 HIS L 8 PHE 0.034 0.002 PHE C 338 TYR 0.027 0.002 TYR A 495 ARG 0.007 0.001 ARG F 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 2) link_NAG-ASN : angle 0.98620 ( 6) hydrogen bonds : bond 0.03540 ( 666) hydrogen bonds : angle 6.02213 ( 1755) SS BOND : bond 0.00464 ( 34) SS BOND : angle 1.25565 ( 69) covalent geometry : bond 0.00550 (23428) covalent geometry : angle 0.59695 (31937) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 62 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.1723 (pmm) cc_final: -0.2270 (pmm) REVERT: C 355 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7740 (ptm160) REVERT: H 204 ASN cc_start: 0.2890 (OUTLIER) cc_final: 0.1365 (m-40) REVERT: A 355 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7793 (ptm160) REVERT: A 405 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: A 450 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6752 (m-40) REVERT: A 466 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7643 (ptp-170) REVERT: F 207 VAL cc_start: -0.4028 (OUTLIER) cc_final: -0.4404 (t) outliers start: 98 outliers final: 72 residues processed: 148 average time/residue: 0.3238 time to fit residues: 78.9214 Evaluate side-chains 137 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 58 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 55 TYR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 224 optimal weight: 30.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN A 506 GLN F 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.226310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.206083 restraints weight = 354367.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.206668 restraints weight = 189056.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.205694 restraints weight = 167833.014| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4534 r_free = 0.4534 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4534 r_free = 0.4534 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23464 Z= 0.145 Angle : 0.537 10.303 32012 Z= 0.281 Chirality : 0.045 0.266 3595 Planarity : 0.004 0.047 4105 Dihedral : 4.316 41.701 3260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.31 % Allowed : 25.26 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2967 helix: -2.30 (0.50), residues: 86 sheet: 0.09 (0.17), residues: 1028 loop : -0.85 (0.15), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 49 HIS 0.002 0.000 HIS I 199 PHE 0.019 0.001 PHE A 565 TYR 0.022 0.001 TYR D 95 ARG 0.007 0.000 ARG E 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 2) link_NAG-ASN : angle 0.97479 ( 6) hydrogen bonds : bond 0.02983 ( 666) hydrogen bonds : angle 5.75604 ( 1755) SS BOND : bond 0.00404 ( 34) SS BOND : angle 0.97847 ( 69) covalent geometry : bond 0.00343 (23428) covalent geometry : angle 0.53593 (31937) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 66 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.1644 (pmm) cc_final: -0.2221 (pmm) REVERT: C 355 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7471 (ptm160) REVERT: C 590 CYS cc_start: 0.1086 (OUTLIER) cc_final: 0.0678 (m) REVERT: H 204 ASN cc_start: 0.2685 (OUTLIER) cc_final: 0.1738 (t0) REVERT: A 355 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7459 (ptm160) REVERT: A 450 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6826 (m-40) REVERT: A 466 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7463 (ttm110) REVERT: F 207 VAL cc_start: -0.3865 (OUTLIER) cc_final: -0.4235 (t) outliers start: 85 outliers final: 67 residues processed: 140 average time/residue: 0.3440 time to fit residues: 78.9474 Evaluate side-chains 139 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 65 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 201 TYR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 52 CYS Chi-restraints excluded: chain G residue 55 TYR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 265 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 208 optimal weight: 40.0000 chunk 81 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 251 optimal weight: 30.0000 chunk 264 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN L 195 GLN A 544 ASN A 580 GLN F 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.219326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.195106 restraints weight = 358195.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.195804 restraints weight = 183261.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.194621 restraints weight = 166365.852| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.130 23464 Z= 0.410 Angle : 0.799 14.043 32012 Z= 0.430 Chirality : 0.053 0.317 3595 Planarity : 0.006 0.060 4105 Dihedral : 5.552 47.613 3260 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.37 % Allowed : 24.21 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 2967 helix: -2.31 (0.53), residues: 74 sheet: -0.53 (0.17), residues: 994 loop : -1.18 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 47 HIS 0.010 0.001 HIS L 8 PHE 0.033 0.003 PHE C 338 TYR 0.044 0.003 TYR A 495 ARG 0.009 0.001 ARG D 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 2) link_NAG-ASN : angle 0.96159 ( 6) hydrogen bonds : bond 0.04958 ( 666) hydrogen bonds : angle 6.68646 ( 1755) SS BOND : bond 0.00682 ( 34) SS BOND : angle 1.88371 ( 69) covalent geometry : bond 0.00969 (23428) covalent geometry : angle 0.79487 (31937) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 61 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.1637 (pmm) cc_final: -0.2188 (pmm) REVERT: C 355 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7880 (ptm160) REVERT: C 590 CYS cc_start: 0.0936 (OUTLIER) cc_final: 0.0579 (m) REVERT: H 115 LEU cc_start: 0.6971 (mt) cc_final: 0.6731 (mt) REVERT: H 155 GLU cc_start: 0.4650 (mm-30) cc_final: 0.4124 (mm-30) REVERT: A 177 MET cc_start: -0.2900 (OUTLIER) cc_final: -0.4217 (mmm) REVERT: A 355 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8027 (ptm160) REVERT: A 405 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: A 450 ASN cc_start: 0.6878 (OUTLIER) cc_final: 0.6367 (m-40) REVERT: A 466 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7583 (ttm110) REVERT: F 4 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6218 (mt) REVERT: F 207 VAL cc_start: -0.4230 (OUTLIER) cc_final: -0.4448 (t) outliers start: 112 outliers final: 93 residues processed: 160 average time/residue: 0.3085 time to fit residues: 80.7193 Evaluate side-chains 157 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 55 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 201 TYR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 55 TYR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 9.9990 chunk 281 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 294 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 234 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN F 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.226593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.204511 restraints weight = 356641.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.204845 restraints weight = 181014.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.203813 restraints weight = 161749.161| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4448 r_free = 0.4448 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4448 r_free = 0.4448 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23464 Z= 0.124 Angle : 0.554 10.923 32012 Z= 0.290 Chirality : 0.045 0.249 3595 Planarity : 0.004 0.049 4105 Dihedral : 4.561 40.670 3260 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.77 % Allowed : 25.69 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 2967 helix: -2.65 (0.46), residues: 86 sheet: -0.23 (0.17), residues: 986 loop : -0.98 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 436 HIS 0.002 0.001 HIS I 199 PHE 0.021 0.001 PHE C 565 TYR 0.020 0.001 TYR D 95 ARG 0.006 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 2) link_NAG-ASN : angle 0.85398 ( 6) hydrogen bonds : bond 0.02954 ( 666) hydrogen bonds : angle 5.86041 ( 1755) SS BOND : bond 0.00437 ( 34) SS BOND : angle 1.13162 ( 69) covalent geometry : bond 0.00291 (23428) covalent geometry : angle 0.55198 (31937) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5934 Ramachandran restraints generated. 2967 Oldfield, 0 Emsley, 2967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 72 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.1591 (pmm) cc_final: -0.2206 (pmm) REVERT: C 355 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7412 (ptm160) REVERT: C 590 CYS cc_start: 0.1094 (OUTLIER) cc_final: 0.0661 (m) REVERT: L 199 HIS cc_start: -0.1291 (m-70) cc_final: -0.1602 (m170) REVERT: H 183 TYR cc_start: 0.4474 (OUTLIER) cc_final: 0.3792 (m-80) REVERT: H 204 ASN cc_start: 0.2947 (OUTLIER) cc_final: 0.1796 (t0) REVERT: A 346 ARG cc_start: 0.6711 (ptp90) cc_final: 0.6149 (ptt90) REVERT: A 355 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7624 (ptm160) REVERT: A 450 ASN cc_start: 0.6250 (OUTLIER) cc_final: 0.5844 (m-40) REVERT: A 590 CYS cc_start: 0.1530 (OUTLIER) cc_final: 0.1119 (m) REVERT: I 164 SER cc_start: 0.5999 (p) cc_final: 0.5786 (t) outliers start: 71 outliers final: 57 residues processed: 132 average time/residue: 0.3442 time to fit residues: 73.3413 Evaluate side-chains 133 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 69 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 55 TYR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 104 ARG Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 201 TYR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 55 TYR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 204 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 1.9990 chunk 250 optimal weight: 40.0000 chunk 71 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 chunk 98 optimal weight: 50.0000 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN F 133 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.228641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.208079 restraints weight = 358813.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.208702 restraints weight = 187057.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.207856 restraints weight = 167869.911| |-----------------------------------------------------------------------------| r_work (final): 0.4534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4534 r_free = 0.4534 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4534 r_free = 0.4534 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23464 Z= 0.108 Angle : 0.515 10.472 32012 Z= 0.267 Chirality : 0.044 0.247 3595 Planarity : 0.004 0.047 4105 Dihedral : 4.155 38.287 3260 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.50 % Allowed : 25.93 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.15), residues: 2967 helix: -2.43 (0.48), residues: 86 sheet: -0.02 (0.17), residues: 986 loop : -0.83 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 436 HIS 0.003 0.000 HIS I 199 PHE 0.021 0.001 PHE C 565 TYR 0.016 0.001 TYR D 95 ARG 0.004 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 2) link_NAG-ASN : angle 1.32053 ( 6) hydrogen bonds : bond 0.02647 ( 666) hydrogen bonds : angle 5.50924 ( 1755) SS BOND : bond 0.00476 ( 34) SS BOND : angle 0.96637 ( 69) covalent geometry : bond 0.00254 (23428) covalent geometry : angle 0.51341 (31937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5807.73 seconds wall clock time: 103 minutes 43.64 seconds (6223.64 seconds total)