Starting phenix.real_space_refine on Thu Feb 5 09:50:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uy9_64607/02_2026/9uy9_64607.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uy9_64607/02_2026/9uy9_64607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uy9_64607/02_2026/9uy9_64607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uy9_64607/02_2026/9uy9_64607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uy9_64607/02_2026/9uy9_64607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uy9_64607/02_2026/9uy9_64607.map" } resolution = 3.5 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= -0.000 sd= 0.003 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 53 5.16 5 C 10117 2.51 5 N 2802 2.21 5 O 3179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16151 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 3819 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 17, 'TRANS': 533} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 778 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 18, 'ASP:plan': 8, 'PHE:plan': 4, 'GLN:plan1': 15, 'ASN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 356 Chain: "B" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 3825 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 17, 'TRANS': 533} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 613 Unresolved non-hydrogen angles: 773 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 17, 'ASP:plan': 8, 'PHE:plan': 4, 'GLN:plan1': 14, 'ASN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 348 Chain: "C" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 3809 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 17, 'TRANS': 533} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 628 Unresolved non-hydrogen angles: 792 Unresolved non-hydrogen dihedrals: 502 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 18, 'ASP:plan': 10, 'PHE:plan': 4, 'GLN:plan1': 14, 'ASN:plan1': 8, 'HIS:plan': 6, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 351 Chain: "H" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 859 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 859 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 859 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 707 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "M" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 707 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "N" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 707 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 96} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 3.67, per 1000 atoms: 0.23 Number of scatterers: 16151 At special positions: 0 Unit cell: (148.072, 156.704, 174.632, 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 53 16.00 O 3179 8.00 N 2802 7.00 C 10117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 206 " distance=2.33 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS B 206 " distance=2.04 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 206 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.52 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 87 " distance=2.52 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 87 " distance=2.52 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: 1.54 Conformation dependent library (CDL) restraints added in 764.7 milliseconds 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 33 sheets defined 14.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 148 through 152 removed outlier: 4.237A pdb=" N GLY A 151 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.061A pdb=" N GLU A 356 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 503 Processing helix chain 'A' and resid 506 through 516 removed outlier: 3.637A pdb=" N VAL A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 removed outlier: 4.115A pdb=" N TYR A 613 " --> pdb=" O TYR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 682 removed outlier: 3.728A pdb=" N LEU A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 342 through 358 removed outlier: 4.493A pdb=" N GLN B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 356 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 503 Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.613A pdb=" N VAL B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 removed outlier: 4.317A pdb=" N TYR B 613 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 657 Processing helix chain 'B' and resid 661 through 682 removed outlier: 3.514A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 679 " --> pdb=" O ASN B 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 343 through 359 removed outlier: 3.850A pdb=" N GLU C 356 " --> pdb=" O HIS C 352 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 503 Processing helix chain 'C' and resid 506 through 516 removed outlier: 3.669A pdb=" N VAL C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 657 Processing helix chain 'C' and resid 661 through 682 removed outlier: 3.714A pdb=" N LEU C 679 " --> pdb=" O ASN C 675 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 301 removed outlier: 6.731A pdb=" N VAL A 84 " --> pdb=" O TRP A 300 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 81 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 379 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 370 " --> pdb=" O TRP A 382 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.695A pdb=" N PHE A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 230 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 removed outlier: 4.172A pdb=" N ARG A 179 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 210 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 183 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS A 206 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS A 95 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS A 287 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 99 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 283 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 282 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 284 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 286 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.557A pdb=" N VAL A 145 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 309 Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 301 removed outlier: 3.828A pdb=" N TRP B 300 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 84 " --> pdb=" O TRP B 300 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 379 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP B 382 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR B 370 " --> pdb=" O TRP B 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 125 removed outlier: 3.578A pdb=" N LYS B 101 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 182 removed outlier: 4.083A pdb=" N ARG B 179 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 210 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LYS B 95 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 287 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 99 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 283 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP B 286 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'B' and resid 307 through 309 Processing sheet with id=AB4, first strand: chain 'B' and resid 364 through 365 removed outlier: 3.709A pdb=" N LYS B 364 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 386 " --> pdb=" O LYS B 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 297 through 301 removed outlier: 6.782A pdb=" N VAL C 84 " --> pdb=" O TRP C 300 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 81 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 379 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 372 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 370 " --> pdb=" O TRP C 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 124 through 125 removed outlier: 3.575A pdb=" N LYS C 101 " --> pdb=" O PHE C 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 179 through 182 removed outlier: 4.063A pdb=" N ARG C 179 " --> pdb=" O ASP C 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP C 210 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LYS C 95 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS C 287 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 99 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C 283 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 286 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU C 272 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN C 256 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 274 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB9, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.708A pdb=" N VAL C 145 " --> pdb=" O TYR C 156 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 156 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET C 147 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 154 " --> pdb=" O MET C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 307 through 309 Processing sheet with id=AC2, first strand: chain 'C' and resid 364 through 365 removed outlier: 3.676A pdb=" N LYS C 364 " --> pdb=" O THR C 386 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 520 through 523 Processing sheet with id=AC4, first strand: chain 'H' and resid 9 through 10 removed outlier: 6.872A pdb=" N ILE H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.612A pdb=" N MET H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 9 through 10 removed outlier: 6.872A pdb=" N ILE I 34 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.612A pdb=" N MET I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 9 through 10 removed outlier: 6.872A pdb=" N ILE J 34 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.612A pdb=" N MET J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.530A pdb=" N SER L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.665A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR L 84 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 101 " --> pdb=" O TYR L 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 4 through 5 removed outlier: 3.531A pdb=" N SER M 69 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 43 through 47 removed outlier: 6.666A pdb=" N TRP M 34 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR M 84 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR M 101 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 4 through 5 removed outlier: 3.530A pdb=" N SER N 69 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 43 through 47 removed outlier: 6.666A pdb=" N TRP N 34 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR N 84 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR N 101 " --> pdb=" O TYR N 85 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1497 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: 2.73 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5432 1.35 - 1.47: 4345 1.47 - 1.59: 6636 1.59 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 16495 Sorted by residual: bond pdb=" CA THR L 50 " pdb=" C THR L 50 " ideal model delta sigma weight residual 1.519 1.493 0.026 1.01e-02 9.80e+03 6.77e+00 bond pdb=" N CYS B 141 " pdb=" CA CYS B 141 " ideal model delta sigma weight residual 1.456 1.475 -0.019 1.21e-02 6.83e+03 2.40e+00 bond pdb=" CA CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sigma weight residual 1.531 1.553 -0.022 1.52e-02 4.33e+03 2.11e+00 bond pdb=" N TYR L 48 " pdb=" CA TYR L 48 " ideal model delta sigma weight residual 1.456 1.474 -0.018 1.33e-02 5.65e+03 1.76e+00 bond pdb=" N SER L 51 " pdb=" CA SER L 51 " ideal model delta sigma weight residual 1.459 1.448 0.011 9.10e-03 1.21e+04 1.48e+00 ... (remaining 16490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 22256 2.06 - 4.11: 257 4.11 - 6.17: 50 6.17 - 8.23: 11 8.23 - 10.28: 2 Bond angle restraints: 22576 Sorted by residual: angle pdb=" N THR L 50 " pdb=" CA THR L 50 " pdb=" C THR L 50 " ideal model delta sigma weight residual 112.72 102.90 9.82 1.28e+00 6.10e-01 5.88e+01 angle pdb=" N SER L 51 " pdb=" CA SER L 51 " pdb=" C SER L 51 " ideal model delta sigma weight residual 112.99 105.45 7.54 1.61e+00 3.86e-01 2.19e+01 angle pdb=" N TYR L 48 " pdb=" CA TYR L 48 " pdb=" C TYR L 48 " ideal model delta sigma weight residual 113.23 118.12 -4.89 1.24e+00 6.50e-01 1.56e+01 angle pdb=" N GLU C 195 " pdb=" CA GLU C 195 " pdb=" C GLU C 195 " ideal model delta sigma weight residual 113.20 108.59 4.61 1.21e+00 6.83e-01 1.45e+01 angle pdb=" N GLN N 88 " pdb=" CA GLN N 88 " pdb=" C GLN N 88 " ideal model delta sigma weight residual 108.99 114.48 -5.49 1.57e+00 4.06e-01 1.22e+01 ... (remaining 22571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8491 17.89 - 35.78: 865 35.78 - 53.67: 205 53.67 - 71.56: 21 71.56 - 89.44: 10 Dihedral angle restraints: 9592 sinusoidal: 2862 harmonic: 6730 Sorted by residual: dihedral pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " pdb=" SG CYS A 206 " pdb=" CB CYS A 206 " ideal model delta sinusoidal sigma weight residual -86.00 -160.82 74.82 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 87 " pdb=" CB CYS N 87 " ideal model delta sinusoidal sigma weight residual -86.00 -122.94 36.94 1 1.00e+01 1.00e-02 1.93e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 87 " pdb=" CB CYS L 87 " ideal model delta sinusoidal sigma weight residual -86.00 -122.89 36.89 1 1.00e+01 1.00e-02 1.92e+01 ... (remaining 9589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1947 0.038 - 0.075: 421 0.075 - 0.113: 201 0.113 - 0.150: 22 0.150 - 0.188: 1 Chirality restraints: 2592 Sorted by residual: chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CG LEU C 380 " pdb=" CB LEU C 380 " pdb=" CD1 LEU C 380 " pdb=" CD2 LEU C 380 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ASN C 176 " pdb=" N ASN C 176 " pdb=" C ASN C 176 " pdb=" CB ASN C 176 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2589 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 169 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO C 170 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 13 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO I 14 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 13 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO H 14 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.025 5.00e-02 4.00e+02 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 23 2.31 - 2.96: 7765 2.96 - 3.60: 22366 3.60 - 4.25: 31625 4.25 - 4.90: 52831 Nonbonded interactions: 114610 Sorted by model distance: nonbonded pdb=" OD1 ASN C 167 " pdb=" OD1 ASP H 55 " model vdw 1.661 3.040 nonbonded pdb=" CG2 THR B 171 " pdb=" O ARG B 180 " model vdw 1.871 3.460 nonbonded pdb=" OD1 ASN C 167 " pdb=" OG SER H 54 " model vdw 2.064 3.040 nonbonded pdb=" CG ASN C 167 " pdb=" OG SER H 54 " model vdw 2.106 3.270 nonbonded pdb=" OH TYR I 60 " pdb=" O ALA I 68 " model vdw 2.209 3.040 ... (remaining 114605 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 45 through 145 or (resid 146 through 150 and (name N or na \ me CA or name C or name O or name CB )) or resid 151 through 168 or (resid 169 a \ nd (name N or name CA or name C or name O or name CB )) or resid 170 through 184 \ or (resid 185 through 187 and (name N or name CA or name C or name O or name CB \ )) or resid 188 or (resid 189 through 191 and (name N or name CA or name C or n \ ame O or name CB )) or resid 192 through 301 or (resid 302 and (name N or name C \ A or name C or name O or name CB )) or resid 303 through 355 or (resid 356 throu \ gh 367 and (name N or name CA or name C or name O or name CB )) or resid 368 thr \ ough 462 or (resid 463 through 464 and (name N or name CA or name C or name O or \ name CB )) or resid 465 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB )) or resid 515 through 517 or (resid 518 through 524 a \ nd (name N or name CA or name C or name O or name CB )) or resid 525 through 533 \ or (resid 534 and (name N or name CA or name C or name O or name CB )) or resid \ 535 through 626 or (resid 627 through 628 and (name N or name CA or name C or n \ ame O or name CB )) or resid 629 through 661 or (resid 662 and (name N or name C \ A or name C or name O or name CB )) or resid 663 through 678 or (resid 679 throu \ gh 681 and (name N or name CA or name C or name O or name CB )) or resid 682)) selection = (chain 'B' and (resid 45 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 or (resid 84 and (name N or name CA or nam \ e C or name O or name CB )) or resid 85 through 145 or (resid 146 through 150 an \ d (name N or name CA or name C or name O or name CB )) or resid 151 through 168 \ or (resid 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 or (resid 171 and (name N or name CA or name C or name O or name CB )) or re \ sid 172 through 184 or (resid 185 through 187 and (name N or name CA or name C o \ r name O or name CB )) or resid 188 or (resid 189 through 191 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 192 through 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 257 or (resid 258 \ and (name N or name CA or name C or name O or name CB )) or resid 259 through 3 \ 55 or (resid 356 through 367 and (name N or name CA or name C or name O or name \ CB )) or resid 368 through 462 or (resid 463 through 464 and (name N or name CA \ or name C or name O or name CB )) or resid 465 through 533 or (resid 534 and (na \ me N or name CA or name C or name O or name CB )) or resid 535 through 581 or (r \ esid 582 and (name N or name CA or name C or name O or name CB )) or resid 583 t \ hrough 613 or (resid 614 through 621 and (name N or name CA or name C or name O \ or name CB )) or resid 622 through 661 or (resid 662 and (name N or name CA or n \ ame C or name O or name CB )) or resid 663 through 682)) selection = (chain 'C' and (resid 45 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 81 or (resid 82 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 170 or (resid 171 and \ (name N or name CA or name C or name O or name CB )) or resid 172 through 257 o \ r (resid 258 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 59 through 480 or (resid 481 and (name N or name CA or name C or name O or name \ CB )) or resid 482 through 493 or (resid 494 through 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 513 or (resid 514 and (na \ me N or name CA or name C or name O or name CB )) or resid 515 through 517 or (r \ esid 518 through 524 and (name N or name CA or name C or name O or name CB )) or \ resid 525 through 581 or (resid 582 and (name N or name CA or name C or name O \ or name CB )) or resid 583 through 598 or (resid 599 and (name N or name CA or n \ ame C or name O or name CB )) or resid 600 through 613 or (resid 614 through 621 \ and (name N or name CA or name C or name O or name CB )) or resid 622 through 6 \ 26 or (resid 627 through 628 and (name N or name CA or name C or name O or name \ CB )) or resid 629 through 678 or (resid 679 through 681 and (name N or name CA \ or name C or name O or name CB )) or resid 682)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.060 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: 0.580 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.180 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.007 0.487 16501 Z= 0.367 Angle : 0.656 28.778 22588 Z= 0.341 Chirality : 0.039 0.188 2592 Planarity : 0.003 0.051 2979 Dihedral : 15.349 89.444 5242 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 30.41 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.18), residues: 2274 helix: 3.30 (0.29), residues: 300 sheet: -0.46 (0.22), residues: 573 loop : -1.90 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 102 TYR 0.009 0.001 TYR L 48 PHE 0.019 0.000 PHE A 235 TRP 0.029 0.002 TRP I 108 HIS 0.009 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00206 (16495) covalent geometry : angle 0.55105 (22576) SS BOND : bond 0.36510 ( 6) SS BOND : angle 15.41721 ( 12) hydrogen bonds : bond 0.22783 ( 511) hydrogen bonds : angle 9.00577 ( 1497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.1551 (ppp) cc_final: 0.1070 (ppp) REVERT: A 669 TYR cc_start: 0.8062 (t80) cc_final: 0.7845 (t80) REVERT: B 147 MET cc_start: 0.0442 (ppp) cc_final: -0.0481 (ppp) REVERT: B 188 HIS cc_start: 0.7759 (t70) cc_final: 0.7486 (t-170) REVERT: B 497 MET cc_start: 0.8717 (tmm) cc_final: 0.8436 (tmm) REVERT: C 663 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8059 (tm-30) REVERT: H 28 THR cc_start: 0.7976 (m) cc_final: 0.7750 (t) REVERT: H 46 GLU cc_start: 0.8742 (tp30) cc_final: 0.8500 (tp30) REVERT: H 114 LEU cc_start: 0.7732 (tt) cc_final: 0.7293 (mp) REVERT: I 55 ASP cc_start: 0.8312 (m-30) cc_final: 0.7526 (p0) REVERT: I 102 ARG cc_start: 0.8567 (tpp80) cc_final: 0.8337 (tpt170) REVERT: J 55 ASP cc_start: 0.7706 (m-30) cc_final: 0.6981 (p0) REVERT: J 102 ARG cc_start: 0.8624 (tpp80) cc_final: 0.8269 (tpt170) REVERT: L 17 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8419 (mp0) REVERT: L 36 GLN cc_start: 0.7549 (tt0) cc_final: 0.6540 (tt0) REVERT: L 61 PHE cc_start: 0.8669 (m-80) cc_final: 0.8065 (m-80) REVERT: M 17 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8229 (mp0) REVERT: M 36 GLN cc_start: 0.7799 (tt0) cc_final: 0.7179 (tt0) REVERT: N 47 ILE cc_start: 0.8403 (mm) cc_final: 0.8098 (tt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1024 time to fit residues: 39.8768 Evaluate side-chains 223 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 476 GLN B 77 HIS B 299 HIS C 77 HIS C 167 ASN H 5 GLN N 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.079763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057373 restraints weight = 70859.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.058694 restraints weight = 39691.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059564 restraints weight = 28832.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.060099 restraints weight = 23913.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060397 restraints weight = 21467.156| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 16501 Z= 0.348 Angle : 0.731 7.631 22588 Z= 0.404 Chirality : 0.046 0.148 2592 Planarity : 0.005 0.065 2979 Dihedral : 4.767 23.363 2470 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.50 % Favored : 90.46 % Rotamer: Outliers : 5.78 % Allowed : 23.84 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2274 helix: 2.51 (0.28), residues: 303 sheet: -0.66 (0.20), residues: 666 loop : -2.25 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 474 TYR 0.028 0.003 TYR A 92 PHE 0.033 0.002 PHE C 244 TRP 0.033 0.003 TRP H 36 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00793 (16495) covalent geometry : angle 0.73050 (22576) SS BOND : bond 0.00638 ( 6) SS BOND : angle 1.64650 ( 12) hydrogen bonds : bond 0.07480 ( 511) hydrogen bonds : angle 5.75240 ( 1497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 210 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.3188 (ppp) cc_final: 0.2809 (ppp) REVERT: A 246 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: B 147 MET cc_start: 0.2003 (ppp) cc_final: 0.1639 (ppp) REVERT: B 246 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6146 (pm20) REVERT: H 46 GLU cc_start: 0.8809 (tp30) cc_final: 0.8585 (tp30) REVERT: I 46 GLU cc_start: 0.8885 (tp30) cc_final: 0.8634 (tp30) REVERT: I 102 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8592 (tpp80) REVERT: I 107 TYR cc_start: 0.8956 (t80) cc_final: 0.8681 (t80) REVERT: J 48 ILE cc_start: 0.8342 (mt) cc_final: 0.8074 (mt) REVERT: L 32 MET cc_start: 0.7993 (mmm) cc_final: 0.6690 (tpp) REVERT: L 52 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7388 (p0) REVERT: L 53 LEU cc_start: 0.9317 (tt) cc_final: 0.8872 (tt) REVERT: L 61 PHE cc_start: 0.8969 (m-80) cc_final: 0.8671 (m-80) REVERT: M 48 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7176 (t80) REVERT: M 92 SER cc_start: 0.7004 (m) cc_final: 0.6559 (p) REVERT: N 48 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6895 (t80) REVERT: N 92 SER cc_start: 0.6812 (m) cc_final: 0.6283 (p) outliers start: 81 outliers final: 36 residues processed: 271 average time/residue: 0.1007 time to fit residues: 42.8988 Evaluate side-chains 231 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 66 ASP Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 40 ARG Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 164 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 77 HIS B 188 HIS C 77 HIS C 228 GLN C 459 ASN C 476 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056015 restraints weight = 77570.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057611 restraints weight = 39426.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058658 restraints weight = 26733.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059301 restraints weight = 21166.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059525 restraints weight = 18457.168| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16501 Z= 0.144 Angle : 0.536 8.923 22588 Z= 0.284 Chirality : 0.041 0.205 2592 Planarity : 0.004 0.051 2979 Dihedral : 3.843 21.587 2470 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.85 % Allowed : 25.05 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.18), residues: 2274 helix: 3.10 (0.27), residues: 324 sheet: -0.41 (0.20), residues: 654 loop : -2.18 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 169 TYR 0.014 0.001 TYR A 92 PHE 0.017 0.001 PHE A 235 TRP 0.032 0.002 TRP H 36 HIS 0.008 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00323 (16495) covalent geometry : angle 0.53562 (22576) SS BOND : bond 0.00424 ( 6) SS BOND : angle 1.21533 ( 12) hydrogen bonds : bond 0.05164 ( 511) hydrogen bonds : angle 4.96527 ( 1497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.3763 (ppp) cc_final: 0.3314 (ppp) REVERT: A 232 MET cc_start: 0.9397 (ptm) cc_final: 0.9059 (ptm) REVERT: A 237 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: B 147 MET cc_start: 0.2346 (ppp) cc_final: 0.1838 (ppp) REVERT: B 232 MET cc_start: 0.9155 (ptm) cc_final: 0.8953 (ptm) REVERT: C 672 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8580 (tm-30) REVERT: H 46 GLU cc_start: 0.8806 (tp30) cc_final: 0.8475 (tp30) REVERT: I 46 GLU cc_start: 0.8845 (tp30) cc_final: 0.8539 (tp30) REVERT: I 48 ILE cc_start: 0.8141 (mt) cc_final: 0.7878 (mt) REVERT: I 102 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8661 (tpp80) REVERT: I 107 TYR cc_start: 0.8893 (t80) cc_final: 0.8635 (t80) REVERT: J 36 TRP cc_start: 0.5296 (OUTLIER) cc_final: 0.3585 (m-10) REVERT: J 48 ILE cc_start: 0.8076 (mt) cc_final: 0.7793 (mt) REVERT: J 81 MET cc_start: 0.8096 (tpt) cc_final: 0.7470 (tpt) REVERT: J 112 THR cc_start: 0.9285 (m) cc_final: 0.9085 (m) REVERT: J 113 THR cc_start: 0.8333 (m) cc_final: 0.8108 (p) REVERT: L 53 LEU cc_start: 0.9280 (tt) cc_final: 0.8818 (tt) REVERT: L 61 PHE cc_start: 0.8943 (m-80) cc_final: 0.8584 (m-80) REVERT: L 74 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8006 (tp) REVERT: M 48 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6812 (t80) REVERT: M 92 SER cc_start: 0.6890 (m) cc_final: 0.6330 (p) REVERT: N 32 MET cc_start: 0.7589 (tpp) cc_final: 0.7375 (mmt) REVERT: N 48 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6649 (t80) REVERT: N 92 SER cc_start: 0.6589 (m) cc_final: 0.6167 (p) outliers start: 54 outliers final: 30 residues processed: 255 average time/residue: 0.0974 time to fit residues: 39.1858 Evaluate side-chains 239 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 40 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 149 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 213 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 198 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 128 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 77 HIS C 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.076225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055415 restraints weight = 77047.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057012 restraints weight = 38951.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.058055 restraints weight = 26337.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058694 restraints weight = 20868.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059090 restraints weight = 18183.584| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16501 Z= 0.144 Angle : 0.525 8.171 22588 Z= 0.276 Chirality : 0.041 0.132 2592 Planarity : 0.004 0.047 2979 Dihedral : 3.654 18.874 2470 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.35 % Allowed : 24.77 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.18), residues: 2274 helix: 3.45 (0.27), residues: 309 sheet: -0.27 (0.21), residues: 609 loop : -2.22 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 102 TYR 0.014 0.001 TYR A 92 PHE 0.016 0.001 PHE C 244 TRP 0.036 0.002 TRP H 36 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00326 (16495) covalent geometry : angle 0.52510 (22576) SS BOND : bond 0.00405 ( 6) SS BOND : angle 1.01928 ( 12) hydrogen bonds : bond 0.04740 ( 511) hydrogen bonds : angle 4.55466 ( 1497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.4379 (ppp) cc_final: 0.3913 (ppp) REVERT: A 228 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: A 232 MET cc_start: 0.9410 (ptm) cc_final: 0.9013 (ptm) REVERT: A 237 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: A 334 MET cc_start: 0.8575 (ttp) cc_final: 0.8367 (ttt) REVERT: B 147 MET cc_start: 0.2701 (ppp) cc_final: 0.2292 (ppp) REVERT: B 188 HIS cc_start: 0.7605 (t70) cc_final: 0.7378 (t-170) REVERT: H 113 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.7225 (p) REVERT: I 36 TRP cc_start: 0.5406 (OUTLIER) cc_final: 0.3787 (m-10) REVERT: I 46 GLU cc_start: 0.8824 (tp30) cc_final: 0.8545 (tp30) REVERT: I 48 ILE cc_start: 0.8140 (mt) cc_final: 0.7889 (mt) REVERT: J 36 TRP cc_start: 0.5299 (OUTLIER) cc_final: 0.3775 (m-10) REVERT: J 48 ILE cc_start: 0.8162 (mt) cc_final: 0.7943 (mt) REVERT: J 81 MET cc_start: 0.8054 (tpt) cc_final: 0.7570 (tpt) REVERT: J 103 TYR cc_start: 0.8413 (t80) cc_final: 0.8205 (t80) REVERT: J 107 TYR cc_start: 0.8810 (t80) cc_final: 0.8484 (t80) REVERT: J 112 THR cc_start: 0.9268 (m) cc_final: 0.9054 (m) REVERT: L 61 PHE cc_start: 0.8918 (m-80) cc_final: 0.8655 (m-80) REVERT: L 74 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7904 (tp) REVERT: L 103 LEU cc_start: 0.7679 (mt) cc_final: 0.7459 (mt) REVERT: M 92 SER cc_start: 0.6960 (m) cc_final: 0.6415 (p) REVERT: N 32 MET cc_start: 0.7498 (tpp) cc_final: 0.6995 (mmt) REVERT: N 48 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6513 (t80) REVERT: N 92 SER cc_start: 0.6634 (m) cc_final: 0.6142 (p) outliers start: 61 outliers final: 35 residues processed: 253 average time/residue: 0.1067 time to fit residues: 42.3027 Evaluate side-chains 244 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 380 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 40 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 120 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 chunk 227 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.072188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051412 restraints weight = 78348.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052871 restraints weight = 40809.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053725 restraints weight = 28235.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054352 restraints weight = 23011.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054669 restraints weight = 20167.726| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 16501 Z= 0.338 Angle : 0.693 9.755 22588 Z= 0.375 Chirality : 0.045 0.192 2592 Planarity : 0.004 0.050 2979 Dihedral : 4.911 24.193 2470 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 5.64 % Allowed : 24.63 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.17), residues: 2274 helix: 2.54 (0.28), residues: 306 sheet: -0.69 (0.19), residues: 690 loop : -2.41 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 169 TYR 0.023 0.002 TYR A 92 PHE 0.034 0.002 PHE C 244 TRP 0.040 0.003 TRP H 36 HIS 0.009 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00772 (16495) covalent geometry : angle 0.69225 (22576) SS BOND : bond 0.00575 ( 6) SS BOND : angle 1.56562 ( 12) hydrogen bonds : bond 0.06657 ( 511) hydrogen bonds : angle 5.18226 ( 1497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.5628 (ppp) cc_final: 0.5384 (ppp) REVERT: A 228 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: A 246 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: B 142 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7998 (t-90) REVERT: B 147 MET cc_start: 0.3770 (OUTLIER) cc_final: 0.3521 (ppp) REVERT: B 188 HIS cc_start: 0.7685 (t70) cc_final: 0.7467 (t-170) REVERT: B 246 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.5996 (pt0) REVERT: C 246 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: H 33 TRP cc_start: 0.8052 (m-10) cc_final: 0.7704 (m-10) REVERT: H 46 GLU cc_start: 0.8852 (tp30) cc_final: 0.8589 (tp30) REVERT: I 33 TRP cc_start: 0.8036 (m-10) cc_final: 0.7739 (m-10) REVERT: I 36 TRP cc_start: 0.5233 (OUTLIER) cc_final: 0.3499 (m-10) REVERT: J 33 TRP cc_start: 0.8177 (m-10) cc_final: 0.7888 (m-10) REVERT: J 36 TRP cc_start: 0.5207 (OUTLIER) cc_final: 0.3862 (m-10) REVERT: J 46 GLU cc_start: 0.8943 (tp30) cc_final: 0.8634 (tp30) REVERT: J 81 MET cc_start: 0.7939 (tpt) cc_final: 0.7636 (tpt) REVERT: L 103 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7539 (mt) outliers start: 79 outliers final: 52 residues processed: 251 average time/residue: 0.1080 time to fit residues: 41.8492 Evaluate side-chains 253 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 663 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 40 ARG Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.053612 restraints weight = 76934.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055136 restraints weight = 38499.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056151 restraints weight = 26119.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056781 restraints weight = 20739.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056989 restraints weight = 18079.458| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16501 Z= 0.141 Angle : 0.556 10.037 22588 Z= 0.289 Chirality : 0.041 0.217 2592 Planarity : 0.004 0.044 2979 Dihedral : 4.034 23.321 2470 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.50 % Allowed : 25.84 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2274 helix: 3.27 (0.27), residues: 312 sheet: -0.47 (0.20), residues: 675 loop : -2.38 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.016 0.001 TYR N 93 PHE 0.019 0.001 PHE C 62 TRP 0.029 0.002 TRP H 36 HIS 0.010 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00321 (16495) covalent geometry : angle 0.55504 (22576) SS BOND : bond 0.00412 ( 6) SS BOND : angle 1.39209 ( 12) hydrogen bonds : bond 0.04970 ( 511) hydrogen bonds : angle 4.56519 ( 1497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.5838 (ppp) cc_final: 0.5521 (ppp) REVERT: A 228 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8408 (mt0) REVERT: A 232 MET cc_start: 0.9336 (ptm) cc_final: 0.8786 (ptm) REVERT: A 237 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6347 (m-30) REVERT: B 147 MET cc_start: 0.3804 (OUTLIER) cc_final: 0.3498 (ppp) REVERT: H 33 TRP cc_start: 0.7813 (m-10) cc_final: 0.7577 (m-10) REVERT: H 46 GLU cc_start: 0.8831 (tp30) cc_final: 0.8572 (tp30) REVERT: I 33 TRP cc_start: 0.7817 (m-10) cc_final: 0.7530 (m-10) REVERT: I 46 GLU cc_start: 0.8719 (tp30) cc_final: 0.8512 (tp30) REVERT: J 102 ARG cc_start: 0.9023 (tpp80) cc_final: 0.8820 (tpp80) REVERT: N 48 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6309 (t80) outliers start: 63 outliers final: 39 residues processed: 254 average time/residue: 0.1046 time to fit residues: 41.6159 Evaluate side-chains 239 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 40 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 69 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 chunk 151 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.073127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052448 restraints weight = 77702.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.053944 restraints weight = 39682.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054912 restraints weight = 27207.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055501 restraints weight = 21795.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.055796 restraints weight = 19160.455| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16501 Z= 0.198 Angle : 0.592 9.900 22588 Z= 0.310 Chirality : 0.042 0.144 2592 Planarity : 0.004 0.050 2979 Dihedral : 4.185 22.154 2470 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 4.93 % Allowed : 25.84 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2274 helix: 3.16 (0.27), residues: 312 sheet: -0.64 (0.20), residues: 663 loop : -2.40 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.017 0.001 TYR A 92 PHE 0.023 0.002 PHE A 244 TRP 0.027 0.002 TRP H 36 HIS 0.010 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00456 (16495) covalent geometry : angle 0.59106 (22576) SS BOND : bond 0.00594 ( 6) SS BOND : angle 1.44948 ( 12) hydrogen bonds : bond 0.05432 ( 511) hydrogen bonds : angle 4.57691 ( 1497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.5998 (ppp) cc_final: 0.5728 (ppp) REVERT: A 228 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: A 232 MET cc_start: 0.9468 (ptm) cc_final: 0.9218 (ptm) REVERT: B 147 MET cc_start: 0.4212 (OUTLIER) cc_final: 0.3901 (ppp) REVERT: H 33 TRP cc_start: 0.8088 (m-10) cc_final: 0.7159 (m-10) REVERT: I 33 TRP cc_start: 0.8012 (m-10) cc_final: 0.7743 (m-10) REVERT: I 36 TRP cc_start: 0.5424 (OUTLIER) cc_final: 0.3680 (m-10) REVERT: I 46 GLU cc_start: 0.8741 (tp30) cc_final: 0.8483 (tp30) REVERT: M 17 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8256 (mp0) REVERT: N 48 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.6351 (t80) outliers start: 69 outliers final: 51 residues processed: 253 average time/residue: 0.1094 time to fit residues: 43.8403 Evaluate side-chains 254 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 40 ARG Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 69 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 38 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.072402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051793 restraints weight = 78552.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053238 restraints weight = 40924.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054158 restraints weight = 28341.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054716 restraints weight = 22979.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055064 restraints weight = 20193.462| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16501 Z= 0.225 Angle : 0.611 10.221 22588 Z= 0.322 Chirality : 0.042 0.142 2592 Planarity : 0.004 0.052 2979 Dihedral : 4.375 24.033 2470 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 5.00 % Allowed : 25.48 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2274 helix: 3.04 (0.27), residues: 312 sheet: -0.72 (0.19), residues: 687 loop : -2.41 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.018 0.001 TYR A 92 PHE 0.025 0.002 PHE C 62 TRP 0.041 0.002 TRP L 34 HIS 0.016 0.002 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00520 (16495) covalent geometry : angle 0.61060 (22576) SS BOND : bond 0.00594 ( 6) SS BOND : angle 1.42653 ( 12) hydrogen bonds : bond 0.05541 ( 511) hydrogen bonds : angle 4.64660 ( 1497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 0.580 Fit side-chains REVERT: A 228 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: A 232 MET cc_start: 0.9417 (ptm) cc_final: 0.9152 (ptm) REVERT: A 237 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: A 669 TYR cc_start: 0.8841 (t80) cc_final: 0.8617 (t80) REVERT: B 147 MET cc_start: 0.4607 (OUTLIER) cc_final: 0.4194 (ppp) REVERT: H 33 TRP cc_start: 0.8339 (m-10) cc_final: 0.7365 (m-10) REVERT: H 40 ARG cc_start: 0.8595 (tmm-80) cc_final: 0.8315 (tmm-80) REVERT: H 46 GLU cc_start: 0.8883 (tp30) cc_final: 0.8612 (tp30) REVERT: H 62 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8796 (mm-40) REVERT: I 33 TRP cc_start: 0.8254 (m-10) cc_final: 0.7964 (m-10) REVERT: I 36 TRP cc_start: 0.5608 (OUTLIER) cc_final: 0.3743 (m-10) REVERT: I 46 GLU cc_start: 0.8740 (tp30) cc_final: 0.8479 (tp30) REVERT: J 36 TRP cc_start: 0.5598 (OUTLIER) cc_final: 0.3723 (m-10) REVERT: J 81 MET cc_start: 0.8159 (tpt) cc_final: 0.7506 (tpt) REVERT: L 17 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8341 (mp0) REVERT: M 17 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8208 (mp0) REVERT: M 74 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7614 (tp) REVERT: N 48 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6598 (t80) outliers start: 70 outliers final: 51 residues processed: 256 average time/residue: 0.1078 time to fit residues: 43.1242 Evaluate side-chains 258 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 489 CYS Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 40 ARG Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 69 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 118 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 209 optimal weight: 0.0370 chunk 112 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.073883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.053370 restraints weight = 77572.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054856 restraints weight = 39845.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.055819 restraints weight = 27384.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056373 restraints weight = 21913.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056745 restraints weight = 19351.802| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.6567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16501 Z= 0.127 Angle : 0.575 10.717 22588 Z= 0.294 Chirality : 0.041 0.232 2592 Planarity : 0.004 0.044 2979 Dihedral : 3.931 22.398 2470 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.85 % Allowed : 26.62 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 2274 helix: 3.47 (0.27), residues: 312 sheet: -0.70 (0.20), residues: 669 loop : -2.36 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.017 0.001 TYR C 669 PHE 0.017 0.001 PHE C 62 TRP 0.042 0.002 TRP L 34 HIS 0.013 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00289 (16495) covalent geometry : angle 0.57473 (22576) SS BOND : bond 0.00405 ( 6) SS BOND : angle 1.29583 ( 12) hydrogen bonds : bond 0.04569 ( 511) hydrogen bonds : angle 4.32067 ( 1497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 228 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8421 (mt0) REVERT: A 232 MET cc_start: 0.9350 (ptm) cc_final: 0.8812 (ptm) REVERT: A 237 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6660 (m-30) REVERT: A 669 TYR cc_start: 0.8828 (t80) cc_final: 0.8584 (t80) REVERT: B 147 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.4210 (ppp) REVERT: H 33 TRP cc_start: 0.8112 (m-10) cc_final: 0.7303 (m-10) REVERT: H 40 ARG cc_start: 0.8613 (tmm-80) cc_final: 0.8375 (tmm-80) REVERT: H 46 GLU cc_start: 0.8879 (tp30) cc_final: 0.8628 (tp30) REVERT: H 62 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8781 (mm-40) REVERT: I 33 TRP cc_start: 0.8039 (m-10) cc_final: 0.7785 (m-10) REVERT: I 46 GLU cc_start: 0.8668 (tp30) cc_final: 0.8390 (tp30) REVERT: I 102 ARG cc_start: 0.8977 (tpp80) cc_final: 0.8501 (tpt170) REVERT: J 36 TRP cc_start: 0.5536 (OUTLIER) cc_final: 0.3893 (m-10) REVERT: J 102 ARG cc_start: 0.8970 (tpp80) cc_final: 0.8383 (tpt170) REVERT: J 103 TYR cc_start: 0.8470 (t80) cc_final: 0.8160 (t80) REVERT: L 17 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8280 (mp0) REVERT: M 17 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8180 (mp0) REVERT: M 74 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7653 (tp) REVERT: N 48 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6350 (t80) outliers start: 54 outliers final: 42 residues processed: 252 average time/residue: 0.1048 time to fit residues: 41.4160 Evaluate side-chains 253 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 69 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 5.9990 chunk 223 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.071974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051299 restraints weight = 78410.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052734 restraints weight = 41125.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053647 restraints weight = 28547.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054206 restraints weight = 23071.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.054487 restraints weight = 20386.664| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16501 Z= 0.259 Angle : 0.639 10.171 22588 Z= 0.335 Chirality : 0.043 0.154 2592 Planarity : 0.004 0.053 2979 Dihedral : 4.421 22.980 2470 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 3.71 % Allowed : 27.27 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.17), residues: 2274 helix: 3.06 (0.27), residues: 312 sheet: -0.81 (0.20), residues: 669 loop : -2.43 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.019 0.002 TYR A 92 PHE 0.028 0.002 PHE C 244 TRP 0.049 0.002 TRP L 34 HIS 0.013 0.002 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00599 (16495) covalent geometry : angle 0.63836 (22576) SS BOND : bond 0.00631 ( 6) SS BOND : angle 1.52526 ( 12) hydrogen bonds : bond 0.05701 ( 511) hydrogen bonds : angle 4.62624 ( 1497) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.536 Fit side-chains REVERT: A 228 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: A 237 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: A 669 TYR cc_start: 0.8854 (t80) cc_final: 0.8642 (t80) REVERT: B 147 MET cc_start: 0.4872 (OUTLIER) cc_final: 0.4582 (ppp) REVERT: H 33 TRP cc_start: 0.8429 (m-10) cc_final: 0.7471 (m-10) REVERT: H 62 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8790 (mm-40) REVERT: I 33 TRP cc_start: 0.8305 (m-10) cc_final: 0.8022 (m-10) REVERT: I 36 TRP cc_start: 0.5587 (OUTLIER) cc_final: 0.3596 (m-10) REVERT: J 36 TRP cc_start: 0.5622 (OUTLIER) cc_final: 0.3872 (m-10) REVERT: L 17 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8311 (mp0) REVERT: M 17 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8211 (mp0) REVERT: M 74 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7811 (tp) REVERT: N 48 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6526 (t80) outliers start: 52 outliers final: 42 residues processed: 245 average time/residue: 0.0986 time to fit residues: 38.0927 Evaluate side-chains 250 residues out of total 2034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 142 HIS Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 489 CYS Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 663 GLU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain I residue 36 TRP Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain J residue 36 TRP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 69 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 205 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.070902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.050275 restraints weight = 78649.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.051681 restraints weight = 41588.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052547 restraints weight = 29022.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053123 restraints weight = 23642.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053351 restraints weight = 20829.858| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 16501 Z= 0.325 Angle : 0.698 10.017 22588 Z= 0.372 Chirality : 0.045 0.271 2592 Planarity : 0.004 0.063 2979 Dihedral : 4.972 27.163 2470 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 4.71 % Allowed : 26.05 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.17), residues: 2274 helix: 2.78 (0.27), residues: 303 sheet: -0.97 (0.19), residues: 669 loop : -2.51 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 60 TYR 0.022 0.002 TYR A 92 PHE 0.035 0.002 PHE C 244 TRP 0.058 0.003 TRP L 34 HIS 0.013 0.002 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00750 (16495) covalent geometry : angle 0.69687 (22576) SS BOND : bond 0.00756 ( 6) SS BOND : angle 1.68927 ( 12) hydrogen bonds : bond 0.06332 ( 511) hydrogen bonds : angle 4.95549 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4015.16 seconds wall clock time: 69 minutes 21.66 seconds (4161.66 seconds total)