Starting phenix.real_space_refine on Thu Jun 4 23:21:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1t_53514/06_2026/9r1t_53514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1t_53514/06_2026/9r1t_53514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r1t_53514/06_2026/9r1t_53514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1t_53514/06_2026/9r1t_53514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r1t_53514/06_2026/9r1t_53514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1t_53514/06_2026/9r1t_53514.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 128 5.16 5 C 10256 2.51 5 N 2672 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15784 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3879 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 16, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3879 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 16, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3879 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 16, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3879 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 16, 'TRANS': 478} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 3.74, per 1000 atoms: 0.24 Number of scatterers: 15784 At special positions: 0 Unit cell: (117.39, 117.39, 121.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 4 15.00 O 2724 8.00 N 2672 7.00 C 10256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 843.6 milliseconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 8 sheets defined 73.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 97 through 103 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.609A pdb=" N VAL A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 166 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.902A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 7.125A pdb=" N VAL A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 225 " --> pdb=" O TRP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.217A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 421 Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 454 through 473 removed outlier: 5.362A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.796A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 576 through 595 Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.697A pdb=" N HIS A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 removed outlier: 3.608A pdb=" N VAL B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 166 Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.940A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 removed outlier: 7.123A pdb=" N VAL B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.221A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 421 Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.508A pdb=" N LEU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 473 removed outlier: 5.360A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.797A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 566 through 576 Processing helix chain 'B' and resid 576 through 595 Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.694A pdb=" N HIS B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 removed outlier: 3.609A pdb=" N VAL C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.940A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 230 removed outlier: 7.125A pdb=" N VAL C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 225 " --> pdb=" O TRP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.222A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 421 Processing helix chain 'C' and resid 424 through 439 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.500A pdb=" N LEU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 473 removed outlier: 5.358A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.798A pdb=" N LYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 545 Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 576 through 595 Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.695A pdb=" N HIS C 603 " --> pdb=" O SER C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 removed outlier: 3.608A pdb=" N VAL D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 166 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.940A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 230 removed outlier: 7.123A pdb=" N VAL D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 225 " --> pdb=" O TRP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 256 through 266 Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.222A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 Proline residue: D 320 - end of helix removed outlier: 3.510A pdb=" N GLN D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 421 Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.500A pdb=" N LEU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 removed outlier: 3.516A pdb=" N MET D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.820A pdb=" N LYS D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 545 Processing helix chain 'D' and resid 566 through 576 Processing helix chain 'D' and resid 576 through 595 Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.694A pdb=" N HIS D 603 " --> pdb=" O SER D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 914 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 495 removed outlier: 6.602A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.248A pdb=" N VAL A 553 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 495 removed outlier: 6.607A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.246A pdb=" N VAL B 553 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 495 removed outlier: 6.607A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.248A pdb=" N VAL C 553 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 495 removed outlier: 6.602A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.245A pdb=" N VAL D 553 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) 1077 hydrogen bonds defined for protein. 3195 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: 2.78 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4960 1.34 - 1.46: 3730 1.46 - 1.58: 7254 1.58 - 1.69: 8 1.69 - 1.81: 224 Bond restraints: 16176 Sorted by residual: bond pdb=" C3' CMP A1001 " pdb=" C4' CMP A1001 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 2.05e+00 bond pdb=" C3' CMP D1001 " pdb=" C4' CMP D1001 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 2.02e+00 bond pdb=" C3' CMP B1001 " pdb=" C4' CMP B1001 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 2.01e+00 bond pdb=" C3' CMP C1001 " pdb=" C4' CMP C1001 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 2.01e+00 bond pdb=" CG TYR D 558 " pdb=" CD1 TYR D 558 " ideal model delta sigma weight residual 1.389 1.413 -0.024 2.10e-02 2.27e+03 1.35e+00 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 21611 1.88 - 3.76: 271 3.76 - 5.64: 40 5.64 - 7.51: 14 7.51 - 9.39: 8 Bond angle restraints: 21944 Sorted by residual: angle pdb=" O1P CMP C1001 " pdb=" P CMP C1001 " pdb=" O2P CMP C1001 " ideal model delta sigma weight residual 109.50 118.89 -9.39 3.00e+00 1.11e-01 9.80e+00 angle pdb=" O1P CMP B1001 " pdb=" P CMP B1001 " pdb=" O2P CMP B1001 " ideal model delta sigma weight residual 109.50 118.88 -9.38 3.00e+00 1.11e-01 9.78e+00 angle pdb=" O1P CMP D1001 " pdb=" P CMP D1001 " pdb=" O2P CMP D1001 " ideal model delta sigma weight residual 109.50 118.86 -9.36 3.00e+00 1.11e-01 9.73e+00 angle pdb=" O1P CMP A1001 " pdb=" P CMP A1001 " pdb=" O2P CMP A1001 " ideal model delta sigma weight residual 109.50 118.83 -9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA ARG A 467 " pdb=" CB ARG A 467 " pdb=" CG ARG A 467 " ideal model delta sigma weight residual 114.10 120.08 -5.98 2.00e+00 2.50e-01 8.93e+00 ... (remaining 21939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8825 25.94 - 51.88: 651 51.88 - 77.81: 40 77.81 - 103.75: 8 103.75 - 129.69: 4 Dihedral angle restraints: 9528 sinusoidal: 3604 harmonic: 5924 Sorted by residual: dihedral pdb=" CA GLU A 335 " pdb=" C GLU A 335 " pdb=" N MET A 336 " pdb=" CA MET A 336 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA GLU B 335 " pdb=" C GLU B 335 " pdb=" N MET B 336 " pdb=" CA MET B 336 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA GLU C 335 " pdb=" C GLU C 335 " pdb=" N MET C 336 " pdb=" CA MET C 336 " ideal model delta harmonic sigma weight residual 180.00 163.99 16.01 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 9525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1618 0.033 - 0.066: 603 0.066 - 0.100: 176 0.100 - 0.133: 44 0.133 - 0.166: 11 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CB VAL B 470 " pdb=" CA VAL B 470 " pdb=" CG1 VAL B 470 " pdb=" CG2 VAL B 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CB THR A 585 " pdb=" CA THR A 585 " pdb=" OG1 THR A 585 " pdb=" CG2 THR A 585 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CB THR C 585 " pdb=" CA THR C 585 " pdb=" OG1 THR C 585 " pdb=" CG2 THR C 585 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 2449 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 464 " 0.005 2.00e-02 2.50e+03 1.26e-02 2.80e+00 pdb=" CG PHE B 464 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 464 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 464 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 464 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 464 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 464 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 464 " -0.005 2.00e-02 2.50e+03 1.26e-02 2.80e+00 pdb=" CG PHE D 464 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE D 464 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 464 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 464 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 464 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 464 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 464 " -0.005 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE A 464 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 464 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 464 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 464 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 464 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 464 " 0.002 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 215 2.65 - 3.22: 15192 3.22 - 3.78: 26298 3.78 - 4.34: 33053 4.34 - 4.90: 55986 Nonbonded interactions: 130744 Sorted by model distance: nonbonded pdb=" OD2 ASP D 433 " pdb=" OH TYR D 558 " model vdw 2.093 3.040 nonbonded pdb=" OE2 GLU A 505 " pdb=" NZ LYS A 525 " model vdw 2.248 3.120 nonbonded pdb=" OH TYR D 411 " pdb=" ND1 HIS D 432 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR A 439 " pdb=" OE1 GLU B 452 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU D 282 " pdb=" ND2 ASN D 300 " model vdw 2.272 3.120 ... (remaining 130739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.032 16176 Z= 0.133 Angle : 0.583 9.392 21944 Z= 0.302 Chirality : 0.040 0.166 2452 Planarity : 0.003 0.029 2740 Dihedral : 16.217 129.691 5696 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.34 % Allowed : 17.43 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1964 helix: 1.46 (0.13), residues: 1356 sheet: -1.52 (0.53), residues: 88 loop : -1.46 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 297 TYR 0.018 0.001 TYR D 576 PHE 0.027 0.002 PHE D 464 TRP 0.010 0.001 TRP A 373 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16176) covalent geometry : angle 0.58321 / 0.30 (21944) hydrogen bonds : bond 0.10549 / 6.85 ( 1077) hydrogen bonds : angle 5.64516 / 4.21 ( 3195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 329 time to evaluate : 0.577 Fit side-chains REVERT: A 149 MET cc_start: 0.7182 (ttp) cc_final: 0.6920 (ttt) REVERT: A 152 MET cc_start: 0.7666 (ppp) cc_final: 0.7430 (tmm) REVERT: A 189 ASP cc_start: 0.8461 (t0) cc_final: 0.8159 (t70) REVERT: A 483 PHE cc_start: 0.7963 (t80) cc_final: 0.7355 (t80) REVERT: A 558 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6351 (t80) REVERT: B 149 MET cc_start: 0.7211 (ttp) cc_final: 0.6889 (ttt) REVERT: B 152 MET cc_start: 0.7665 (ppp) cc_final: 0.7414 (tmm) REVERT: B 189 ASP cc_start: 0.8427 (t0) cc_final: 0.8112 (t70) REVERT: B 483 PHE cc_start: 0.7992 (t80) cc_final: 0.7351 (t80) REVERT: B 558 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6350 (t80) REVERT: C 149 MET cc_start: 0.7153 (ttp) cc_final: 0.6811 (ttt) REVERT: C 152 MET cc_start: 0.7645 (ppp) cc_final: 0.7390 (tmm) REVERT: C 189 ASP cc_start: 0.8433 (t0) cc_final: 0.8112 (t70) REVERT: C 558 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6354 (t80) REVERT: D 149 MET cc_start: 0.7140 (ttp) cc_final: 0.6750 (ttm) REVERT: D 152 MET cc_start: 0.7662 (ppp) cc_final: 0.7421 (tmm) REVERT: D 483 PHE cc_start: 0.7864 (t80) cc_final: 0.7534 (t80) outliers start: 21 outliers final: 14 residues processed: 337 average time/residue: 0.1003 time to fit residues: 54.7279 Evaluate side-chains 308 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 ASN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.210446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.170595 restraints weight = 18153.022| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.71 r_work: 0.3568 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16176 Z= 0.164 Angle : 0.568 9.067 21944 Z= 0.293 Chirality : 0.040 0.132 2452 Planarity : 0.004 0.034 2740 Dihedral : 7.641 132.603 2268 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 16.48 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1964 helix: 1.50 (0.14), residues: 1364 sheet: -1.58 (0.53), residues: 88 loop : -1.67 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 590 TYR 0.013 0.001 TYR A 407 PHE 0.035 0.002 PHE D 569 TRP 0.012 0.001 TRP A 330 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (16176) covalent geometry : angle 0.56824 / 0.29 (21944) hydrogen bonds : bond 0.04083 / 2.72 ( 1077) hydrogen bonds : angle 4.76330 / 3.55 ( 3195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 0.650 Fit side-chains REVERT: A 149 MET cc_start: 0.7040 (ttp) cc_final: 0.6643 (ttm) REVERT: A 152 MET cc_start: 0.7541 (ppp) cc_final: 0.7333 (tmm) REVERT: A 376 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7804 (mtm) REVERT: A 558 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6382 (t80) REVERT: B 149 MET cc_start: 0.7030 (ttp) cc_final: 0.6630 (ttm) REVERT: B 152 MET cc_start: 0.7526 (ppp) cc_final: 0.7304 (tmm) REVERT: B 376 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7812 (mtm) REVERT: B 558 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6381 (t80) REVERT: C 149 MET cc_start: 0.7026 (ttp) cc_final: 0.6634 (ttm) REVERT: C 152 MET cc_start: 0.7532 (ppp) cc_final: 0.7320 (tmm) REVERT: C 376 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7815 (mtm) REVERT: C 558 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6392 (t80) REVERT: D 149 MET cc_start: 0.7009 (ttp) cc_final: 0.6604 (ttm) REVERT: D 152 MET cc_start: 0.7544 (ppp) cc_final: 0.7332 (tmm) REVERT: D 376 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7801 (mtm) REVERT: D 483 PHE cc_start: 0.7854 (t80) cc_final: 0.7618 (t80) outliers start: 29 outliers final: 19 residues processed: 302 average time/residue: 0.1010 time to fit residues: 49.1873 Evaluate side-chains 308 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 282 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 376 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 185 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.211040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.168608 restraints weight = 18252.865| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.81 r_work: 0.3538 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16176 Z= 0.154 Angle : 0.544 8.145 21944 Z= 0.279 Chirality : 0.040 0.137 2452 Planarity : 0.003 0.035 2740 Dihedral : 7.575 133.931 2254 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.53 % Allowed : 17.30 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1964 helix: 1.57 (0.14), residues: 1340 sheet: -1.51 (0.54), residues: 88 loop : -1.56 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 590 TYR 0.010 0.001 TYR D 434 PHE 0.025 0.001 PHE D 569 TRP 0.009 0.001 TRP C 330 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16176) covalent geometry : angle 0.54383 / 0.28 (21944) hydrogen bonds : bond 0.03914 / 2.62 ( 1077) hydrogen bonds : angle 4.60116 / 3.44 ( 3195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 318 time to evaluate : 0.609 Fit side-chains REVERT: A 376 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: A 558 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6251 (t80) REVERT: B 126 ARG cc_start: 0.8475 (ttt-90) cc_final: 0.8267 (ttp-170) REVERT: B 226 PHE cc_start: 0.7784 (t80) cc_final: 0.7566 (t80) REVERT: B 376 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7949 (mtm) REVERT: B 558 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6268 (t80) REVERT: C 126 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.8274 (ttp-170) REVERT: C 226 PHE cc_start: 0.7819 (t80) cc_final: 0.7609 (t80) REVERT: C 376 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7956 (mtm) REVERT: C 558 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6238 (t80) REVERT: D 126 ARG cc_start: 0.8472 (ttt-90) cc_final: 0.8262 (ttp-170) REVERT: D 149 MET cc_start: 0.7063 (ttp) cc_final: 0.6645 (ttt) REVERT: D 189 ASP cc_start: 0.8162 (t0) cc_final: 0.7763 (t0) REVERT: D 226 PHE cc_start: 0.7790 (t80) cc_final: 0.7586 (t80) REVERT: D 376 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7960 (mtm) REVERT: D 483 PHE cc_start: 0.7899 (t80) cc_final: 0.7599 (t80) outliers start: 24 outliers final: 16 residues processed: 325 average time/residue: 0.1105 time to fit residues: 56.3095 Evaluate side-chains 325 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 302 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 10 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.210553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.170205 restraints weight = 18130.303| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.70 r_work: 0.3515 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16176 Z= 0.155 Angle : 0.548 8.027 21944 Z= 0.281 Chirality : 0.040 0.144 2452 Planarity : 0.003 0.035 2740 Dihedral : 7.588 134.422 2252 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.97 % Allowed : 17.62 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1964 helix: 1.49 (0.13), residues: 1364 sheet: -1.48 (0.55), residues: 88 loop : -1.80 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 590 TYR 0.011 0.001 TYR D 434 PHE 0.018 0.001 PHE D 569 TRP 0.009 0.001 TRP B 330 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16176) covalent geometry : angle 0.54829 / 0.28 (21944) hydrogen bonds : bond 0.03869 / 2.59 ( 1077) hydrogen bonds : angle 4.55917 / 3.41 ( 3195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 316 time to evaluate : 0.430 Fit side-chains REVERT: A 149 MET cc_start: 0.7057 (ttp) cc_final: 0.6741 (ttm) REVERT: A 376 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7942 (mtm) REVERT: A 558 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6330 (t80) REVERT: B 149 MET cc_start: 0.7044 (ttp) cc_final: 0.6752 (ttm) REVERT: B 376 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7965 (mtm) REVERT: B 483 PHE cc_start: 0.7957 (t80) cc_final: 0.7467 (t80) REVERT: B 558 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6339 (t80) REVERT: C 149 MET cc_start: 0.7026 (ttp) cc_final: 0.6717 (ttm) REVERT: C 376 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7959 (mtm) REVERT: C 437 HIS cc_start: 0.7170 (t70) cc_final: 0.6893 (t-170) REVERT: C 483 PHE cc_start: 0.7934 (t80) cc_final: 0.7430 (t80) REVERT: C 558 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6338 (t80) REVERT: D 376 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: D 483 PHE cc_start: 0.7913 (t80) cc_final: 0.7710 (t80) outliers start: 31 outliers final: 23 residues processed: 328 average time/residue: 0.1164 time to fit residues: 58.3534 Evaluate side-chains 333 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 55 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 HIS ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.209647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169274 restraints weight = 18276.658| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.69 r_work: 0.3514 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16176 Z= 0.165 Angle : 0.568 8.030 21944 Z= 0.288 Chirality : 0.040 0.152 2452 Planarity : 0.003 0.035 2740 Dihedral : 7.627 134.967 2252 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.48 % Allowed : 18.00 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 1964 helix: 1.44 (0.13), residues: 1364 sheet: -1.44 (0.56), residues: 88 loop : -1.82 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 267 TYR 0.013 0.001 TYR B 439 PHE 0.018 0.001 PHE A 464 TRP 0.009 0.001 TRP A 330 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (16176) covalent geometry : angle 0.56797 / 0.29 (21944) hydrogen bonds : bond 0.03938 / 2.65 ( 1077) hydrogen bonds : angle 4.55139 / 3.40 ( 3195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 306 time to evaluate : 0.635 Fit side-chains REVERT: A 376 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7999 (mtm) REVERT: A 558 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6375 (t80) REVERT: B 376 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: B 437 HIS cc_start: 0.7278 (t-170) cc_final: 0.6876 (t-170) REVERT: B 483 PHE cc_start: 0.7989 (t80) cc_final: 0.7553 (t80) REVERT: B 558 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6322 (t80) REVERT: C 376 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: C 437 HIS cc_start: 0.7280 (t70) cc_final: 0.6890 (t-170) REVERT: C 483 PHE cc_start: 0.7970 (t80) cc_final: 0.7483 (t80) REVERT: C 558 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6367 (t80) REVERT: D 376 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7989 (mtm) REVERT: D 406 GLN cc_start: 0.7879 (mp10) cc_final: 0.7446 (mt0) outliers start: 39 outliers final: 28 residues processed: 323 average time/residue: 0.1087 time to fit residues: 55.5882 Evaluate side-chains 329 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 109 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.206975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165920 restraints weight = 18046.251| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.67 r_work: 0.3469 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16176 Z= 0.209 Angle : 0.599 10.036 21944 Z= 0.304 Chirality : 0.042 0.155 2452 Planarity : 0.003 0.034 2740 Dihedral : 7.688 135.244 2252 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.35 % Allowed : 18.77 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1964 helix: 1.36 (0.13), residues: 1364 sheet: -1.41 (0.56), residues: 88 loop : -1.84 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 267 TYR 0.016 0.001 TYR B 439 PHE 0.021 0.002 PHE A 464 TRP 0.009 0.001 TRP A 373 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (16176) covalent geometry : angle 0.59921 / 0.30 (21944) hydrogen bonds : bond 0.04098 / 2.75 ( 1077) hydrogen bonds : angle 4.59622 / 3.43 ( 3195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7464 (ppp) cc_final: 0.7247 (tmm) REVERT: A 376 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: A 558 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 376 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8128 (mtt) REVERT: B 437 HIS cc_start: 0.7535 (t-170) cc_final: 0.7035 (t-170) REVERT: B 558 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6343 (t80) REVERT: C 226 PHE cc_start: 0.7727 (t80) cc_final: 0.7508 (t80) REVERT: C 376 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8110 (mtt) REVERT: C 558 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6365 (t80) REVERT: D 152 MET cc_start: 0.7497 (ppp) cc_final: 0.7255 (tmm) REVERT: D 376 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8085 (mtt) REVERT: D 406 GLN cc_start: 0.7926 (mp10) cc_final: 0.7458 (mt0) outliers start: 37 outliers final: 30 residues processed: 313 average time/residue: 0.1050 time to fit residues: 52.2101 Evaluate side-chains 335 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 0.0570 chunk 84 optimal weight: 0.4980 chunk 186 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 193 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 HIS ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.211103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.171602 restraints weight = 18110.551| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.67 r_work: 0.3526 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16176 Z= 0.127 Angle : 0.555 10.590 21944 Z= 0.282 Chirality : 0.040 0.157 2452 Planarity : 0.003 0.034 2740 Dihedral : 7.637 134.841 2252 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.72 % Allowed : 20.42 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1964 helix: 1.44 (0.13), residues: 1364 sheet: -1.23 (0.57), residues: 88 loop : -1.83 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 267 TYR 0.017 0.001 TYR D 439 PHE 0.022 0.001 PHE C 464 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (16176) covalent geometry : angle 0.55491 / 0.28 (21944) hydrogen bonds : bond 0.03713 / 2.51 ( 1077) hydrogen bonds : angle 4.53939 / 3.39 ( 3195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 308 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7460 (ppp) cc_final: 0.7163 (tmm) REVERT: A 406 GLN cc_start: 0.7870 (mp10) cc_final: 0.7386 (mt0) REVERT: A 558 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6300 (t80) REVERT: B 152 MET cc_start: 0.7490 (ppp) cc_final: 0.7255 (tmm) REVERT: B 406 GLN cc_start: 0.7894 (mp10) cc_final: 0.7399 (mt0) REVERT: B 437 HIS cc_start: 0.7265 (t70) cc_final: 0.6849 (t-170) REVERT: B 483 PHE cc_start: 0.7764 (t80) cc_final: 0.7397 (t80) REVERT: B 558 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6188 (t80) REVERT: C 152 MET cc_start: 0.7508 (ppp) cc_final: 0.7269 (tmm) REVERT: C 323 GLN cc_start: 0.8085 (mt0) cc_final: 0.7797 (mt0) REVERT: C 406 GLN cc_start: 0.7879 (mp10) cc_final: 0.7373 (mt0) REVERT: C 437 HIS cc_start: 0.7225 (t70) cc_final: 0.6828 (t70) REVERT: C 483 PHE cc_start: 0.7972 (t80) cc_final: 0.7740 (t80) REVERT: C 558 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6281 (t80) REVERT: D 152 MET cc_start: 0.7469 (ppp) cc_final: 0.7209 (tmm) REVERT: D 406 GLN cc_start: 0.7899 (mp10) cc_final: 0.7418 (mt0) REVERT: D 483 PHE cc_start: 0.7964 (t80) cc_final: 0.7707 (t80) outliers start: 27 outliers final: 24 residues processed: 322 average time/residue: 0.1018 time to fit residues: 52.3049 Evaluate side-chains 317 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 145 TRP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 0.0570 chunk 173 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 188 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.211863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170005 restraints weight = 18243.289| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.74 r_work: 0.3592 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16176 Z= 0.128 Angle : 0.558 10.341 21944 Z= 0.283 Chirality : 0.040 0.165 2452 Planarity : 0.003 0.034 2740 Dihedral : 7.539 134.999 2246 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.04 % Allowed : 20.29 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.19), residues: 1964 helix: 1.50 (0.14), residues: 1364 sheet: -1.25 (0.58), residues: 88 loop : -1.80 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 270 TYR 0.014 0.001 TYR D 439 PHE 0.025 0.001 PHE D 186 TRP 0.009 0.001 TRP D 330 HIS 0.003 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16176) covalent geometry : angle 0.55821 / 0.28 (21944) hydrogen bonds : bond 0.03710 / 2.51 ( 1077) hydrogen bonds : angle 4.53234 / 3.38 ( 3195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 303 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7451 (ppp) cc_final: 0.7204 (tmm) REVERT: A 376 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7808 (mtm) REVERT: A 406 GLN cc_start: 0.7726 (mp10) cc_final: 0.7169 (mt0) REVERT: A 483 PHE cc_start: 0.7918 (t80) cc_final: 0.7475 (t80) REVERT: A 558 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6078 (t80) REVERT: B 152 MET cc_start: 0.7464 (ppp) cc_final: 0.7251 (tmm) REVERT: B 323 GLN cc_start: 0.8018 (mt0) cc_final: 0.7802 (mt0) REVERT: B 376 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7841 (mtm) REVERT: B 406 GLN cc_start: 0.7777 (mp10) cc_final: 0.7190 (mt0) REVERT: B 437 HIS cc_start: 0.7256 (t70) cc_final: 0.6802 (t-170) REVERT: B 483 PHE cc_start: 0.7784 (t80) cc_final: 0.7514 (t80) REVERT: B 558 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6076 (t80) REVERT: C 152 MET cc_start: 0.7470 (ppp) cc_final: 0.7254 (tmm) REVERT: C 323 GLN cc_start: 0.8027 (mt0) cc_final: 0.7747 (mt0) REVERT: C 376 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7836 (mtm) REVERT: C 406 GLN cc_start: 0.7754 (mp10) cc_final: 0.7204 (mt0) REVERT: C 437 HIS cc_start: 0.7250 (t70) cc_final: 0.6788 (t70) REVERT: C 483 PHE cc_start: 0.7959 (t80) cc_final: 0.7701 (t80) REVERT: C 558 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6141 (t80) REVERT: D 152 MET cc_start: 0.7487 (ppp) cc_final: 0.7269 (tmm) REVERT: D 376 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7793 (mtm) outliers start: 32 outliers final: 23 residues processed: 315 average time/residue: 0.1092 time to fit residues: 53.7131 Evaluate side-chains 333 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 166 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 156 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.211271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.171906 restraints weight = 18155.912| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.67 r_work: 0.3545 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16176 Z= 0.143 Angle : 0.579 10.358 21944 Z= 0.293 Chirality : 0.041 0.172 2452 Planarity : 0.003 0.034 2740 Dihedral : 7.572 135.143 2246 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.97 % Allowed : 20.67 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1964 helix: 1.65 (0.13), residues: 1340 sheet: -1.28 (0.57), residues: 88 loop : -1.56 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 267 TYR 0.012 0.001 TYR B 439 PHE 0.020 0.001 PHE C 464 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16176) covalent geometry : angle 0.57894 / 0.29 (21944) hydrogen bonds : bond 0.03740 / 2.52 ( 1077) hydrogen bonds : angle 4.50808 / 3.36 ( 3195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7452 (ppp) cc_final: 0.7207 (tmm) REVERT: A 406 GLN cc_start: 0.7876 (mp10) cc_final: 0.7368 (mt0) REVERT: A 483 PHE cc_start: 0.7879 (t80) cc_final: 0.7374 (t80) REVERT: A 558 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6281 (t80) REVERT: B 152 MET cc_start: 0.7462 (ppp) cc_final: 0.7170 (tmm) REVERT: B 437 HIS cc_start: 0.7347 (t70) cc_final: 0.6949 (t70) REVERT: B 483 PHE cc_start: 0.7802 (t80) cc_final: 0.7472 (t80) REVERT: B 558 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6220 (t80) REVERT: C 152 MET cc_start: 0.7437 (ppp) cc_final: 0.7116 (tmm) REVERT: C 437 HIS cc_start: 0.7230 (t70) cc_final: 0.6804 (t70) REVERT: C 483 PHE cc_start: 0.7935 (t80) cc_final: 0.7697 (t80) REVERT: C 558 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6277 (t80) REVERT: D 152 MET cc_start: 0.7438 (ppp) cc_final: 0.7177 (tmm) outliers start: 31 outliers final: 28 residues processed: 306 average time/residue: 0.1063 time to fit residues: 51.1553 Evaluate side-chains 321 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 145 TRP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.209853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.167858 restraints weight = 18153.280| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.77 r_work: 0.3546 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16176 Z= 0.167 Angle : 0.599 10.492 21944 Z= 0.303 Chirality : 0.041 0.179 2452 Planarity : 0.003 0.034 2740 Dihedral : 7.596 135.349 2246 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.23 % Allowed : 20.42 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 1964 helix: 1.62 (0.13), residues: 1340 sheet: -1.33 (0.57), residues: 88 loop : -1.54 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 267 TYR 0.013 0.001 TYR B 439 PHE 0.031 0.002 PHE D 186 TRP 0.010 0.001 TRP A 145 HIS 0.002 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16176) covalent geometry : angle 0.59868 / 0.30 (21944) hydrogen bonds : bond 0.03854 / 2.60 ( 1077) hydrogen bonds : angle 4.51051 / 3.36 ( 3195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 302 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7469 (ppp) cc_final: 0.7223 (tmm) REVERT: A 186 PHE cc_start: 0.8572 (m-80) cc_final: 0.8352 (m-10) REVERT: A 376 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8014 (mtm) REVERT: A 406 GLN cc_start: 0.7809 (mp10) cc_final: 0.7207 (mt0) REVERT: A 483 PHE cc_start: 0.7957 (t80) cc_final: 0.7597 (t80) REVERT: A 558 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6177 (t80) REVERT: B 152 MET cc_start: 0.7502 (ppp) cc_final: 0.7268 (tmm) REVERT: B 376 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8033 (mtm) REVERT: B 437 HIS cc_start: 0.7505 (t70) cc_final: 0.6917 (t-170) REVERT: B 483 PHE cc_start: 0.7921 (t80) cc_final: 0.7649 (t80) REVERT: B 558 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6094 (t80) REVERT: C 152 MET cc_start: 0.7483 (ppp) cc_final: 0.7236 (tmm) REVERT: C 376 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8020 (mtm) REVERT: C 437 HIS cc_start: 0.7461 (t70) cc_final: 0.6830 (t70) REVERT: C 483 PHE cc_start: 0.8038 (t80) cc_final: 0.7768 (t80) REVERT: C 558 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6180 (t80) REVERT: D 152 MET cc_start: 0.7518 (ppp) cc_final: 0.7296 (tmm) REVERT: D 376 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7933 (mtm) outliers start: 35 outliers final: 28 residues processed: 315 average time/residue: 0.1137 time to fit residues: 56.1610 Evaluate side-chains 324 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 558 TYR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 558 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 507 THR Chi-restraints excluded: chain C residue 558 TYR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.210691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.168235 restraints weight = 18083.067| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.70 r_work: 0.3485 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16176 Z= 0.146 Angle : 0.591 10.492 21944 Z= 0.300 Chirality : 0.040 0.173 2452 Planarity : 0.003 0.033 2740 Dihedral : 7.575 135.163 2246 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.29 % Allowed : 20.80 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 1964 helix: 1.61 (0.13), residues: 1340 sheet: -1.27 (0.58), residues: 88 loop : -1.56 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 267 TYR 0.011 0.001 TYR B 439 PHE 0.022 0.001 PHE D 483 TRP 0.011 0.001 TRP A 145 HIS 0.016 0.001 HIS D 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16176) covalent geometry : angle 0.59117 / 0.30 (21944) hydrogen bonds : bond 0.03786 / 2.56 ( 1077) hydrogen bonds : angle 4.50562 / 3.36 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.48 seconds wall clock time: 61 minutes 42.95 seconds (3702.95 seconds total)