Starting phenix.real_space_refine on Thu Aug 6 17:02:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1t_53514/08_2026/9r1t_53514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1t_53514/08_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_53514/08_2026/9r1t_53514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1t_53514/08_2026/9r1t_53514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r1t_53514/08_2026/9r1t_53514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1t_53514/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.18 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: 0.89 Conformation dependent library (CDL) restraints added in 511.5 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: 0.46 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: 2.56 Time building geometry restraints manager: 1.26 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=" C4' CMP B1001 " pdb=" C5' CMP B1001 " ideal model delta sigma weight residual 1.524 1.497 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C4' CMP A1001 " pdb=" C5' CMP A1001 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C4' CMP C1001 " pdb=" C5' CMP C1001 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C4' CMP D1001 " pdb=" C5' CMP D1001 " ideal model delta sigma weight residual 1.524 1.498 0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C3' CMP A1001 " pdb=" C4' CMP A1001 " ideal model delta sigma weight residual 1.524 1.500 0.024 2.00e-02 2.50e+03 1.50e+00 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 21678 2.08 - 4.16: 197 4.16 - 6.24: 38 6.24 - 8.32: 15 8.32 - 10.41: 16 Bond angle restraints: 21944 Sorted by residual: angle pdb=" C1' CMP C1001 " pdb=" C2' CMP C1001 " pdb=" C3' CMP C1001 " ideal model delta sigma weight residual 111.00 100.59 10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C1' CMP B1001 " pdb=" C2' CMP B1001 " pdb=" C3' CMP B1001 " ideal model delta sigma weight residual 111.00 100.60 10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C1' CMP A1001 " pdb=" C2' CMP A1001 " pdb=" C3' CMP A1001 " ideal model delta sigma weight residual 111.00 100.62 10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C1' CMP D1001 " pdb=" C2' CMP D1001 " pdb=" C3' CMP D1001 " ideal model delta sigma weight residual 111.00 100.63 10.37 3.00e+00 1.11e-01 1.19e+01 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 ... (remaining 21939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 8301 17.64 - 35.27: 963 35.27 - 52.91: 231 52.91 - 70.55: 25 70.55 - 88.18: 8 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 - 0.054: 2052 0.054 - 0.109: 365 0.109 - 0.163: 29 0.163 - 0.218: 2 0.218 - 0.272: 4 Chirality restraints: 2452 Sorted by residual: chirality pdb=" C2' CMP C1001 " pdb=" C1' CMP C1001 " pdb=" C3' CMP C1001 " pdb=" O2' CMP C1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2' CMP B1001 " pdb=" C1' CMP B1001 " pdb=" C3' CMP B1001 " pdb=" O2' CMP B1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2' CMP A1001 " pdb=" C1' CMP A1001 " pdb=" C3' CMP A1001 " pdb=" O2' CMP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.84e+00 ... (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: 0.05 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: 2.850 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.190 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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= 0.134 Angle : 0.628 10.405 21944 Z= 0.305 Chirality : 0.041 0.272 2452 Planarity : 0.003 0.029 2740 Dihedral : 15.863 88.184 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 0.00280 / 0.13 (16176) covalent geometry : angle 0.62777 / 0.31 (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 : 0.500 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: 0.0954 time to fit residues: 52.3110 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 : 0.571 ------------------------------------------------------------------------------- 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... ** 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.210413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170196 restraints weight = 18143.686| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.69 r_work: 0.3567 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0787 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= 0.163 Angle : 0.598 8.330 21944 Z= 0.293 Chirality : 0.041 0.154 2452 Planarity : 0.004 0.034 2740 Dihedral : 5.129 59.653 2268 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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: 0.83 (0.19), residues: 1964 helix: 1.50 (0.14), residues: 1364 sheet: -1.58 (0.53), residues: 88 loop : -1.65 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.00368 / 0.16 (16176) covalent geometry : angle 0.59809 / 0.29 (21944) hydrogen bonds : bond 0.04115 / 2.74 ( 1077) hydrogen bonds : angle 4.76571 / 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 318 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 289 time to evaluate : 0.496 Fit side-chains REVERT: A 149 MET cc_start: 0.7037 (ttp) cc_final: 0.6639 (ttm) REVERT: A 376 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7791 (mtm) REVERT: A 558 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6384 (t80) REVERT: B 149 MET cc_start: 0.7028 (ttp) cc_final: 0.6631 (ttm) REVERT: B 152 MET cc_start: 0.7540 (ppp) cc_final: 0.7327 (tmm) REVERT: B 376 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7796 (mtm) REVERT: B 558 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6380 (t80) REVERT: C 149 MET cc_start: 0.7022 (ttp) cc_final: 0.6626 (ttm) REVERT: C 152 MET cc_start: 0.7549 (ppp) cc_final: 0.7343 (tmm) REVERT: C 376 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7795 (mtm) REVERT: C 558 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6374 (t80) REVERT: D 149 MET cc_start: 0.7054 (ttp) cc_final: 0.6660 (ttm) REVERT: D 152 MET cc_start: 0.7556 (ppp) cc_final: 0.7348 (tmm) REVERT: D 376 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7801 (mtm) REVERT: D 483 PHE cc_start: 0.7858 (t80) cc_final: 0.7620 (t80) outliers start: 29 outliers final: 18 residues processed: 301 average time/residue: 0.0934 time to fit residues: 45.4671 Evaluate side-chains 308 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 48 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 139 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 193 ASN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.211166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.170109 restraints weight = 18226.024| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.70 r_work: 0.3509 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1035 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= 0.149 Angle : 0.574 8.896 21944 Z= 0.279 Chirality : 0.040 0.150 2452 Planarity : 0.003 0.035 2740 Dihedral : 4.927 58.493 2254 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.59 % Allowed : 17.37 % Favored : 81.04 % 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: 1.56 (0.14), residues: 1340 sheet: -1.47 (0.54), residues: 88 loop : -1.54 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 297 TYR 0.010 0.001 TYR D 434 PHE 0.024 0.001 PHE D 569 TRP 0.009 0.001 TRP C 330 HIS 0.004 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16176) covalent geometry : angle 0.57396 / 0.28 (21944) hydrogen bonds : bond 0.03903 / 2.61 ( 1077) hydrogen bonds : angle 4.60106 / 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 341 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 316 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7866 (mtm) REVERT: A 558 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6365 (t80) REVERT: B 152 MET cc_start: 0.7595 (ppp) cc_final: 0.7383 (tmm) REVERT: B 376 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7886 (mtm) REVERT: B 558 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6383 (t80) REVERT: C 152 MET cc_start: 0.7599 (ppp) cc_final: 0.7387 (tmm) REVERT: C 376 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7893 (mtm) REVERT: D 149 MET cc_start: 0.7100 (ttp) cc_final: 0.6694 (ttt) REVERT: D 152 MET cc_start: 0.7601 (ppp) cc_final: 0.7384 (tmm) REVERT: D 189 ASP cc_start: 0.7889 (t0) cc_final: 0.7491 (t0) REVERT: D 376 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7898 (mtm) REVERT: D 483 PHE cc_start: 0.7825 (t80) cc_final: 0.7498 (t80) outliers start: 25 outliers final: 19 residues processed: 324 average time/residue: 0.1074 time to fit residues: 54.3683 Evaluate side-chains 323 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 298 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 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=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: 0.5980 chunk 85 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 10 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 = 0.4309 r_free = 0.4309 target = 0.211096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171153 restraints weight = 18127.159| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.69 r_work: 0.3523 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1189 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= 0.139 Angle : 0.573 8.963 21944 Z= 0.279 Chirality : 0.040 0.144 2452 Planarity : 0.003 0.035 2740 Dihedral : 4.893 58.020 2252 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.91 % Allowed : 17.81 % Favored : 80.28 % 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: 0.79 (0.19), residues: 1964 helix: 1.49 (0.13), residues: 1364 sheet: -1.40 (0.55), residues: 88 loop : -1.79 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 580 TYR 0.010 0.001 TYR D 434 PHE 0.016 0.001 PHE D 569 TRP 0.008 0.001 TRP C 330 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16176) covalent geometry : angle 0.57328 / 0.28 (21944) hydrogen bonds : bond 0.03805 / 2.56 ( 1077) hydrogen bonds : angle 4.54434 / 3.39 ( 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 341 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 311 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.6930 (ttp) cc_final: 0.6613 (ttm) REVERT: A 483 PHE cc_start: 0.7945 (t80) cc_final: 0.7449 (t80) REVERT: A 558 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6352 (t80) REVERT: B 149 MET cc_start: 0.7210 (ttp) cc_final: 0.6820 (ttm) REVERT: B 437 HIS cc_start: 0.7164 (t70) cc_final: 0.6897 (t-170) REVERT: B 483 PHE cc_start: 0.7928 (t80) cc_final: 0.7417 (t80) REVERT: B 558 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6367 (t80) REVERT: C 149 MET cc_start: 0.7100 (ttp) cc_final: 0.6706 (ttm) REVERT: C 483 PHE cc_start: 0.7920 (t80) cc_final: 0.7407 (t80) REVERT: D 483 PHE cc_start: 0.7868 (t80) cc_final: 0.7658 (t80) outliers start: 30 outliers final: 24 residues processed: 328 average time/residue: 0.1187 time to fit residues: 60.6439 Evaluate side-chains 319 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 293 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.3980 chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.210091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168977 restraints weight = 18228.196| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.71 r_work: 0.3489 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1265 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 : 0.588 8.524 21944 Z= 0.285 Chirality : 0.040 0.150 2452 Planarity : 0.003 0.034 2740 Dihedral : 4.933 58.677 2252 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.42 % Allowed : 17.81 % Favored : 79.77 % 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 (0.18), residues: 1964 helix: 1.48 (0.13), residues: 1364 sheet: -1.32 (0.57), residues: 88 loop : -1.82 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 267 TYR 0.013 0.001 TYR B 439 PHE 0.019 0.001 PHE B 464 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 0.00349 / 0.15 (16176) covalent geometry : angle 0.58795 / 0.28 (21944) hydrogen bonds : bond 0.03870 / 2.60 ( 1077) hydrogen bonds : angle 4.52296 / 3.38 ( 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 338 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: A 483 PHE cc_start: 0.7998 (t80) cc_final: 0.7566 (t80) REVERT: A 558 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6326 (t80) REVERT: B 376 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7998 (mtm) REVERT: B 406 GLN cc_start: 0.7868 (mp10) cc_final: 0.7394 (mt0) REVERT: B 437 HIS cc_start: 0.7308 (t70) cc_final: 0.6907 (t-170) REVERT: B 483 PHE cc_start: 0.7980 (t80) cc_final: 0.7552 (t80) REVERT: B 558 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6339 (t80) REVERT: C 376 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7978 (mtm) REVERT: C 406 GLN cc_start: 0.7852 (mp10) cc_final: 0.7380 (mt0) REVERT: C 483 PHE cc_start: 0.7982 (t80) cc_final: 0.7522 (t80) REVERT: D 149 MET cc_start: 0.7116 (ttp) cc_final: 0.6800 (ttm) REVERT: D 376 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: D 406 GLN cc_start: 0.7873 (mp10) cc_final: 0.7434 (mt0) outliers start: 38 outliers final: 28 residues processed: 319 average time/residue: 0.1097 time to fit residues: 55.6080 Evaluate side-chains 326 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 32 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.209230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166587 restraints weight = 18000.392| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.81 r_work: 0.3478 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1375 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= 0.161 Angle : 0.600 9.678 21944 Z= 0.291 Chirality : 0.041 0.159 2452 Planarity : 0.003 0.034 2740 Dihedral : 4.959 59.106 2252 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.04 % Allowed : 18.83 % Favored : 79.13 % 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: 0.78 (0.19), residues: 1964 helix: 1.48 (0.13), residues: 1364 sheet: -1.17 (0.59), residues: 88 loop : -1.81 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 267 TYR 0.016 0.001 TYR D 439 PHE 0.022 0.001 PHE A 464 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 0.00365 / 0.16 (16176) covalent geometry : angle 0.60048 / 0.29 (21944) hydrogen bonds : bond 0.03901 / 2.63 ( 1077) hydrogen bonds : angle 4.52966 / 3.39 ( 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 328 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7179 (ttp) cc_final: 0.6745 (ttm) REVERT: A 152 MET cc_start: 0.7569 (ppp) cc_final: 0.7348 (tmm) REVERT: A 376 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8048 (mtm) REVERT: A 483 PHE cc_start: 0.8059 (t80) cc_final: 0.7715 (t80) REVERT: A 558 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6388 (t80) REVERT: B 376 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8065 (mtm) REVERT: B 406 GLN cc_start: 0.7838 (mp10) cc_final: 0.7314 (mt0) REVERT: B 483 PHE cc_start: 0.8060 (t80) cc_final: 0.7701 (t80) REVERT: B 558 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6370 (t80) REVERT: C 376 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (mtm) REVERT: C 406 GLN cc_start: 0.7829 (mp10) cc_final: 0.7303 (mt0) REVERT: C 483 PHE cc_start: 0.8064 (t80) cc_final: 0.7679 (t80) REVERT: D 376 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8053 (mtm) REVERT: D 406 GLN cc_start: 0.7840 (mp10) cc_final: 0.7345 (mt0) outliers start: 32 outliers final: 26 residues processed: 310 average time/residue: 0.1122 time to fit residues: 55.3579 Evaluate side-chains 315 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 = 0.210199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.166734 restraints weight = 18038.077| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.65 r_work: 0.3478 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16176 Z= 0.142 Angle : 0.592 9.084 21944 Z= 0.287 Chirality : 0.041 0.162 2452 Planarity : 0.003 0.034 2740 Dihedral : 4.774 58.743 2246 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.23 % Allowed : 19.47 % Favored : 78.31 % 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: 0.79 (0.19), residues: 1964 helix: 1.48 (0.13), residues: 1364 sheet: -1.10 (0.60), residues: 88 loop : -1.81 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 267 TYR 0.017 0.001 TYR D 439 PHE 0.019 0.001 PHE A 464 TRP 0.009 0.001 TRP D 330 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16176) covalent geometry : angle 0.59206 / 0.29 (21944) hydrogen bonds : bond 0.03783 / 2.55 ( 1077) hydrogen bonds : angle 4.51258 / 3.37 ( 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 319 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7539 (ppp) cc_final: 0.7305 (tmm) REVERT: A 323 GLN cc_start: 0.8085 (mt0) cc_final: 0.7879 (mt0) REVERT: A 376 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7900 (mtm) REVERT: A 483 PHE cc_start: 0.8031 (t80) cc_final: 0.7697 (t80) REVERT: A 558 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6313 (t80) REVERT: B 152 MET cc_start: 0.7549 (ppp) cc_final: 0.7320 (tmm) REVERT: B 376 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7997 (mtm) REVERT: B 406 GLN cc_start: 0.7897 (mp10) cc_final: 0.7358 (mt0) REVERT: B 437 HIS cc_start: 0.7344 (t-170) cc_final: 0.6883 (t-170) REVERT: B 483 PHE cc_start: 0.8031 (t80) cc_final: 0.7686 (t80) REVERT: B 558 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6219 (t80) REVERT: C 152 MET cc_start: 0.7550 (ppp) cc_final: 0.7329 (tmm) REVERT: C 376 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7972 (mtm) REVERT: C 406 GLN cc_start: 0.7878 (mp10) cc_final: 0.7354 (mt0) REVERT: C 483 PHE cc_start: 0.8031 (t80) cc_final: 0.7659 (t80) REVERT: D 376 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7908 (mtm) outliers start: 35 outliers final: 28 residues processed: 300 average time/residue: 0.1107 time to fit residues: 52.8414 Evaluate side-chains 323 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 289 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 0.0970 chunk 173 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 184 optimal weight: 0.0370 chunk 124 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4313 r_free = 0.4313 target = 0.211783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.168744 restraints weight = 18201.585| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.67 r_work: 0.3496 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16176 Z= 0.128 Angle : 0.589 10.962 21944 Z= 0.283 Chirality : 0.040 0.163 2452 Planarity : 0.003 0.033 2740 Dihedral : 4.747 59.760 2246 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.23 % Allowed : 19.27 % Favored : 78.50 % 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: 0.86 (0.19), residues: 1964 helix: 1.54 (0.13), residues: 1364 sheet: -1.00 (0.61), residues: 88 loop : -1.81 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 267 TYR 0.012 0.001 TYR D 439 PHE 0.019 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 0.00279 / 0.13 (16176) covalent geometry : angle 0.58917 / 0.28 (21944) hydrogen bonds : bond 0.03705 / 2.51 ( 1077) hydrogen bonds : angle 4.47870 / 3.35 ( 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 331 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 296 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7564 (ppp) cc_final: 0.7339 (tmm) REVERT: A 323 GLN cc_start: 0.8047 (mt0) cc_final: 0.7841 (mt0) REVERT: A 376 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7837 (mtm) REVERT: A 483 PHE cc_start: 0.7995 (t80) cc_final: 0.7666 (t80) REVERT: A 558 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6211 (t80) REVERT: B 152 MET cc_start: 0.7560 (ppp) cc_final: 0.7292 (tmm) REVERT: B 376 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7901 (mtm) REVERT: B 437 HIS cc_start: 0.7272 (t-170) cc_final: 0.6929 (t-170) REVERT: B 483 PHE cc_start: 0.8013 (t80) cc_final: 0.7711 (t80) REVERT: B 512 MET cc_start: 0.8629 (ptm) cc_final: 0.8363 (ptm) REVERT: B 558 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6123 (t80) REVERT: C 152 MET cc_start: 0.7574 (ppp) cc_final: 0.7328 (tmm) REVERT: C 376 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7911 (mtm) REVERT: C 483 PHE cc_start: 0.8023 (t80) cc_final: 0.7690 (t80) REVERT: D 376 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7850 (mtm) outliers start: 35 outliers final: 28 residues processed: 311 average time/residue: 0.1174 time to fit residues: 57.1947 Evaluate side-chains 321 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 chunk 182 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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 = 0.210653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171202 restraints weight = 18130.975| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.68 r_work: 0.3548 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16176 Z= 0.141 Angle : 0.607 10.722 21944 Z= 0.292 Chirality : 0.041 0.172 2452 Planarity : 0.003 0.033 2740 Dihedral : 4.771 59.772 2246 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.35 % Allowed : 19.21 % Favored : 78.44 % 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: 0.87 (0.19), residues: 1964 helix: 1.54 (0.13), residues: 1364 sheet: -1.05 (0.61), residues: 88 loop : -1.79 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 270 TYR 0.013 0.001 TYR B 439 PHE 0.019 0.001 PHE B 464 TRP 0.008 0.001 TRP A 330 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16176) covalent geometry : angle 0.60669 / 0.29 (21944) hydrogen bonds : bond 0.03751 / 2.54 ( 1077) hydrogen bonds : angle 4.48201 / 3.35 ( 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 329 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 292 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7450 (ppp) cc_final: 0.7183 (tmm) REVERT: A 323 GLN cc_start: 0.8080 (mt0) cc_final: 0.7873 (mt0) REVERT: A 483 PHE cc_start: 0.7957 (t80) cc_final: 0.7651 (t80) REVERT: A 558 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.6374 (t80) REVERT: B 152 MET cc_start: 0.7439 (ppp) cc_final: 0.7174 (tmm) REVERT: B 437 HIS cc_start: 0.7179 (t-170) cc_final: 0.6854 (t-170) REVERT: B 483 PHE cc_start: 0.7979 (t80) cc_final: 0.7662 (t80) REVERT: B 512 MET cc_start: 0.8556 (ptm) cc_final: 0.8345 (ptm) REVERT: B 558 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6155 (t80) REVERT: C 152 MET cc_start: 0.7497 (ppp) cc_final: 0.7223 (tmm) REVERT: C 483 PHE cc_start: 0.7966 (t80) cc_final: 0.7611 (t80) REVERT: D 483 PHE cc_start: 0.7882 (t80) cc_final: 0.7582 (t80) outliers start: 37 outliers final: 30 residues processed: 307 average time/residue: 0.1224 time to fit residues: 58.5787 Evaluate side-chains 315 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 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 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 145 TRP Chi-restraints excluded: chain D residue 147 LEU 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 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: 0.9980 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 ASN ** 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 = 0.4295 r_free = 0.4295 target = 0.209377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.169585 restraints weight = 18141.444| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.69 r_work: 0.3503 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1594 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= 0.160 Angle : 0.620 10.702 21944 Z= 0.299 Chirality : 0.041 0.172 2452 Planarity : 0.004 0.059 2740 Dihedral : 4.785 59.256 2246 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.23 % Allowed : 19.72 % Favored : 78.05 % 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: 1.49 (0.13), residues: 1364 sheet: -1.08 (0.61), residues: 88 loop : -1.76 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 270 TYR 0.013 0.001 TYR B 439 PHE 0.060 0.002 PHE C 186 TRP 0.008 0.001 TRP C 330 HIS 0.004 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (16176) covalent geometry : angle 0.61983 / 0.30 (21944) hydrogen bonds : bond 0.03842 / 2.60 ( 1077) hydrogen bonds : angle 4.50320 / 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 325 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7550 (ppp) cc_final: 0.7302 (tmm) REVERT: A 323 GLN cc_start: 0.8088 (mt0) cc_final: 0.7880 (mt0) REVERT: A 376 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: A 558 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6354 (t80) REVERT: B 152 MET cc_start: 0.7519 (ppp) cc_final: 0.7257 (tmm) REVERT: B 376 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7895 (mtm) REVERT: B 437 HIS cc_start: 0.7303 (t-170) cc_final: 0.6900 (t-170) REVERT: B 558 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6177 (t80) REVERT: C 152 MET cc_start: 0.7560 (ppp) cc_final: 0.7284 (tmm) REVERT: C 376 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7877 (mtm) REVERT: D 376 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7835 (mtm) outliers start: 35 outliers final: 29 residues processed: 301 average time/residue: 0.1128 time to fit residues: 53.5027 Evaluate side-chains 320 residues out of total 1792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 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 145 TRP Chi-restraints excluded: chain D residue 147 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 11 optimal weight: 20.0000 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 126 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 174 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 HIS ** 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** ** D 136 HIS ** 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 = 0.210913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171132 restraints weight = 18033.702| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.67 r_work: 0.3537 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16176 Z= 0.140 Angle : 0.614 10.653 21944 Z= 0.297 Chirality : 0.041 0.172 2452 Planarity : 0.004 0.094 2740 Dihedral : 4.765 58.906 2246 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.29 % Allowed : 20.55 % Favored : 77.16 % 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: 1.04 (0.19), residues: 1964 helix: 1.64 (0.13), residues: 1336 sheet: -1.04 (0.61), residues: 88 loop : -1.45 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 270 TYR 0.011 0.001 TYR B 439 PHE 0.046 0.002 PHE A 186 TRP 0.009 0.001 TRP A 145 HIS 0.003 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16176) covalent geometry : angle 0.61353 / 0.30 (21944) hydrogen bonds : bond 0.03756 / 2.55 ( 1077) hydrogen bonds : angle 4.50558 / 3.35 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.63 seconds wall clock time: 60 minutes 39.87 seconds (3639.87 seconds total)