Starting phenix.real_space_refine on Wed Mar 4 17:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oi2_70502/03_2026/9oi2_70502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oi2_70502/03_2026/9oi2_70502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oi2_70502/03_2026/9oi2_70502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oi2_70502/03_2026/9oi2_70502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oi2_70502/03_2026/9oi2_70502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oi2_70502/03_2026/9oi2_70502.map" } resolution = 2.8 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= 0.017 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 9247 2.51 5 N 2566 2.21 5 O 2769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14649 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2415 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 301} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 11, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1334 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2382 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 12, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2392 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 20, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 11, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1330 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.38, per 1000 atoms: 0.23 Number of scatterers: 14649 At special positions: 0 Unit cell: (96.278, 132.25, 150.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 2769 8.00 N 2566 7.00 C 9247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS B 463 " distance=2.07 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS D 463 " distance=2.04 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 463 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 98 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 664.3 milliseconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 45 sheets defined 22.5% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.905A pdb=" N GLU A 68 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.580A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 Processing helix chain 'B' and resid 400 through 453 removed outlier: 3.564A pdb=" N GLU B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.677A pdb=" N TYR B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 64 through 71 removed outlier: 3.950A pdb=" N GLU C 68 " --> pdb=" O PRO C 65 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU C 69 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE C 71 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 105 removed outlier: 3.632A pdb=" N LEU C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 400 through 453 Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 488 through 495 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 64 through 68 removed outlier: 3.669A pdb=" N GLU E 68 " --> pdb=" O PRO E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'F' and resid 363 through 384 removed outlier: 3.551A pdb=" N LYS F 384 " --> pdb=" O SER F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 452 removed outlier: 3.573A pdb=" N GLU F 431 " --> pdb=" O LEU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 481 Processing helix chain 'F' and resid 484 through 496 removed outlier: 3.735A pdb=" N TYR F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU F 490 " --> pdb=" O PRO F 486 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU F 491 " --> pdb=" O LYS F 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 64 through 67 removed outlier: 4.041A pdb=" N LYS H 67 " --> pdb=" O ALA H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 89 through 93 removed outlier: 4.140A pdb=" N THR H 93 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.023A pdb=" N TYR H 115 " --> pdb=" O MET H 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 111 through 116 removed outlier: 3.801A pdb=" N TYR I 115 " --> pdb=" O MET I 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 30 Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.567A pdb=" N SER L 29 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.018A pdb=" N LEU A 41 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N CYS A 274 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.560A pdb=" N LEU A 50 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 79 " --> pdb=" O ILE A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 114 Processing sheet with id=AA8, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.475A pdb=" N CYS A 135 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AB1, first strand: chain 'A' and resid 160 through 165 Processing sheet with id=AB2, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AB3, first strand: chain 'B' and resid 456 through 458 Processing sheet with id=AB4, first strand: chain 'D' and resid 357 through 362 removed outlier: 3.789A pdb=" N ASN D 354 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 14 through 16 removed outlier: 4.217A pdb=" N ASP C 14 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB7, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB8, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.474A pdb=" N LEU C 41 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N CYS C 274 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.449A pdb=" N LEU C 50 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 79 " --> pdb=" O ILE C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.659A pdb=" N GLU C 171 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU C 175 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.659A pdb=" N GLU C 171 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AC5, first strand: chain 'C' and resid 160 through 165 Processing sheet with id=AC6, first strand: chain 'C' and resid 278 through 279 Processing sheet with id=AC7, first strand: chain 'F' and resid 357 through 362 removed outlier: 6.618A pdb=" N CYS F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AD1, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AD2, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.147A pdb=" N LEU E 41 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N CYS E 274 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 50 through 52 removed outlier: 6.723A pdb=" N LEU E 50 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE E 79 " --> pdb=" O ILE E 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 108 through 110 removed outlier: 6.302A pdb=" N SER E 257 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU E 171 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU E 175 " --> pdb=" O PRO E 250 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 113 through 114 removed outlier: 3.725A pdb=" N GLU E 171 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AD7, first strand: chain 'E' and resid 160 through 165 Processing sheet with id=AD8, first strand: chain 'E' and resid 283 through 285 removed outlier: 3.773A pdb=" N CYS E 278 " --> pdb=" O ILE E 285 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.640A pdb=" N GLY H 10 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.544A pdb=" N GLY I 10 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.536A pdb=" N TRP J 34 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.471A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 23 634 hydrogen bonds defined for protein. 1677 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: 2.68 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4823 1.35 - 1.48: 3907 1.48 - 1.60: 6183 1.60 - 1.73: 0 1.73 - 1.85: 90 Bond restraints: 15003 Sorted by residual: bond pdb=" C ALA D 456 " pdb=" N LYS D 457 " ideal model delta sigma weight residual 1.330 1.445 -0.116 1.32e-02 5.74e+03 7.68e+01 bond pdb=" C LYS D 457 " pdb=" N GLU D 458 " ideal model delta sigma weight residual 1.331 1.419 -0.089 1.37e-02 5.33e+03 4.20e+01 bond pdb=" CA SER C 206 " pdb=" CB SER C 206 " ideal model delta sigma weight residual 1.533 1.476 0.057 1.69e-02 3.50e+03 1.15e+01 bond pdb=" CA TYR A 157 " pdb=" C TYR A 157 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.31e-02 5.83e+03 9.70e+00 bond pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.27e-02 6.20e+03 8.40e+00 ... (remaining 14998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 19979 2.35 - 4.69: 373 4.69 - 7.04: 46 7.04 - 9.39: 12 9.39 - 11.73: 5 Bond angle restraints: 20415 Sorted by residual: angle pdb=" C TYR A 157 " pdb=" CA TYR A 157 " pdb=" CB TYR A 157 " ideal model delta sigma weight residual 110.33 105.33 5.00 1.02e+00 9.61e-01 2.40e+01 angle pdb=" O ALA D 456 " pdb=" C ALA D 456 " pdb=" N LYS D 457 " ideal model delta sigma weight residual 123.17 129.01 -5.84 1.21e+00 6.83e-01 2.33e+01 angle pdb=" C LYS B 449 " pdb=" CA LYS B 449 " pdb=" CB LYS B 449 " ideal model delta sigma weight residual 110.88 103.55 7.33 1.57e+00 4.06e-01 2.18e+01 angle pdb=" N ASN A 293 " pdb=" CA ASN A 293 " pdb=" C ASN A 293 " ideal model delta sigma weight residual 111.87 105.57 6.30 1.41e+00 5.03e-01 2.00e+01 angle pdb=" CA ASN A 159 " pdb=" C ASN A 159 " pdb=" O ASN A 159 " ideal model delta sigma weight residual 121.99 117.32 4.67 1.14e+00 7.69e-01 1.67e+01 ... (remaining 20410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 7471 17.13 - 34.25: 980 34.25 - 51.38: 282 51.38 - 68.50: 73 68.50 - 85.63: 13 Dihedral angle restraints: 8819 sinusoidal: 3282 harmonic: 5537 Sorted by residual: dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 67 " pdb=" CB CYS A 67 " ideal model delta sinusoidal sigma weight residual 93.00 176.19 -83.19 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS C 42 " pdb=" SG CYS C 42 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual -86.00 -8.03 -77.97 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS C 4 " pdb=" SG CYS C 4 " pdb=" SG CYS D 463 " pdb=" CB CYS D 463 " ideal model delta sinusoidal sigma weight residual 93.00 51.35 41.65 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 8816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2216 0.144 - 0.288: 16 0.288 - 0.431: 3 0.431 - 0.575: 0 0.575 - 0.719: 1 Chirality restraints: 2236 Sorted by residual: chirality pdb=" CG LEU H 18 " pdb=" CB LEU H 18 " pdb=" CD1 LEU H 18 " pdb=" CD2 LEU H 18 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA PHE B 464 " pdb=" N PHE B 464 " pdb=" C PHE B 464 " pdb=" CB PHE B 464 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA VAL D 344 " pdb=" N VAL D 344 " pdb=" C VAL D 344 " pdb=" CB VAL D 344 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 2233 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 19 " -0.594 9.50e-02 1.11e+02 2.66e-01 4.33e+01 pdb=" NE ARG H 19 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG H 19 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG H 19 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 19 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 382 " 0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C ILE D 382 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE D 382 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU D 383 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 207 " 0.378 9.50e-02 1.11e+02 1.69e-01 1.76e+01 pdb=" NE ARG A 207 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 207 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 207 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 207 " 0.013 2.00e-02 2.50e+03 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 382 2.69 - 3.24: 12985 3.24 - 3.79: 23120 3.79 - 4.35: 30687 4.35 - 4.90: 52527 Nonbonded interactions: 119701 Sorted by model distance: nonbonded pdb=" OG SER A 308 " pdb=" OE2 GLU B 423 " model vdw 2.134 3.040 nonbonded pdb=" O SER C 107 " pdb=" OG SER C 107 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR E 7 " pdb=" O ILE F 332 " model vdw 2.170 3.040 nonbonded pdb=" N GLN L 16 " pdb=" OE1 GLN L 16 " model vdw 2.175 3.120 nonbonded pdb=" OE1 GLN E 104 " pdb=" NH2 ARG E 258 " model vdw 2.194 3.120 ... (remaining 119696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 through 169 or (resid 170 thro \ ugh 171 and (name N or name CA or name C or name O or name CB )) or resid 172 th \ rough 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) \ or resid 185 through 211 or (resid 212 and (name N or name CA or name C or name \ O or name CB )) or resid 213 through 220 or (resid 221 through 223 and (name N \ or name CA or name C or name O or name CB )) or resid 224 through 259 or resid 2 \ 62 through 270 or (resid 271 through 273 and (name N or name CA or name C or nam \ e O or name CB )) or resid 274 through 321)) selection = (chain 'C' and (resid 1 through 211 or (resid 212 and (name N or name CA or name \ C or name O or name CB )) or resid 213 through 270 or (resid 271 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 through 321) \ ) selection = (chain 'E' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 183 or (resid 184 and (name N or na \ me CA or name C or name O or name CB )) or resid 185 through 272 or (resid 273 a \ nd (name N or name CA or name C or name O or name CB )) or resid 274 through 321 \ )) } ncs_group { reference = (chain 'B' and (resid 328 through 382 or (resid 383 and (name N or name CA or na \ me C or name O or name CB )) or resid 384 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 394 or (resid \ 395 and (name N or name CA or name C or name O or name CB )) or resid 396 throug \ h 468 or (resid 469 and (name N or name CA or name C or name O or name CB )) or \ resid 470 through 496)) selection = (chain 'D' and (resid 328 through 354 or (resid 355 and (name N or name CA or na \ me C or name O or name CB )) or resid 356 through 382 or (resid 383 and (name N \ or name CA or name C or name O or name CB )) or resid 384 through 496)) selection = (chain 'F' and (resid 328 through 336 or (resid 337 and (name N or name CA or na \ me C or name O or name CB )) or resid 338 through 354 or (resid 355 and (name N \ or name CA or name C or name O or name CB )) or resid 356 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 throug \ h 496)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.006 0.116 15020 Z= 0.294 Angle : 0.767 11.733 20449 Z= 0.444 Chirality : 0.051 0.719 2236 Planarity : 0.008 0.266 2649 Dihedral : 17.169 85.626 5240 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 2.57 % Allowed : 30.39 % Favored : 67.04 % Cbeta Deviations : 0.06 % 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: -0.27 (0.19), residues: 1900 helix: 1.39 (0.27), residues: 378 sheet: 0.24 (0.24), residues: 455 loop : -0.97 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 496 TYR 0.019 0.002 TYR B 348 PHE 0.015 0.002 PHE C 111 TRP 0.016 0.001 TRP F 347 HIS 0.007 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00562 (15003) covalent geometry : angle 0.76400 (20415) SS BOND : bond 0.01073 ( 17) SS BOND : angle 1.92792 ( 34) hydrogen bonds : bond 0.14083 ( 614) hydrogen bonds : angle 6.44092 ( 1677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 303 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 100 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7459 (tm-30) REVERT: A 203 SER cc_start: 0.8377 (m) cc_final: 0.7986 (p) REVERT: B 465 GLU cc_start: 0.7533 (tp30) cc_final: 0.7219 (tp30) REVERT: C 168 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8163 (mttm) REVERT: D 343 MET cc_start: 0.8679 (ttp) cc_final: 0.8461 (ttp) REVERT: D 383 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: D 429 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6764 (mt-10) outliers start: 39 outliers final: 24 residues processed: 332 average time/residue: 0.6750 time to fit residues: 243.0622 Evaluate side-chains 326 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 348 TYR Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 451 GLN C 268 ASN D 397 ASN D 451 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104305 restraints weight = 21292.513| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.81 r_work: 0.3240 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15020 Z= 0.156 Angle : 0.567 10.754 20449 Z= 0.291 Chirality : 0.043 0.140 2236 Planarity : 0.004 0.043 2649 Dihedral : 6.016 59.971 2127 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.21 % Allowed : 26.25 % Favored : 69.54 % 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: 0.06 (0.19), residues: 1900 helix: 1.87 (0.27), residues: 382 sheet: 0.31 (0.24), residues: 487 loop : -0.80 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 496 TYR 0.012 0.001 TYR D 350 PHE 0.014 0.002 PHE B 335 TRP 0.010 0.001 TRP F 347 HIS 0.004 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00368 (15003) covalent geometry : angle 0.56460 (20415) SS BOND : bond 0.00476 ( 17) SS BOND : angle 1.47704 ( 34) hydrogen bonds : bond 0.04672 ( 614) hydrogen bonds : angle 4.94382 ( 1677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 310 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7598 (tptm) REVERT: A 160 LEU cc_start: 0.8095 (tp) cc_final: 0.7868 (pp) REVERT: B 449 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8351 (mtmt) REVERT: C 204 HIS cc_start: 0.8551 (m-70) cc_final: 0.8287 (m90) REVERT: C 206 SER cc_start: 0.8492 (t) cc_final: 0.8247 (p) REVERT: D 343 MET cc_start: 0.8608 (ttp) cc_final: 0.8407 (ttp) REVERT: F 423 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7579 (mt-10) REVERT: H 118 LEU cc_start: 0.8365 (mt) cc_final: 0.8019 (mt) REVERT: I 85 MET cc_start: 0.7311 (mtt) cc_final: 0.7038 (mtt) REVERT: I 99 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7301 (p) REVERT: J 72 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7078 (tt) outliers start: 64 outliers final: 32 residues processed: 344 average time/residue: 0.6169 time to fit residues: 230.4651 Evaluate side-chains 336 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 348 TYR Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 36 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 GLN C 268 ASN D 495 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102574 restraints weight = 21553.814| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.83 r_work: 0.3216 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15020 Z= 0.208 Angle : 0.574 10.660 20449 Z= 0.295 Chirality : 0.044 0.142 2236 Planarity : 0.004 0.041 2649 Dihedral : 5.235 58.615 2095 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.95 % Allowed : 26.12 % Favored : 69.93 % 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: 0.05 (0.19), residues: 1900 helix: 1.91 (0.27), residues: 384 sheet: 0.23 (0.24), residues: 472 loop : -0.79 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 496 TYR 0.023 0.002 TYR B 445 PHE 0.017 0.002 PHE B 335 TRP 0.009 0.001 TRP I 121 HIS 0.004 0.001 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00497 (15003) covalent geometry : angle 0.57149 (20415) SS BOND : bond 0.00664 ( 17) SS BOND : angle 1.53479 ( 34) hydrogen bonds : bond 0.04711 ( 614) hydrogen bonds : angle 4.84271 ( 1677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7616 (tptm) REVERT: B 445 TYR cc_start: 0.8630 (t80) cc_final: 0.8406 (t80) REVERT: B 449 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8325 (mtmt) REVERT: C 204 HIS cc_start: 0.8585 (m-70) cc_final: 0.8334 (m90) REVERT: C 206 SER cc_start: 0.8477 (t) cc_final: 0.8261 (p) REVERT: D 343 MET cc_start: 0.8636 (ttp) cc_final: 0.8435 (mtp) REVERT: H 21 SER cc_start: 0.8314 (p) cc_final: 0.8075 (p) REVERT: H 118 LEU cc_start: 0.8412 (mt) cc_final: 0.8060 (mt) REVERT: I 85 MET cc_start: 0.7347 (mtt) cc_final: 0.7028 (mtt) REVERT: I 99 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7388 (p) REVERT: J 72 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7088 (tt) outliers start: 60 outliers final: 34 residues processed: 354 average time/residue: 0.6672 time to fit residues: 256.1351 Evaluate side-chains 353 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 316 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 89 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 179 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 144 optimal weight: 0.0570 chunk 111 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 140 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 451 GLN C 268 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN F 386 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103876 restraints weight = 21481.468| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.82 r_work: 0.3241 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15020 Z= 0.119 Angle : 0.524 9.268 20449 Z= 0.269 Chirality : 0.042 0.132 2236 Planarity : 0.004 0.044 2649 Dihedral : 4.915 58.969 2092 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.01 % Allowed : 26.51 % Favored : 69.47 % 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: 0.22 (0.19), residues: 1900 helix: 2.09 (0.27), residues: 384 sheet: 0.32 (0.25), residues: 468 loop : -0.68 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 307 TYR 0.019 0.001 TYR B 445 PHE 0.012 0.001 PHE C 111 TRP 0.009 0.001 TRP F 418 HIS 0.004 0.001 HIS F 352 Details of bonding type rmsd covalent geometry : bond 0.00278 (15003) covalent geometry : angle 0.52189 (20415) SS BOND : bond 0.00577 ( 17) SS BOND : angle 1.30068 ( 34) hydrogen bonds : bond 0.04166 ( 614) hydrogen bonds : angle 4.68815 ( 1677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 323 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7556 (tptm) REVERT: B 445 TYR cc_start: 0.8589 (t80) cc_final: 0.8319 (t80) REVERT: C 22 LYS cc_start: 0.8359 (mttt) cc_final: 0.8138 (mttt) REVERT: C 168 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8135 (mttm) REVERT: C 204 HIS cc_start: 0.8551 (m-70) cc_final: 0.8298 (m90) REVERT: C 206 SER cc_start: 0.8450 (t) cc_final: 0.8234 (p) REVERT: C 231 THR cc_start: 0.8942 (t) cc_final: 0.8727 (t) REVERT: D 343 MET cc_start: 0.8639 (ttp) cc_final: 0.8423 (mtp) REVERT: D 429 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7037 (mt-10) REVERT: F 429 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: H 21 SER cc_start: 0.8251 (p) cc_final: 0.8033 (p) REVERT: H 118 LEU cc_start: 0.8361 (mt) cc_final: 0.8014 (mt) REVERT: I 85 MET cc_start: 0.7379 (mtt) cc_final: 0.7110 (mtt) REVERT: I 99 THR cc_start: 0.7554 (OUTLIER) cc_final: 0.7324 (p) REVERT: J 72 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7031 (tt) outliers start: 61 outliers final: 35 residues processed: 356 average time/residue: 0.6655 time to fit residues: 257.0427 Evaluate side-chains 356 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 348 TYR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 97 optimal weight: 2.9990 chunk 140 optimal weight: 0.0870 chunk 139 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 172 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 0.0980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 451 GLN B 461 ASN C 28 HIS C 268 ASN D 451 GLN D 495 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103435 restraints weight = 21526.940| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.84 r_work: 0.3231 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15020 Z= 0.143 Angle : 0.546 9.217 20449 Z= 0.278 Chirality : 0.042 0.266 2236 Planarity : 0.004 0.044 2649 Dihedral : 4.697 59.753 2090 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.41 % Allowed : 25.92 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1900 helix: 2.06 (0.27), residues: 384 sheet: 0.35 (0.25), residues: 468 loop : -0.63 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.018 0.001 TYR B 445 PHE 0.013 0.001 PHE B 335 TRP 0.009 0.001 TRP F 418 HIS 0.008 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00339 (15003) covalent geometry : angle 0.54346 (20415) SS BOND : bond 0.00622 ( 17) SS BOND : angle 1.50295 ( 34) hydrogen bonds : bond 0.04202 ( 614) hydrogen bonds : angle 4.68693 ( 1677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7614 (tptm) REVERT: A 190 LEU cc_start: 0.8756 (mt) cc_final: 0.8508 (mp) REVERT: B 445 TYR cc_start: 0.8578 (t80) cc_final: 0.8340 (t80) REVERT: C 22 LYS cc_start: 0.8365 (mttt) cc_final: 0.8140 (mttt) REVERT: C 168 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8148 (mttm) REVERT: C 204 HIS cc_start: 0.8544 (m-70) cc_final: 0.8263 (m90) REVERT: C 206 SER cc_start: 0.8387 (t) cc_final: 0.8165 (p) REVERT: D 343 MET cc_start: 0.8611 (ttp) cc_final: 0.8400 (mtp) REVERT: D 429 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7047 (mt-10) REVERT: D 449 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8477 (ttmt) REVERT: F 429 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: H 21 SER cc_start: 0.8252 (p) cc_final: 0.8033 (p) REVERT: H 118 LEU cc_start: 0.8402 (mt) cc_final: 0.8049 (mt) REVERT: I 85 MET cc_start: 0.7400 (mtt) cc_final: 0.7168 (mtt) REVERT: I 99 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7313 (p) REVERT: J 72 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7020 (tt) outliers start: 67 outliers final: 39 residues processed: 351 average time/residue: 0.6597 time to fit residues: 251.1358 Evaluate side-chains 363 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 348 TYR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 429 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 185 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 76 optimal weight: 0.0770 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 451 GLN B 461 ASN C 28 HIS C 268 ASN D 451 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103110 restraints weight = 21371.582| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.83 r_work: 0.3230 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15020 Z= 0.159 Angle : 0.564 10.766 20449 Z= 0.286 Chirality : 0.043 0.272 2236 Planarity : 0.004 0.045 2649 Dihedral : 4.592 59.596 2087 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.41 % Allowed : 26.38 % Favored : 69.21 % 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: 0.26 (0.19), residues: 1900 helix: 2.05 (0.27), residues: 384 sheet: 0.36 (0.25), residues: 468 loop : -0.63 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.018 0.001 TYR B 445 PHE 0.014 0.001 PHE B 335 TRP 0.008 0.001 TRP I 47 HIS 0.009 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00381 (15003) covalent geometry : angle 0.55998 (20415) SS BOND : bond 0.00690 ( 17) SS BOND : angle 1.69549 ( 34) hydrogen bonds : bond 0.04241 ( 614) hydrogen bonds : angle 4.69378 ( 1677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7574 (tptm) REVERT: A 190 LEU cc_start: 0.8784 (mt) cc_final: 0.8531 (mp) REVERT: B 445 TYR cc_start: 0.8576 (t80) cc_final: 0.8330 (t80) REVERT: C 22 LYS cc_start: 0.8372 (mttt) cc_final: 0.8151 (mttt) REVERT: C 168 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8153 (mttm) REVERT: C 204 HIS cc_start: 0.8578 (m-70) cc_final: 0.8318 (m90) REVERT: C 206 SER cc_start: 0.8384 (t) cc_final: 0.8158 (p) REVERT: D 449 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8483 (ttmt) REVERT: H 21 SER cc_start: 0.8240 (p) cc_final: 0.8020 (p) REVERT: H 118 LEU cc_start: 0.8412 (mt) cc_final: 0.8060 (mt) REVERT: I 85 MET cc_start: 0.7317 (mtt) cc_final: 0.7111 (mtt) REVERT: I 99 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7308 (p) REVERT: I 129 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.6783 (p) REVERT: J 72 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7010 (tt) outliers start: 67 outliers final: 44 residues processed: 351 average time/residue: 0.6678 time to fit residues: 253.8862 Evaluate side-chains 353 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 348 TYR Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 384 LYS Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 66 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 160 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 28 HIS C 268 ASN D 451 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103280 restraints weight = 21387.713| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.83 r_work: 0.3229 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15020 Z= 0.165 Angle : 0.563 10.951 20449 Z= 0.287 Chirality : 0.043 0.260 2236 Planarity : 0.004 0.045 2649 Dihedral : 4.392 58.991 2084 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.41 % Allowed : 26.51 % Favored : 69.08 % 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: 0.25 (0.19), residues: 1900 helix: 2.00 (0.27), residues: 384 sheet: 0.36 (0.25), residues: 468 loop : -0.61 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 216 TYR 0.017 0.001 TYR B 445 PHE 0.014 0.001 PHE B 335 TRP 0.009 0.001 TRP D 340 HIS 0.008 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00395 (15003) covalent geometry : angle 0.55927 (20415) SS BOND : bond 0.00696 ( 17) SS BOND : angle 1.58561 ( 34) hydrogen bonds : bond 0.04293 ( 614) hydrogen bonds : angle 4.69724 ( 1677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 310 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 119 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7599 (tptm) REVERT: A 190 LEU cc_start: 0.8817 (mt) cc_final: 0.8551 (mp) REVERT: A 251 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7898 (ttt90) REVERT: B 445 TYR cc_start: 0.8554 (t80) cc_final: 0.8309 (t80) REVERT: C 22 LYS cc_start: 0.8390 (mttt) cc_final: 0.8169 (mttt) REVERT: C 168 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8146 (mttm) REVERT: C 204 HIS cc_start: 0.8554 (m-70) cc_final: 0.8302 (m90) REVERT: C 206 SER cc_start: 0.8350 (t) cc_final: 0.8132 (p) REVERT: H 21 SER cc_start: 0.8242 (p) cc_final: 0.8022 (p) REVERT: H 85 MET cc_start: 0.8015 (mtp) cc_final: 0.7751 (tpp) REVERT: H 118 LEU cc_start: 0.8421 (mt) cc_final: 0.8053 (mt) REVERT: I 129 VAL cc_start: 0.7262 (OUTLIER) cc_final: 0.6788 (p) REVERT: J 72 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7003 (tt) outliers start: 67 outliers final: 44 residues processed: 346 average time/residue: 0.6688 time to fit residues: 251.3901 Evaluate side-chains 350 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 160 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 116 optimal weight: 0.0060 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 100 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN C 28 HIS C 268 ASN D 451 GLN E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103564 restraints weight = 21404.558| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.82 r_work: 0.3235 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15020 Z= 0.137 Angle : 0.547 9.770 20449 Z= 0.280 Chirality : 0.042 0.223 2236 Planarity : 0.003 0.045 2649 Dihedral : 4.347 59.096 2084 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.75 % Allowed : 27.17 % Favored : 69.08 % 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: 0.32 (0.19), residues: 1900 helix: 2.12 (0.27), residues: 384 sheet: 0.29 (0.24), residues: 486 loop : -0.54 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 216 TYR 0.016 0.001 TYR B 445 PHE 0.012 0.001 PHE B 335 TRP 0.008 0.001 TRP D 340 HIS 0.007 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00328 (15003) covalent geometry : angle 0.54472 (20415) SS BOND : bond 0.00650 ( 17) SS BOND : angle 1.44307 ( 34) hydrogen bonds : bond 0.04115 ( 614) hydrogen bonds : angle 4.64827 ( 1677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8150 (mt-10) REVERT: A 190 LEU cc_start: 0.8812 (mt) cc_final: 0.8556 (mp) REVERT: A 251 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7916 (ttt90) REVERT: A 298 THR cc_start: 0.8189 (p) cc_final: 0.7969 (m) REVERT: B 445 TYR cc_start: 0.8573 (t80) cc_final: 0.8303 (t80) REVERT: C 22 LYS cc_start: 0.8368 (mttt) cc_final: 0.8138 (mttt) REVERT: C 168 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8156 (mttm) REVERT: C 204 HIS cc_start: 0.8547 (m-70) cc_final: 0.8295 (m90) REVERT: C 206 SER cc_start: 0.8339 (t) cc_final: 0.8117 (p) REVERT: D 424 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8278 (tp) REVERT: D 449 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8477 (ttmt) REVERT: F 403 MET cc_start: 0.8155 (mmp) cc_final: 0.7913 (mmt) REVERT: H 21 SER cc_start: 0.8223 (p) cc_final: 0.7993 (p) REVERT: H 97 TYR cc_start: 0.8350 (m-80) cc_final: 0.8087 (m-80) REVERT: H 118 LEU cc_start: 0.8394 (mt) cc_final: 0.8040 (mt) REVERT: I 129 VAL cc_start: 0.7235 (OUTLIER) cc_final: 0.6764 (p) REVERT: J 72 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6986 (tt) REVERT: L 45 LEU cc_start: 0.8830 (tp) cc_final: 0.8544 (tt) outliers start: 57 outliers final: 43 residues processed: 343 average time/residue: 0.6738 time to fit residues: 250.4971 Evaluate side-chains 355 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 307 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 177 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 451 GLN B 461 ASN C 28 HIS C 268 ASN D 451 GLN D 495 ASN E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102960 restraints weight = 21462.600| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.82 r_work: 0.3221 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15020 Z= 0.173 Angle : 0.575 10.728 20449 Z= 0.292 Chirality : 0.043 0.222 2236 Planarity : 0.004 0.045 2649 Dihedral : 4.408 58.855 2084 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.75 % Allowed : 27.04 % Favored : 69.21 % 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: 0.32 (0.19), residues: 1900 helix: 2.12 (0.27), residues: 384 sheet: 0.36 (0.25), residues: 468 loop : -0.57 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 216 TYR 0.024 0.001 TYR A 197 PHE 0.015 0.002 PHE B 335 TRP 0.013 0.001 TRP D 340 HIS 0.008 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00415 (15003) covalent geometry : angle 0.57220 (20415) SS BOND : bond 0.00662 ( 17) SS BOND : angle 1.59439 ( 34) hydrogen bonds : bond 0.04308 ( 614) hydrogen bonds : angle 4.68752 ( 1677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 310 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7395 (tm-30) REVERT: A 115 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8137 (mt-10) REVERT: A 119 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7580 (tptm) REVERT: A 190 LEU cc_start: 0.8824 (mt) cc_final: 0.8566 (mp) REVERT: A 251 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7914 (ttt90) REVERT: A 285 ILE cc_start: 0.8554 (mt) cc_final: 0.8312 (mp) REVERT: B 403 MET cc_start: 0.8231 (mmm) cc_final: 0.8005 (mmt) REVERT: B 445 TYR cc_start: 0.8538 (t80) cc_final: 0.8285 (t80) REVERT: C 22 LYS cc_start: 0.8378 (mttt) cc_final: 0.8148 (mttt) REVERT: C 168 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8132 (mttm) REVERT: C 204 HIS cc_start: 0.8570 (m-70) cc_final: 0.8359 (m90) REVERT: C 206 SER cc_start: 0.8334 (t) cc_final: 0.8119 (p) REVERT: D 403 MET cc_start: 0.8355 (mmm) cc_final: 0.8129 (mmm) REVERT: D 424 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8270 (tp) REVERT: D 449 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8437 (ttmt) REVERT: H 21 SER cc_start: 0.8239 (p) cc_final: 0.8016 (p) REVERT: H 85 MET cc_start: 0.7946 (mtp) cc_final: 0.7664 (tpp) REVERT: H 118 LEU cc_start: 0.8427 (mt) cc_final: 0.8062 (mt) REVERT: I 129 VAL cc_start: 0.7258 (OUTLIER) cc_final: 0.6782 (p) REVERT: J 72 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6974 (tt) REVERT: L 45 LEU cc_start: 0.8821 (tp) cc_final: 0.8570 (tt) outliers start: 57 outliers final: 42 residues processed: 342 average time/residue: 0.6701 time to fit residues: 248.7463 Evaluate side-chains 356 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 308 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 133 optimal weight: 0.0970 chunk 160 optimal weight: 0.0970 chunk 9 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.0870 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 451 GLN B 461 ASN C 28 HIS C 268 ASN D 451 GLN E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104853 restraints weight = 21421.719| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.82 r_work: 0.3255 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15020 Z= 0.105 Angle : 0.536 10.262 20449 Z= 0.272 Chirality : 0.042 0.181 2236 Planarity : 0.003 0.045 2649 Dihedral : 4.236 57.976 2084 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.16 % Allowed : 27.70 % Favored : 69.14 % 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: 0.42 (0.19), residues: 1900 helix: 2.30 (0.27), residues: 384 sheet: 0.29 (0.25), residues: 476 loop : -0.48 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.022 0.001 TYR A 197 PHE 0.010 0.001 PHE C 111 TRP 0.009 0.001 TRP D 340 HIS 0.007 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00243 (15003) covalent geometry : angle 0.53350 (20415) SS BOND : bond 0.00602 ( 17) SS BOND : angle 1.25845 ( 34) hydrogen bonds : bond 0.03838 ( 614) hydrogen bonds : angle 4.58031 ( 1677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7414 (tm-30) REVERT: A 119 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7579 (tptm) REVERT: A 190 LEU cc_start: 0.8793 (mt) cc_final: 0.8529 (mp) REVERT: A 285 ILE cc_start: 0.8474 (mt) cc_final: 0.8256 (mp) REVERT: B 445 TYR cc_start: 0.8508 (t80) cc_final: 0.8296 (t80) REVERT: C 22 LYS cc_start: 0.8377 (mttt) cc_final: 0.8130 (mttm) REVERT: C 168 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8121 (mttm) REVERT: C 204 HIS cc_start: 0.8523 (m-70) cc_final: 0.8272 (m90) REVERT: C 206 SER cc_start: 0.8320 (t) cc_final: 0.8086 (p) REVERT: C 231 THR cc_start: 0.8961 (t) cc_final: 0.8752 (t) REVERT: D 424 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8271 (tp) REVERT: D 429 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7014 (mt-10) REVERT: D 449 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8485 (ttmt) REVERT: E 317 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8346 (mt) REVERT: H 21 SER cc_start: 0.8204 (p) cc_final: 0.7972 (p) REVERT: H 85 MET cc_start: 0.7924 (mtp) cc_final: 0.7631 (tpp) REVERT: H 97 TYR cc_start: 0.8299 (m-80) cc_final: 0.8078 (m-80) REVERT: H 118 LEU cc_start: 0.8351 (mt) cc_final: 0.7993 (mt) REVERT: I 129 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6756 (p) REVERT: J 72 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6932 (tt) REVERT: L 45 LEU cc_start: 0.8776 (tp) cc_final: 0.8513 (tt) outliers start: 48 outliers final: 30 residues processed: 345 average time/residue: 0.6635 time to fit residues: 248.5566 Evaluate side-chains 345 residues out of total 1655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 348 TYR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 149 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.0020 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 451 GLN C 28 HIS C 268 ASN D 451 GLN D 495 ASN E 266 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 ASN ** F 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102605 restraints weight = 21363.545| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.82 r_work: 0.3239 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15020 Z= 0.205 Angle : 0.602 12.434 20449 Z= 0.306 Chirality : 0.044 0.212 2236 Planarity : 0.004 0.045 2649 Dihedral : 4.444 59.408 2084 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.76 % Allowed : 28.42 % Favored : 68.82 % 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: 0.32 (0.19), residues: 1900 helix: 2.08 (0.27), residues: 385 sheet: 0.39 (0.25), residues: 462 loop : -0.57 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 216 TYR 0.024 0.002 TYR A 197 PHE 0.016 0.002 PHE B 335 TRP 0.021 0.001 TRP D 340 HIS 0.007 0.001 HIS C 28 Details of bonding type rmsd covalent geometry : bond 0.00493 (15003) covalent geometry : angle 0.59848 (20415) SS BOND : bond 0.00701 ( 17) SS BOND : angle 1.62733 ( 34) hydrogen bonds : bond 0.04454 ( 614) hydrogen bonds : angle 4.69937 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5648.70 seconds wall clock time: 96 minutes 57.32 seconds (5817.32 seconds total)