Starting phenix.real_space_refine on Wed Nov 19 23:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b2z_7036/11_2025/6b2z_7036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b2z_7036/11_2025/6b2z_7036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b2z_7036/11_2025/6b2z_7036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b2z_7036/11_2025/6b2z_7036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b2z_7036/11_2025/6b2z_7036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b2z_7036/11_2025/6b2z_7036.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9678 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 14214 2.51 5 N 3422 2.21 5 O 3682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21436 Number of models: 1 Model: "" Number of chains: 38 Chain: "1" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "3" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "4" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "5" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "6" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "7" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 522 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "8" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "9" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "0" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 410 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "a" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1971 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain: "b" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 639 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 5, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "d" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 411 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 49} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "e" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Chain: "f" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 528 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 63} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "i" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain: "k" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 180 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "C" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "D" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "E" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "G" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "H" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "I" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 522 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "J" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "K" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 410 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "M" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1971 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain: "N" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 639 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 5, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "O" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 411 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 49} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Chain: "Q" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 528 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 63} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "S" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 473 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain: "T" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 180 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Time building chain proxies: 5.02, per 1000 atoms: 0.23 Number of scatterers: 21436 At special positions: 0 Unit cell: (136.74, 189.74, 129.32, 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 118 16.00 O 3682 8.00 N 3422 7.00 C 14214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 912.8 milliseconds 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 0 sheets defined 92.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain '1' and resid 1 through 15 removed outlier: 3.618A pdb=" N TYR 1 9 " --> pdb=" O LEU 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 40 removed outlier: 4.172A pdb=" N ALA 1 22 " --> pdb=" O GLY 1 18 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG 1 39 " --> pdb=" O ASN 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 74 Proline residue: 1 49 - end of helix removed outlier: 3.868A pdb=" N THR 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS 1 65 " --> pdb=" O THR 1 61 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL 1 68 " --> pdb=" O PHE 1 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER 1 69 " --> pdb=" O CYS 1 65 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE 1 74 " --> pdb=" O PHE 1 70 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 15 Processing helix chain '2' and resid 16 through 18 No H-bonds generated for 'chain '2' and resid 16 through 18' Processing helix chain '2' and resid 19 through 39 removed outlier: 3.647A pdb=" N ILE 2 24 " --> pdb=" O LEU 2 20 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY 2 25 " --> pdb=" O GLY 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 75 Proline residue: 2 49 - end of helix removed outlier: 5.252A pdb=" N THR 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY 2 62 " --> pdb=" O SER 2 58 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS 2 65 " --> pdb=" O THR 2 61 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 15 removed outlier: 4.332A pdb=" N TYR 3 9 " --> pdb=" O LEU 3 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE 3 10 " --> pdb=" O ALA 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 40 removed outlier: 3.867A pdb=" N ALA 3 22 " --> pdb=" O GLY 3 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE 3 24 " --> pdb=" O LEU 3 20 " (cutoff:3.500A) Processing helix chain '3' and resid 43 through 75 Proline residue: 3 49 - end of helix removed outlier: 5.629A pdb=" N CYS 3 65 " --> pdb=" O THR 3 61 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU 3 66 " --> pdb=" O GLY 3 62 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 removed outlier: 3.705A pdb=" N TYR 4 9 " --> pdb=" O LEU 4 5 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR 4 16 " --> pdb=" O ALA 4 12 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 40 removed outlier: 3.697A pdb=" N GLY 4 23 " --> pdb=" O LEU 4 19 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA 4 27 " --> pdb=" O GLY 4 23 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG 4 39 " --> pdb=" O ASN 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 74 Proline residue: 4 49 - end of helix removed outlier: 4.552A pdb=" N THR 4 61 " --> pdb=" O LEU 4 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY 4 62 " --> pdb=" O SER 4 58 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 15 removed outlier: 3.613A pdb=" N ALA 5 7 " --> pdb=" O LEU 5 3 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR 5 9 " --> pdb=" O LEU 5 5 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 40 removed outlier: 4.078A pdb=" N ALA 5 22 " --> pdb=" O GLY 5 18 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA 5 27 " --> pdb=" O GLY 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 74 Proline residue: 5 49 - end of helix removed outlier: 3.540A pdb=" N LEU 5 57 " --> pdb=" O LEU 5 53 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL 5 68 " --> pdb=" O PHE 5 64 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER 5 69 " --> pdb=" O CYS 5 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE 5 74 " --> pdb=" O PHE 5 70 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 15 removed outlier: 3.584A pdb=" N TYR 6 9 " --> pdb=" O LEU 6 5 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 40 removed outlier: 4.108A pdb=" N ALA 6 22 " --> pdb=" O GLY 6 18 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA 6 27 " --> pdb=" O GLY 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 74 Proline residue: 6 49 - end of helix removed outlier: 3.579A pdb=" N GLY 6 62 " --> pdb=" O SER 6 58 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS 6 65 " --> pdb=" O THR 6 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE 6 74 " --> pdb=" O PHE 6 70 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 15 removed outlier: 3.545A pdb=" N TYR 7 9 " --> pdb=" O LEU 7 5 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 40 removed outlier: 4.174A pdb=" N ALA 7 22 " --> pdb=" O GLY 7 18 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA 7 27 " --> pdb=" O GLY 7 23 " (cutoff:3.500A) Processing helix chain '7' and resid 43 through 72 Proline residue: 7 49 - end of helix removed outlier: 3.671A pdb=" N CYS 7 65 " --> pdb=" O THR 7 61 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 16 removed outlier: 4.061A pdb=" N THR 8 16 " --> pdb=" O ALA 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 40 removed outlier: 4.027A pdb=" N ALA 8 22 " --> pdb=" O GLY 8 18 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA 8 27 " --> pdb=" O GLY 8 23 " (cutoff:3.500A) Processing helix chain '8' and resid 43 through 74 Proline residue: 8 49 - end of helix removed outlier: 4.403A pdb=" N CYS 8 65 " --> pdb=" O THR 8 61 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU 8 66 " --> pdb=" O GLY 8 62 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 15 Processing helix chain '9' and resid 18 through 40 removed outlier: 4.077A pdb=" N ALA 9 22 " --> pdb=" O GLY 9 18 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA 9 27 " --> pdb=" O GLY 9 23 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG 9 39 " --> pdb=" O ASN 9 35 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 74 Proline residue: 9 49 - end of helix removed outlier: 3.860A pdb=" N CYS 9 65 " --> pdb=" O THR 9 61 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 16 removed outlier: 3.574A pdb=" N ALA 0 7 " --> pdb=" O LEU 0 3 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR 0 16 " --> pdb=" O ALA 0 12 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 38 removed outlier: 4.237A pdb=" N ALA 0 22 " --> pdb=" O GLY 0 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA 0 27 " --> pdb=" O GLY 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 42 No H-bonds generated for 'chain '0' and resid 40 through 42' Processing helix chain '0' and resid 43 through 72 Proline residue: 0 49 - end of helix removed outlier: 3.820A pdb=" N THR 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY 0 62 " --> pdb=" O SER 0 58 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS 0 65 " --> pdb=" O THR 0 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 30 through 48 removed outlier: 3.810A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 7 removed outlier: 3.585A pdb=" N PHE a 6 " --> pdb=" O LEU a 3 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU a 7 " --> pdb=" O ASP a 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 3 through 7' Processing helix chain 'a' and resid 27 through 43 Processing helix chain 'a' and resid 58 through 74 removed outlier: 3.959A pdb=" N GLN a 62 " --> pdb=" O TRP a 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR a 66 " --> pdb=" O GLN a 62 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET a 72 " --> pdb=" O THR a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 84 No H-bonds generated for 'chain 'a' and resid 82 through 84' Processing helix chain 'a' and resid 85 through 99 removed outlier: 3.891A pdb=" N PHE a 93 " --> pdb=" O ILE a 89 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE a 96 " --> pdb=" O LEU a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 101 through 105 Processing helix chain 'a' and resid 114 through 138 removed outlier: 3.500A pdb=" N SER a 120 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU a 132 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 146 removed outlier: 3.738A pdb=" N PHE a 142 " --> pdb=" O TRP a 139 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL a 146 " --> pdb=" O SER a 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 151 through 153 No H-bonds generated for 'chain 'a' and resid 151 through 153' Processing helix chain 'a' and resid 154 through 168 removed outlier: 3.864A pdb=" N GLU a 162 " --> pdb=" O LEU a 158 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER a 165 " --> pdb=" O ILE a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 199 removed outlier: 3.862A pdb=" N LEU a 173 " --> pdb=" O ARG a 169 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY a 174 " --> pdb=" O ALA a 170 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU a 177 " --> pdb=" O LEU a 173 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN a 197 " --> pdb=" O GLY a 193 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 206 Processing helix chain 'a' and resid 209 through 247 removed outlier: 4.121A pdb=" N LEU a 213 " --> pdb=" O GLY a 209 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE a 224 " --> pdb=" O MET a 220 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA a 225 " --> pdb=" O MET a 221 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN a 230 " --> pdb=" O ILE a 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY a 231 " --> pdb=" O GLY a 227 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA a 235 " --> pdb=" O GLY a 231 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA a 239 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU a 242 " --> pdb=" O THR a 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 22 removed outlier: 4.274A pdb=" N ASN b 16 " --> pdb=" O LYS b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 47 removed outlier: 3.539A pdb=" N ILE b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 101 removed outlier: 4.111A pdb=" N ILE b 57 " --> pdb=" O ASN b 53 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU b 58 " --> pdb=" O ASP b 54 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA b 74 " --> pdb=" O ALA b 70 " (cutoff:3.500A) Proline residue: b 75 - end of helix removed outlier: 3.991A pdb=" N ARG b 96 " --> pdb=" O LEU b 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 230 Processing helix chain 'd' and resid 245 through 253 Processing helix chain 'd' and resid 253 through 267 removed outlier: 4.117A pdb=" N ASP d 257 " --> pdb=" O LYS d 253 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 49 removed outlier: 4.310A pdb=" N UNK e 12 " --> pdb=" O UNK e 8 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N UNK e 13 " --> pdb=" O UNK e 9 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N UNK e 14 " --> pdb=" O UNK e 10 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N UNK e 19 " --> pdb=" O UNK e 15 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N UNK e 39 " --> pdb=" O UNK e 35 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N UNK e 40 " --> pdb=" O UNK e 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N UNK e 41 " --> pdb=" O UNK e 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK e 42 " --> pdb=" O UNK e 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 31 removed outlier: 3.907A pdb=" N ALA f 25 " --> pdb=" O ALA f 21 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL f 28 " --> pdb=" O ILE f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 56 removed outlier: 3.585A pdb=" N TYR f 55 " --> pdb=" O TYR f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 63 through 85 removed outlier: 3.874A pdb=" N TRP f 67 " --> pdb=" O GLY f 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 13 Processing helix chain 'g' and resid 13 through 44 removed outlier: 3.898A pdb=" N UNK g 28 " --> pdb=" O UNK g 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N UNK g 29 " --> pdb=" O UNK g 25 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N UNK g 30 " --> pdb=" O UNK g 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK g 31 " --> pdb=" O UNK g 27 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N UNK g 33 " --> pdb=" O UNK g 29 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N UNK g 38 " --> pdb=" O UNK g 34 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N UNK g 39 " --> pdb=" O UNK g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 73 removed outlier: 3.787A pdb=" N UNK g 52 " --> pdb=" O UNK g 48 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N UNK g 53 " --> pdb=" O UNK g 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N UNK g 54 " --> pdb=" O UNK g 50 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N UNK g 57 " --> pdb=" O UNK g 53 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N UNK g 67 " --> pdb=" O UNK g 63 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N UNK g 68 " --> pdb=" O UNK g 64 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N UNK g 71 " --> pdb=" O UNK g 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 79 Processing helix chain 'g' and resid 83 through 104 removed outlier: 4.024A pdb=" N UNK g 87 " --> pdb=" O UNK g 83 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N UNK g 91 " --> pdb=" O UNK g 87 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N UNK g 92 " --> pdb=" O UNK g 88 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N UNK g 93 " --> pdb=" O UNK g 89 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNK g 94 " --> pdb=" O UNK g 90 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 35 Processing helix chain 'k' and resid 17 through 27 removed outlier: 4.058A pdb=" N THR k 21 " --> pdb=" O LEU k 17 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU k 22 " --> pdb=" O ALA k 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU k 27 " --> pdb=" O GLY k 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 removed outlier: 3.617A pdb=" N TYR C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 40 removed outlier: 4.172A pdb=" N ALA C 22 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 74 Proline residue: C 49 - end of helix removed outlier: 3.867A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 69 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 19 through 39 removed outlier: 3.647A pdb=" N ILE D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 75 Proline residue: D 49 - end of helix removed outlier: 5.252A pdb=" N THR D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 15 removed outlier: 4.332A pdb=" N TYR E 9 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 40 removed outlier: 3.867A pdb=" N ALA E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 75 Proline residue: E 49 - end of helix removed outlier: 5.629A pdb=" N CYS E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.705A pdb=" N TYR F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 40 removed outlier: 3.697A pdb=" N GLY F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA F 27 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG F 39 " --> pdb=" O ASN F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 74 Proline residue: F 49 - end of helix removed outlier: 4.551A pdb=" N THR F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.612A pdb=" N ALA G 7 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 40 removed outlier: 4.077A pdb=" N ALA G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA G 27 " --> pdb=" O GLY G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 74 Proline residue: G 49 - end of helix removed outlier: 3.540A pdb=" N LEU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL G 68 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER G 69 " --> pdb=" O CYS G 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 74 " --> pdb=" O PHE G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.585A pdb=" N TYR H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 40 removed outlier: 4.108A pdb=" N ALA H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA H 27 " --> pdb=" O GLY H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 74 Proline residue: H 49 - end of helix removed outlier: 3.580A pdb=" N GLY H 62 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE H 74 " --> pdb=" O PHE H 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 15 removed outlier: 3.545A pdb=" N TYR I 9 " --> pdb=" O LEU I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 40 removed outlier: 4.176A pdb=" N ALA I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA I 27 " --> pdb=" O GLY I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 72 Proline residue: I 49 - end of helix removed outlier: 3.671A pdb=" N CYS I 65 " --> pdb=" O THR I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 16 removed outlier: 4.062A pdb=" N THR J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 40 removed outlier: 4.026A pdb=" N ALA J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 74 Proline residue: J 49 - end of helix removed outlier: 4.403A pdb=" N CYS J 65 " --> pdb=" O THR J 61 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 18 through 40 removed outlier: 4.076A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG K 39 " --> pdb=" O ASN K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 74 Proline residue: K 49 - end of helix removed outlier: 3.860A pdb=" N CYS K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.575A pdb=" N ALA B 7 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 38 removed outlier: 4.237A pdb=" N ALA B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA B 27 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 72 Proline residue: B 49 - end of helix removed outlier: 3.820A pdb=" N THR B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 30 Processing helix chain 'L' and resid 30 through 48 removed outlier: 3.810A pdb=" N LEU L 38 " --> pdb=" O MET L 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 7 removed outlier: 3.585A pdb=" N PHE M 6 " --> pdb=" O LEU M 3 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU M 7 " --> pdb=" O ASP M 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 3 through 7' Processing helix chain 'M' and resid 27 through 43 Processing helix chain 'M' and resid 58 through 74 removed outlier: 3.961A pdb=" N GLN M 62 " --> pdb=" O TRP M 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR M 66 " --> pdb=" O GLN M 62 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET M 72 " --> pdb=" O THR M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'M' and resid 85 through 99 removed outlier: 3.891A pdb=" N PHE M 93 " --> pdb=" O ILE M 89 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE M 96 " --> pdb=" O LEU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 105 Processing helix chain 'M' and resid 114 through 138 removed outlier: 3.501A pdb=" N SER M 120 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU M 132 " --> pdb=" O GLY M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 146 removed outlier: 3.738A pdb=" N PHE M 142 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL M 146 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 153 No H-bonds generated for 'chain 'M' and resid 151 through 153' Processing helix chain 'M' and resid 154 through 168 removed outlier: 3.865A pdb=" N GLU M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER M 165 " --> pdb=" O ILE M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 199 removed outlier: 3.861A pdb=" N LEU M 173 " --> pdb=" O ARG M 169 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY M 174 " --> pdb=" O ALA M 170 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU M 177 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN M 197 " --> pdb=" O GLY M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 206 Processing helix chain 'M' and resid 209 through 247 removed outlier: 4.122A pdb=" N LEU M 213 " --> pdb=" O GLY M 209 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE M 224 " --> pdb=" O MET M 220 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA M 225 " --> pdb=" O MET M 221 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN M 230 " --> pdb=" O ILE M 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY M 231 " --> pdb=" O GLY M 227 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA M 235 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA M 239 " --> pdb=" O ALA M 235 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU M 242 " --> pdb=" O THR M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 22 removed outlier: 4.275A pdb=" N ASN N 16 " --> pdb=" O LYS N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 47 removed outlier: 3.539A pdb=" N ILE N 42 " --> pdb=" O ALA N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 101 removed outlier: 4.111A pdb=" N ILE N 57 " --> pdb=" O ASN N 53 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU N 58 " --> pdb=" O ASP N 54 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA N 74 " --> pdb=" O ALA N 70 " (cutoff:3.500A) Proline residue: N 75 - end of helix removed outlier: 3.991A pdb=" N ARG N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 230 Processing helix chain 'O' and resid 245 through 253 Processing helix chain 'O' and resid 253 through 267 removed outlier: 4.117A pdb=" N ASP O 257 " --> pdb=" O LYS O 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 49 removed outlier: 4.309A pdb=" N UNK P 12 " --> pdb=" O UNK P 8 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N UNK P 13 " --> pdb=" O UNK P 9 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N UNK P 14 " --> pdb=" O UNK P 10 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N UNK P 19 " --> pdb=" O UNK P 15 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N UNK P 39 " --> pdb=" O UNK P 35 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N UNK P 40 " --> pdb=" O UNK P 36 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N UNK P 41 " --> pdb=" O UNK P 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N UNK P 42 " --> pdb=" O UNK P 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 31 removed outlier: 3.907A pdb=" N ALA Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL Q 28 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 56 removed outlier: 3.585A pdb=" N TYR Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 85 removed outlier: 3.874A pdb=" N TRP Q 67 " --> pdb=" O GLY Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 13 Processing helix chain 'R' and resid 13 through 44 removed outlier: 3.898A pdb=" N UNK R 28 " --> pdb=" O UNK R 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N UNK R 29 " --> pdb=" O UNK R 25 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N UNK R 30 " --> pdb=" O UNK R 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK R 31 " --> pdb=" O UNK R 27 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N UNK R 33 " --> pdb=" O UNK R 29 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N UNK R 38 " --> pdb=" O UNK R 34 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N UNK R 39 " --> pdb=" O UNK R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 73 removed outlier: 3.787A pdb=" N UNK R 52 " --> pdb=" O UNK R 48 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N UNK R 53 " --> pdb=" O UNK R 49 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N UNK R 54 " --> pdb=" O UNK R 50 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N UNK R 57 " --> pdb=" O UNK R 53 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N UNK R 67 " --> pdb=" O UNK R 63 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N UNK R 68 " --> pdb=" O UNK R 64 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N UNK R 71 " --> pdb=" O UNK R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 79 Processing helix chain 'R' and resid 83 through 104 removed outlier: 4.023A pdb=" N UNK R 87 " --> pdb=" O UNK R 83 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N UNK R 91 " --> pdb=" O UNK R 87 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N UNK R 92 " --> pdb=" O UNK R 88 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N UNK R 93 " --> pdb=" O UNK R 89 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N UNK R 94 " --> pdb=" O UNK R 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 35 Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.058A pdb=" N THR T 21 " --> pdb=" O LEU T 17 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) 1673 hydrogen bonds defined for protein. 4965 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: 3.62 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5676 1.34 - 1.45: 3607 1.45 - 1.57: 12325 1.57 - 1.69: 0 1.69 - 1.81: 214 Bond restraints: 21822 Sorted by residual: bond pdb=" N GLU 3 59 " pdb=" CA GLU 3 59 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" N GLU E 59 " pdb=" CA GLU E 59 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CG1 ILE a 69 " pdb=" CD1 ILE a 69 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.40e+00 bond pdb=" CG1 ILE M 69 " pdb=" CD1 ILE M 69 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.25e+00 bond pdb=" C ASN S 42 " pdb=" N ASP S 43 " ideal model delta sigma weight residual 1.333 1.300 0.033 1.50e-02 4.44e+03 4.81e+00 ... (remaining 21817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 29112 3.39 - 6.79: 417 6.79 - 10.18: 101 10.18 - 13.57: 4 13.57 - 16.96: 4 Bond angle restraints: 29638 Sorted by residual: angle pdb=" N PRO N 11 " pdb=" CA PRO N 11 " pdb=" CB PRO N 11 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.42e+01 angle pdb=" N PRO b 11 " pdb=" CA PRO b 11 " pdb=" CB PRO b 11 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.42e+01 angle pdb=" N PRO N 23 " pdb=" CA PRO N 23 " pdb=" CB PRO N 23 " ideal model delta sigma weight residual 103.25 110.08 -6.83 1.05e+00 9.07e-01 4.24e+01 angle pdb=" N PRO b 23 " pdb=" CA PRO b 23 " pdb=" CB PRO b 23 " ideal model delta sigma weight residual 103.25 110.05 -6.80 1.05e+00 9.07e-01 4.20e+01 angle pdb=" C GLN k 16 " pdb=" N LEU k 17 " pdb=" CA LEU k 17 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 ... (remaining 29633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.61: 11860 14.61 - 29.22: 639 29.22 - 43.84: 153 43.84 - 58.45: 12 58.45 - 73.06: 16 Dihedral angle restraints: 12680 sinusoidal: 4206 harmonic: 8474 Sorted by residual: dihedral pdb=" CA UNK g 80 " pdb=" C UNK g 80 " pdb=" N UNK g 81 " pdb=" CA UNK g 81 " ideal model delta harmonic sigma weight residual 180.00 149.13 30.87 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA UNK R 80 " pdb=" C UNK R 80 " pdb=" N UNK R 81 " pdb=" CA UNK R 81 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA SER a 108 " pdb=" C SER a 108 " pdb=" N PHE a 109 " pdb=" CA PHE a 109 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3129 0.073 - 0.146: 473 0.146 - 0.219: 64 0.219 - 0.292: 10 0.292 - 0.365: 2 Chirality restraints: 3678 Sorted by residual: chirality pdb=" CB ILE C 43 " pdb=" CA ILE C 43 " pdb=" CG1 ILE C 43 " pdb=" CG2 ILE C 43 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE 1 43 " pdb=" CA ILE 1 43 " pdb=" CG1 ILE 1 43 " pdb=" CG2 ILE 1 43 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA PRO N 23 " pdb=" N PRO N 23 " pdb=" C PRO N 23 " pdb=" CB PRO N 23 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 3675 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK g 80 " 0.031 2.00e-02 2.50e+03 6.13e-02 3.75e+01 pdb=" C UNK g 80 " -0.106 2.00e-02 2.50e+03 pdb=" O UNK g 80 " 0.040 2.00e-02 2.50e+03 pdb=" N UNK g 81 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK R 80 " 0.031 2.00e-02 2.50e+03 6.12e-02 3.75e+01 pdb=" C UNK R 80 " -0.106 2.00e-02 2.50e+03 pdb=" O UNK R 80 " 0.040 2.00e-02 2.50e+03 pdb=" N UNK R 81 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE M 224 " -0.014 2.00e-02 2.50e+03 2.17e-02 8.26e+00 pdb=" CG PHE M 224 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE M 224 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE M 224 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE M 224 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE M 224 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE M 224 " -0.004 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6333 2.81 - 3.33: 21433 3.33 - 3.86: 35610 3.86 - 4.38: 38997 4.38 - 4.90: 67753 Nonbonded interactions: 170126 Sorted by model distance: nonbonded pdb=" O SER G 58 " pdb=" OG1 THR G 61 " model vdw 2.290 3.040 nonbonded pdb=" O SER 5 58 " pdb=" OG1 THR 5 61 " model vdw 2.290 3.040 nonbonded pdb=" O MET A 10 " pdb=" OG1 THR A 14 " model vdw 2.328 3.040 nonbonded pdb=" O MET L 10 " pdb=" OG1 THR L 14 " model vdw 2.328 3.040 nonbonded pdb=" OG SER M 1 " pdb=" OD2 ASP M 4 " model vdw 2.332 3.040 ... (remaining 170121 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 '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) selection = (chain 'B' and resid 2 through 73) selection = (chain 'C' and resid 2 through 73) selection = (chain 'D' and resid 2 through 73) selection = (chain 'E' and resid 2 through 73) selection = (chain 'F' and resid 2 through 73) selection = (chain 'G' and resid 2 through 73) selection = (chain 'H' and resid 2 through 73) selection = (chain 'I' and resid 2 through 73) selection = (chain 'J' and resid 2 through 73) selection = (chain 'K' and resid 2 through 73) } ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = chain 'O' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'e' } ncs_group { reference = chain 'Q' selection = chain 'f' } ncs_group { reference = chain 'R' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'i' } ncs_group { reference = chain 'T' selection = chain 'k' } 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.080 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.008 0.106 21822 Z= 0.325 Angle : 1.137 16.965 29638 Z= 0.595 Chirality : 0.056 0.365 3678 Planarity : 0.008 0.061 3644 Dihedral : 10.484 73.061 7240 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.05 % Favored : 95.72 % Rotamer: Outliers : 0.69 % Allowed : 3.46 % Favored : 95.85 % 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: -3.66 (0.13), residues: 2618 helix: -2.03 (0.09), residues: 2050 sheet: None (None), residues: 0 loop : -3.17 (0.21), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 84 TYR 0.039 0.003 TYR M 32 PHE 0.044 0.004 PHE M 224 TRP 0.037 0.003 TRP M 234 HIS 0.010 0.002 HIS f 68 Details of bonding type rmsd covalent geometry : bond 0.00761 (21822) covalent geometry : angle 1.13655 (29638) hydrogen bonds : bond 0.10553 ( 1673) hydrogen bonds : angle 5.72962 ( 4965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1011 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 16 THR cc_start: 0.9119 (p) cc_final: 0.8826 (t) REVERT: 2 58 SER cc_start: 0.8981 (t) cc_final: 0.8617 (p) REVERT: 3 45 ASP cc_start: 0.8496 (m-30) cc_final: 0.8169 (t70) REVERT: 4 40 ASN cc_start: 0.8983 (t0) cc_final: 0.8404 (t0) REVERT: 4 43 ILE cc_start: 0.9055 (tp) cc_final: 0.8512 (tt) REVERT: 4 59 GLU cc_start: 0.8962 (tp30) cc_final: 0.8757 (tp30) REVERT: 4 72 LEU cc_start: 0.8408 (mt) cc_final: 0.8074 (mt) REVERT: 5 3 LEU cc_start: 0.8908 (tp) cc_final: 0.8524 (tt) REVERT: 5 16 THR cc_start: 0.9032 (p) cc_final: 0.8821 (t) REVERT: 5 28 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8812 (tp) REVERT: 5 64 PHE cc_start: 0.8460 (m-10) cc_final: 0.8164 (m-80) REVERT: 6 39 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7918 (ttm110) REVERT: 6 46 THR cc_start: 0.8705 (m) cc_final: 0.8319 (p) REVERT: 6 65 CYS cc_start: 0.8960 (m) cc_final: 0.8437 (m) REVERT: 6 72 LEU cc_start: 0.9181 (mt) cc_final: 0.8937 (mt) REVERT: 7 2 GLN cc_start: 0.7574 (tp-100) cc_final: 0.6988 (pm20) REVERT: 7 35 ASN cc_start: 0.8975 (m-40) cc_final: 0.8155 (t0) REVERT: 7 44 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8421 (tptm) REVERT: 7 67 MET cc_start: 0.8671 (ptm) cc_final: 0.7866 (mtp) REVERT: 8 67 MET cc_start: 0.8640 (ptm) cc_final: 0.8064 (mtp) REVERT: 9 39 ARG cc_start: 0.8729 (ttm170) cc_final: 0.8524 (mtp180) REVERT: 9 43 ILE cc_start: 0.8001 (tp) cc_final: 0.7727 (mt) REVERT: 9 46 THR cc_start: 0.7698 (m) cc_final: 0.7371 (p) REVERT: 0 5 LEU cc_start: 0.8725 (tp) cc_final: 0.8185 (tp) REVERT: 0 9 TYR cc_start: 0.7888 (m-80) cc_final: 0.7666 (m-80) REVERT: 0 19 LEU cc_start: 0.8964 (tp) cc_final: 0.8696 (pp) REVERT: 0 47 VAL cc_start: 0.8682 (t) cc_final: 0.8298 (t) REVERT: A 3 GLN cc_start: 0.7473 (tp-100) cc_final: 0.7182 (tp-100) REVERT: a 74 LYS cc_start: 0.8922 (ttpt) cc_final: 0.8664 (ttpt) REVERT: a 85 TYR cc_start: 0.8710 (m-80) cc_final: 0.8501 (m-80) REVERT: a 186 LEU cc_start: 0.9334 (tp) cc_final: 0.9010 (tp) REVERT: b 72 TYR cc_start: 0.7927 (m-10) cc_final: 0.7600 (m-10) REVERT: d 280 ASN cc_start: 0.8185 (p0) cc_final: 0.7844 (p0) REVERT: f 59 ASP cc_start: 0.7969 (t0) cc_final: 0.7661 (t70) REVERT: i 1 MET cc_start: 0.6110 (ttp) cc_final: 0.4827 (tpt) REVERT: i 11 LYS cc_start: 0.8911 (pttt) cc_final: 0.8404 (mmtt) REVERT: i 27 MET cc_start: 0.8426 (tpp) cc_final: 0.8225 (tpp) REVERT: D 16 THR cc_start: 0.9144 (p) cc_final: 0.8838 (t) REVERT: D 58 SER cc_start: 0.8962 (t) cc_final: 0.8622 (p) REVERT: E 45 ASP cc_start: 0.8513 (m-30) cc_final: 0.8154 (t70) REVERT: F 40 ASN cc_start: 0.9007 (t0) cc_final: 0.8404 (t0) REVERT: F 43 ILE cc_start: 0.9079 (tp) cc_final: 0.8539 (tt) REVERT: F 59 GLU cc_start: 0.8940 (tp30) cc_final: 0.8731 (tp30) REVERT: F 61 THR cc_start: 0.9582 (p) cc_final: 0.9345 (t) REVERT: F 72 LEU cc_start: 0.8447 (mt) cc_final: 0.8106 (mt) REVERT: G 3 LEU cc_start: 0.8880 (tp) cc_final: 0.8460 (tt) REVERT: G 16 THR cc_start: 0.9050 (p) cc_final: 0.8848 (t) REVERT: G 28 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8764 (tp) REVERT: G 64 PHE cc_start: 0.8405 (m-10) cc_final: 0.8114 (m-80) REVERT: H 39 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7899 (ttm110) REVERT: H 46 THR cc_start: 0.8639 (m) cc_final: 0.8318 (p) REVERT: H 65 CYS cc_start: 0.8989 (m) cc_final: 0.8414 (m) REVERT: H 72 LEU cc_start: 0.9217 (mt) cc_final: 0.8947 (mt) REVERT: I 2 GLN cc_start: 0.7555 (tp-100) cc_final: 0.6959 (pm20) REVERT: I 9 TYR cc_start: 0.7409 (m-10) cc_final: 0.7119 (m-10) REVERT: I 35 ASN cc_start: 0.8966 (m-40) cc_final: 0.8118 (t0) REVERT: I 44 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8340 (tmtt) REVERT: I 67 MET cc_start: 0.8673 (ptm) cc_final: 0.7866 (mtp) REVERT: J 8 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8305 (mtmm) REVERT: J 43 ILE cc_start: 0.8204 (tp) cc_final: 0.7572 (tp) REVERT: J 67 MET cc_start: 0.8599 (ptm) cc_final: 0.8060 (mtp) REVERT: K 39 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8468 (mtp180) REVERT: K 43 ILE cc_start: 0.7978 (tp) cc_final: 0.7690 (mt) REVERT: K 46 THR cc_start: 0.7579 (m) cc_final: 0.7240 (p) REVERT: B 5 LEU cc_start: 0.8698 (tp) cc_final: 0.8186 (tp) REVERT: B 9 TYR cc_start: 0.7922 (m-80) cc_final: 0.7699 (m-80) REVERT: B 47 VAL cc_start: 0.8637 (t) cc_final: 0.8255 (t) REVERT: B 69 SER cc_start: 0.9255 (t) cc_final: 0.9008 (p) REVERT: L 3 GLN cc_start: 0.7413 (tp-100) cc_final: 0.7137 (tp-100) REVERT: L 8 TYR cc_start: 0.8544 (m-80) cc_final: 0.8337 (m-80) REVERT: M 74 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8679 (ttpt) REVERT: M 186 LEU cc_start: 0.9357 (tp) cc_final: 0.9018 (tp) REVERT: N 72 TYR cc_start: 0.7916 (m-10) cc_final: 0.7586 (m-10) REVERT: O 280 ASN cc_start: 0.8219 (p0) cc_final: 0.7864 (p0) REVERT: Q 59 ASP cc_start: 0.8007 (t0) cc_final: 0.7699 (t70) REVERT: Q 76 PHE cc_start: 0.8472 (t80) cc_final: 0.8198 (t80) REVERT: S 1 MET cc_start: 0.6133 (ttp) cc_final: 0.4832 (tpt) REVERT: S 11 LYS cc_start: 0.8928 (pttt) cc_final: 0.8290 (mmtt) REVERT: S 27 MET cc_start: 0.8438 (tpp) cc_final: 0.8224 (tpp) outliers start: 14 outliers final: 0 residues processed: 1013 average time/residue: 0.1424 time to fit residues: 230.6027 Evaluate side-chains 745 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 743 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 28 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN A 29 GLN a 71 ASN a 180 ASN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN L 29 GLN M 71 ASN M 180 ASN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.142488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104110 restraints weight = 37898.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107456 restraints weight = 17934.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109476 restraints weight = 11417.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110610 restraints weight = 8879.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111330 restraints weight = 7769.454| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21822 Z= 0.149 Angle : 0.717 11.304 29638 Z= 0.349 Chirality : 0.043 0.280 3678 Planarity : 0.005 0.060 3644 Dihedral : 4.892 25.512 3088 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.70 % Allowed : 16.68 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.15), residues: 2618 helix: -0.05 (0.11), residues: 2036 sheet: None (None), residues: 0 loop : -2.20 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 39 TYR 0.017 0.002 TYR f 31 PHE 0.031 0.002 PHE I 55 TRP 0.012 0.001 TRP M 234 HIS 0.005 0.001 HIS f 68 Details of bonding type rmsd covalent geometry : bond 0.00324 (21822) covalent geometry : angle 0.71699 (29638) hydrogen bonds : bond 0.04223 ( 1673) hydrogen bonds : angle 4.27827 ( 4965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 841 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 16 THR cc_start: 0.9242 (p) cc_final: 0.8976 (t) REVERT: 3 45 ASP cc_start: 0.8521 (m-30) cc_final: 0.8246 (t70) REVERT: 4 40 ASN cc_start: 0.8936 (t0) cc_final: 0.7862 (t0) REVERT: 4 43 ILE cc_start: 0.9094 (tp) cc_final: 0.8575 (tt) REVERT: 4 59 GLU cc_start: 0.8700 (tp30) cc_final: 0.8400 (tp30) REVERT: 4 61 THR cc_start: 0.9568 (p) cc_final: 0.9305 (t) REVERT: 5 2 GLN cc_start: 0.7542 (mt0) cc_final: 0.7217 (pm20) REVERT: 5 28 ILE cc_start: 0.9221 (mt) cc_final: 0.9007 (tp) REVERT: 5 64 PHE cc_start: 0.8442 (m-10) cc_final: 0.8234 (m-80) REVERT: 6 46 THR cc_start: 0.8711 (m) cc_final: 0.8492 (p) REVERT: 6 72 LEU cc_start: 0.9202 (mt) cc_final: 0.8976 (tp) REVERT: 7 2 GLN cc_start: 0.7604 (tp-100) cc_final: 0.7178 (pm20) REVERT: 7 9 TYR cc_start: 0.7403 (m-10) cc_final: 0.7199 (m-10) REVERT: 7 67 MET cc_start: 0.8691 (ptm) cc_final: 0.7901 (mtp) REVERT: 8 9 TYR cc_start: 0.8452 (m-10) cc_final: 0.8191 (m-10) REVERT: 8 64 PHE cc_start: 0.8994 (m-10) cc_final: 0.8687 (m-10) REVERT: 8 67 MET cc_start: 0.8536 (ptm) cc_final: 0.8002 (mtp) REVERT: 9 35 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8614 (m-40) REVERT: 9 43 ILE cc_start: 0.8240 (tp) cc_final: 0.7914 (mt) REVERT: 9 46 THR cc_start: 0.7615 (m) cc_final: 0.7295 (p) REVERT: 0 5 LEU cc_start: 0.8721 (tp) cc_final: 0.8052 (pp) REVERT: A 3 GLN cc_start: 0.7160 (tp-100) cc_final: 0.6352 (tp40) REVERT: A 8 TYR cc_start: 0.8393 (m-80) cc_final: 0.8159 (m-80) REVERT: a 57 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7112 (ttt180) REVERT: a 68 THR cc_start: 0.9091 (t) cc_final: 0.8787 (m) REVERT: a 85 TYR cc_start: 0.8521 (m-80) cc_final: 0.8305 (m-80) REVERT: a 94 MET cc_start: 0.8981 (mmt) cc_final: 0.8700 (mmt) REVERT: a 186 LEU cc_start: 0.9159 (tp) cc_final: 0.8815 (tp) REVERT: b 72 TYR cc_start: 0.7945 (m-10) cc_final: 0.7542 (m-10) REVERT: b 82 ASP cc_start: 0.8509 (m-30) cc_final: 0.8303 (m-30) REVERT: i 1 MET cc_start: 0.6095 (ttp) cc_final: 0.4741 (tpt) REVERT: i 11 LYS cc_start: 0.8918 (pttt) cc_final: 0.8216 (mmtt) REVERT: i 42 ASN cc_start: 0.8676 (m-40) cc_final: 0.8404 (m-40) REVERT: C 39 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7719 (tpp80) REVERT: D 16 THR cc_start: 0.9165 (p) cc_final: 0.8919 (t) REVERT: D 67 MET cc_start: 0.8049 (mmm) cc_final: 0.7429 (mmm) REVERT: E 45 ASP cc_start: 0.8538 (m-30) cc_final: 0.8271 (t70) REVERT: F 40 ASN cc_start: 0.8913 (t0) cc_final: 0.7851 (t0) REVERT: F 43 ILE cc_start: 0.9100 (tp) cc_final: 0.8600 (tt) REVERT: F 59 GLU cc_start: 0.8690 (tp30) cc_final: 0.8398 (tp30) REVERT: F 61 THR cc_start: 0.9560 (p) cc_final: 0.9315 (t) REVERT: G 2 GLN cc_start: 0.7635 (mt0) cc_final: 0.7306 (pm20) REVERT: G 28 ILE cc_start: 0.9237 (mt) cc_final: 0.9019 (tp) REVERT: G 64 PHE cc_start: 0.8423 (m-10) cc_final: 0.8040 (m-80) REVERT: H 39 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7720 (ttm110) REVERT: H 46 THR cc_start: 0.8697 (m) cc_final: 0.8460 (p) REVERT: H 72 LEU cc_start: 0.9222 (mt) cc_final: 0.8957 (tp) REVERT: I 2 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7116 (pm20) REVERT: I 9 TYR cc_start: 0.7326 (m-10) cc_final: 0.7109 (m-10) REVERT: I 67 MET cc_start: 0.8656 (ptm) cc_final: 0.7881 (mtp) REVERT: J 8 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8419 (mtmm) REVERT: J 39 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7672 (ttm170) REVERT: J 64 PHE cc_start: 0.8999 (m-10) cc_final: 0.8697 (m-10) REVERT: J 67 MET cc_start: 0.8557 (ptm) cc_final: 0.8007 (mtp) REVERT: K 35 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8575 (m-40) REVERT: K 59 GLU cc_start: 0.8423 (tp30) cc_final: 0.8218 (tp30) REVERT: B 5 LEU cc_start: 0.8719 (tp) cc_final: 0.8015 (pp) REVERT: B 69 SER cc_start: 0.9177 (t) cc_final: 0.8928 (p) REVERT: L 3 GLN cc_start: 0.7147 (tp-100) cc_final: 0.6303 (tp40) REVERT: M 57 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7092 (ttt180) REVERT: M 68 THR cc_start: 0.9072 (t) cc_final: 0.8765 (m) REVERT: M 94 MET cc_start: 0.8975 (mmt) cc_final: 0.8747 (mmt) REVERT: M 186 LEU cc_start: 0.9164 (tp) cc_final: 0.8826 (tp) REVERT: N 72 TYR cc_start: 0.7965 (m-10) cc_final: 0.7572 (m-10) REVERT: Q 59 ASP cc_start: 0.7941 (t0) cc_final: 0.7647 (t70) REVERT: S 1 MET cc_start: 0.6032 (ttp) cc_final: 0.4610 (tpt) REVERT: S 11 LYS cc_start: 0.8921 (pttt) cc_final: 0.8207 (mmtt) REVERT: S 25 TYR cc_start: 0.8177 (t80) cc_final: 0.7891 (t80) REVERT: S 42 ASN cc_start: 0.8654 (m-40) cc_final: 0.8364 (m-40) outliers start: 75 outliers final: 35 residues processed: 871 average time/residue: 0.1305 time to fit residues: 186.4678 Evaluate side-chains 757 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 720 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 69 SER Chi-restraints excluded: chain 3 residue 55 PHE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 65 CYS Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 256 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 257 optimal weight: 0.0370 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 2 GLN ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN K 2 GLN ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101930 restraints weight = 38544.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105260 restraints weight = 18525.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107250 restraints weight = 11948.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108293 restraints weight = 9348.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109035 restraints weight = 8257.721| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21822 Z= 0.145 Angle : 0.692 10.101 29638 Z= 0.336 Chirality : 0.042 0.258 3678 Planarity : 0.004 0.062 3644 Dihedral : 4.592 23.804 3084 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.24 % Allowed : 20.53 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2618 helix: 0.57 (0.11), residues: 2048 sheet: None (None), residues: 0 loop : -2.18 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 239 TYR 0.021 0.002 TYR a 32 PHE 0.038 0.002 PHE 7 55 TRP 0.010 0.001 TRP M 234 HIS 0.006 0.001 HIS f 68 Details of bonding type rmsd covalent geometry : bond 0.00323 (21822) covalent geometry : angle 0.69207 (29638) hydrogen bonds : bond 0.04043 ( 1673) hydrogen bonds : angle 4.08386 ( 4965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 766 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 33 LEU cc_start: 0.9182 (tp) cc_final: 0.8938 (tt) REVERT: 4 40 ASN cc_start: 0.8806 (t0) cc_final: 0.7786 (t0) REVERT: 4 43 ILE cc_start: 0.9062 (tp) cc_final: 0.8592 (tt) REVERT: 4 59 GLU cc_start: 0.8637 (tp30) cc_final: 0.8361 (tp30) REVERT: 4 61 THR cc_start: 0.9582 (p) cc_final: 0.9280 (t) REVERT: 4 72 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8062 (mm) REVERT: 5 2 GLN cc_start: 0.7617 (mt0) cc_final: 0.7360 (pm20) REVERT: 5 64 PHE cc_start: 0.8492 (m-10) cc_final: 0.8168 (m-80) REVERT: 6 57 LEU cc_start: 0.8644 (tp) cc_final: 0.8328 (tp) REVERT: 6 72 LEU cc_start: 0.9207 (mt) cc_final: 0.8971 (tp) REVERT: 7 2 GLN cc_start: 0.7817 (tp-100) cc_final: 0.7151 (pm20) REVERT: 7 67 MET cc_start: 0.8727 (ptm) cc_final: 0.7915 (mtp) REVERT: 8 43 ILE cc_start: 0.8083 (tp) cc_final: 0.7518 (tp) REVERT: 8 64 PHE cc_start: 0.8991 (m-10) cc_final: 0.8694 (m-10) REVERT: 8 67 MET cc_start: 0.8555 (ptm) cc_final: 0.7999 (mtp) REVERT: 8 72 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7943 (mm) REVERT: 9 35 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8572 (m-40) REVERT: 9 43 ILE cc_start: 0.8215 (tp) cc_final: 0.7929 (mt) REVERT: 9 46 THR cc_start: 0.7520 (m) cc_final: 0.7301 (p) REVERT: 0 5 LEU cc_start: 0.8660 (tp) cc_final: 0.7744 (tp) REVERT: 0 9 TYR cc_start: 0.7829 (m-80) cc_final: 0.7167 (m-80) REVERT: A 3 GLN cc_start: 0.7120 (tp-100) cc_final: 0.6861 (tp40) REVERT: a 68 THR cc_start: 0.9124 (t) cc_final: 0.8846 (m) REVERT: a 94 MET cc_start: 0.9038 (mmt) cc_final: 0.8815 (mmt) REVERT: a 186 LEU cc_start: 0.9156 (tp) cc_final: 0.8761 (tp) REVERT: b 72 TYR cc_start: 0.7931 (m-10) cc_final: 0.7511 (m-10) REVERT: b 82 ASP cc_start: 0.8498 (m-30) cc_final: 0.8252 (m-30) REVERT: i 1 MET cc_start: 0.6214 (ttp) cc_final: 0.4801 (tpt) REVERT: i 11 LYS cc_start: 0.8815 (pttt) cc_final: 0.8090 (mmtt) REVERT: C 39 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7714 (tpp80) REVERT: D 33 LEU cc_start: 0.9168 (tp) cc_final: 0.8946 (tt) REVERT: D 67 MET cc_start: 0.8173 (mmm) cc_final: 0.7952 (mmm) REVERT: E 67 MET cc_start: 0.8717 (tmm) cc_final: 0.8516 (tmm) REVERT: F 40 ASN cc_start: 0.8786 (t0) cc_final: 0.7771 (t0) REVERT: F 43 ILE cc_start: 0.9078 (tp) cc_final: 0.8630 (tt) REVERT: F 59 GLU cc_start: 0.8619 (tp30) cc_final: 0.8333 (tp30) REVERT: F 61 THR cc_start: 0.9579 (p) cc_final: 0.9331 (t) REVERT: F 72 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7990 (mm) REVERT: G 2 GLN cc_start: 0.7774 (mt0) cc_final: 0.7291 (pm20) REVERT: H 39 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7752 (ttm110) REVERT: H 57 LEU cc_start: 0.8623 (tp) cc_final: 0.8286 (tp) REVERT: H 72 LEU cc_start: 0.9168 (mt) cc_final: 0.8953 (tp) REVERT: I 2 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7160 (pm20) REVERT: I 55 PHE cc_start: 0.8800 (t80) cc_final: 0.8577 (t80) REVERT: I 67 MET cc_start: 0.8631 (ptm) cc_final: 0.7834 (mtp) REVERT: J 64 PHE cc_start: 0.9027 (m-10) cc_final: 0.8805 (m-10) REVERT: J 67 MET cc_start: 0.8532 (ptm) cc_final: 0.7982 (mtp) REVERT: K 35 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8495 (m-40) REVERT: B 5 LEU cc_start: 0.8652 (tp) cc_final: 0.7802 (tp) REVERT: B 9 TYR cc_start: 0.7842 (m-80) cc_final: 0.7189 (m-80) REVERT: B 69 SER cc_start: 0.9149 (t) cc_final: 0.8928 (p) REVERT: L 3 GLN cc_start: 0.7080 (tp-100) cc_final: 0.6755 (tp40) REVERT: M 68 THR cc_start: 0.9112 (t) cc_final: 0.8848 (m) REVERT: M 186 LEU cc_start: 0.9192 (tp) cc_final: 0.8776 (tp) REVERT: N 72 TYR cc_start: 0.7925 (m-10) cc_final: 0.7507 (m-10) REVERT: S 1 MET cc_start: 0.6202 (ttp) cc_final: 0.4744 (tpt) REVERT: S 11 LYS cc_start: 0.8808 (pttt) cc_final: 0.8090 (mmtt) REVERT: T 8 MET cc_start: 0.6794 (tpt) cc_final: 0.6584 (tpt) outliers start: 86 outliers final: 50 residues processed: 799 average time/residue: 0.1295 time to fit residues: 170.8607 Evaluate side-chains 759 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 704 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 70 PHE Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 69 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 61 THR Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 257 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.107863 restraints weight = 38827.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106824 restraints weight = 20850.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107061 restraints weight = 23039.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108465 restraints weight = 15277.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109005 restraints weight = 12595.722| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21822 Z= 0.195 Angle : 0.701 10.082 29638 Z= 0.345 Chirality : 0.043 0.230 3678 Planarity : 0.004 0.063 3644 Dihedral : 4.463 27.626 3084 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.08 % Allowed : 23.05 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2618 helix: 0.82 (0.11), residues: 2060 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 23 TYR 0.020 0.002 TYR a 166 PHE 0.050 0.002 PHE 7 55 TRP 0.015 0.001 TRP M 234 HIS 0.007 0.001 HIS f 68 Details of bonding type rmsd covalent geometry : bond 0.00460 (21822) covalent geometry : angle 0.70065 (29638) hydrogen bonds : bond 0.04103 ( 1673) hydrogen bonds : angle 4.05157 ( 4965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 745 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 40 ASN cc_start: 0.8798 (t0) cc_final: 0.7986 (t0) REVERT: 4 43 ILE cc_start: 0.9094 (tp) cc_final: 0.8847 (tt) REVERT: 4 59 GLU cc_start: 0.8703 (tp30) cc_final: 0.8245 (tp30) REVERT: 4 72 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7931 (mm) REVERT: 5 2 GLN cc_start: 0.7688 (mt0) cc_final: 0.7310 (pm20) REVERT: 5 55 PHE cc_start: 0.9232 (t80) cc_final: 0.8978 (t80) REVERT: 5 64 PHE cc_start: 0.8620 (m-10) cc_final: 0.8330 (m-80) REVERT: 7 2 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7174 (pm20) REVERT: 7 8 LYS cc_start: 0.8158 (mttp) cc_final: 0.7957 (mtpp) REVERT: 7 14 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8387 (tp) REVERT: 7 67 MET cc_start: 0.8791 (ptm) cc_final: 0.7936 (mtp) REVERT: 8 43 ILE cc_start: 0.8047 (tp) cc_final: 0.7498 (tp) REVERT: 8 64 PHE cc_start: 0.8995 (m-10) cc_final: 0.8650 (m-10) REVERT: 8 67 MET cc_start: 0.8623 (ptm) cc_final: 0.8123 (mtp) REVERT: 0 5 LEU cc_start: 0.8724 (tp) cc_final: 0.7805 (tp) REVERT: 0 9 TYR cc_start: 0.7860 (m-80) cc_final: 0.7272 (m-80) REVERT: A 3 GLN cc_start: 0.7361 (tp-100) cc_final: 0.7071 (tp40) REVERT: A 8 TYR cc_start: 0.8365 (m-80) cc_final: 0.7978 (m-80) REVERT: a 68 THR cc_start: 0.9227 (t) cc_final: 0.8988 (m) REVERT: a 94 MET cc_start: 0.8928 (mmt) cc_final: 0.8475 (mmt) REVERT: a 186 LEU cc_start: 0.9281 (tp) cc_final: 0.8877 (tp) REVERT: b 72 TYR cc_start: 0.8026 (m-10) cc_final: 0.7666 (m-10) REVERT: b 87 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8573 (ttmm) REVERT: i 1 MET cc_start: 0.6189 (ttp) cc_final: 0.4594 (tpt) REVERT: i 11 LYS cc_start: 0.8961 (pttt) cc_final: 0.8075 (mmpt) REVERT: C 39 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7813 (tpp80) REVERT: D 67 MET cc_start: 0.8207 (mmm) cc_final: 0.7976 (mmm) REVERT: E 67 MET cc_start: 0.8712 (tmm) cc_final: 0.8480 (tmm) REVERT: F 40 ASN cc_start: 0.8777 (t0) cc_final: 0.7968 (t0) REVERT: F 43 ILE cc_start: 0.9095 (tp) cc_final: 0.8841 (tt) REVERT: F 59 GLU cc_start: 0.8610 (tp30) cc_final: 0.8175 (tp30) REVERT: F 72 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8086 (mm) REVERT: G 2 GLN cc_start: 0.7711 (mt0) cc_final: 0.7292 (pm20) REVERT: G 55 PHE cc_start: 0.9214 (t80) cc_final: 0.8923 (t80) REVERT: H 72 LEU cc_start: 0.9137 (mt) cc_final: 0.8788 (mt) REVERT: I 2 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7150 (pm20) REVERT: I 8 LYS cc_start: 0.8259 (mttp) cc_final: 0.7913 (mtpp) REVERT: I 14 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8389 (tp) REVERT: I 67 MET cc_start: 0.8734 (ptm) cc_final: 0.7872 (mtp) REVERT: J 1 MET cc_start: 0.8332 (mtm) cc_final: 0.7844 (tmm) REVERT: J 8 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8329 (mtmm) REVERT: J 59 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8771 (mm-30) REVERT: J 64 PHE cc_start: 0.9054 (m-10) cc_final: 0.8743 (m-10) REVERT: J 67 MET cc_start: 0.8619 (ptm) cc_final: 0.8135 (mtp) REVERT: B 5 LEU cc_start: 0.8665 (tp) cc_final: 0.7649 (tp) REVERT: B 9 TYR cc_start: 0.7885 (m-80) cc_final: 0.7279 (m-80) REVERT: L 3 GLN cc_start: 0.7431 (tp-100) cc_final: 0.7164 (tp40) REVERT: L 18 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8642 (tt) REVERT: M 68 THR cc_start: 0.9215 (t) cc_final: 0.8987 (m) REVERT: M 186 LEU cc_start: 0.9300 (tp) cc_final: 0.8904 (tp) REVERT: N 72 TYR cc_start: 0.8032 (m-10) cc_final: 0.7678 (m-10) REVERT: N 87 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8577 (ttmm) REVERT: O 247 ASP cc_start: 0.8417 (m-30) cc_final: 0.8118 (m-30) REVERT: O 250 THR cc_start: 0.8857 (m) cc_final: 0.8600 (p) REVERT: S 1 MET cc_start: 0.6123 (ttp) cc_final: 0.4552 (tpt) REVERT: S 11 LYS cc_start: 0.8918 (pttt) cc_final: 0.8045 (mmpt) REVERT: S 25 TYR cc_start: 0.8192 (t80) cc_final: 0.7965 (t80) outliers start: 103 outliers final: 67 residues processed: 782 average time/residue: 0.1291 time to fit residues: 167.4386 Evaluate side-chains 773 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 701 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 69 SER Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 6 residue 20 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 7 residue 14 ILE Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain S residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 194 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 269 optimal weight: 30.0000 chunk 263 optimal weight: 30.0000 chunk 164 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 2 GLN 9 2 GLN ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109569 restraints weight = 38479.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108946 restraints weight = 19587.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109255 restraints weight = 21823.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.110270 restraints weight = 14862.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111459 restraints weight = 12383.633| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21822 Z= 0.152 Angle : 0.685 12.283 29638 Z= 0.332 Chirality : 0.042 0.288 3678 Planarity : 0.004 0.067 3644 Dihedral : 4.385 28.447 3084 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.94 % Allowed : 23.99 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2618 helix: 0.99 (0.11), residues: 2070 sheet: None (None), residues: 0 loop : -1.83 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 23 TYR 0.016 0.001 TYR S 24 PHE 0.050 0.002 PHE I 55 TRP 0.010 0.001 TRP M 234 HIS 0.005 0.001 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00353 (21822) covalent geometry : angle 0.68500 (29638) hydrogen bonds : bond 0.03952 ( 1673) hydrogen bonds : angle 3.96942 ( 4965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 746 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 40 ASN cc_start: 0.8744 (t0) cc_final: 0.7887 (t0) REVERT: 4 43 ILE cc_start: 0.9063 (tp) cc_final: 0.8682 (tt) REVERT: 4 59 GLU cc_start: 0.8570 (tp30) cc_final: 0.8212 (tp30) REVERT: 4 72 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7949 (mm) REVERT: 5 2 GLN cc_start: 0.7672 (mt0) cc_final: 0.7228 (pm20) REVERT: 7 2 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7158 (pm20) REVERT: 7 14 ILE cc_start: 0.8638 (mm) cc_final: 0.8407 (tp) REVERT: 7 67 MET cc_start: 0.8611 (ptm) cc_final: 0.7825 (mtp) REVERT: 8 43 ILE cc_start: 0.8098 (tp) cc_final: 0.7583 (tp) REVERT: 8 50 MET cc_start: 0.8389 (mtm) cc_final: 0.8133 (ptp) REVERT: 8 64 PHE cc_start: 0.8914 (m-10) cc_final: 0.8600 (m-10) REVERT: 8 67 MET cc_start: 0.8572 (ptm) cc_final: 0.8120 (mtp) REVERT: 0 5 LEU cc_start: 0.8763 (tp) cc_final: 0.7935 (tp) REVERT: 0 9 TYR cc_start: 0.7748 (m-80) cc_final: 0.7228 (m-80) REVERT: a 68 THR cc_start: 0.9221 (t) cc_final: 0.8983 (m) REVERT: a 186 LEU cc_start: 0.9243 (tp) cc_final: 0.8828 (tp) REVERT: a 199 MET cc_start: 0.8401 (mtt) cc_final: 0.8150 (mtt) REVERT: b 72 TYR cc_start: 0.8030 (m-10) cc_final: 0.7662 (m-10) REVERT: b 87 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8500 (ttmm) REVERT: i 1 MET cc_start: 0.6180 (ttp) cc_final: 0.4569 (tpt) REVERT: i 11 LYS cc_start: 0.8983 (pttt) cc_final: 0.8069 (mmpt) REVERT: i 25 TYR cc_start: 0.8148 (t80) cc_final: 0.7846 (t80) REVERT: C 39 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7800 (tpp80) REVERT: D 67 MET cc_start: 0.8159 (mmm) cc_final: 0.7887 (mmm) REVERT: E 67 MET cc_start: 0.8700 (tmm) cc_final: 0.8451 (tmm) REVERT: F 40 ASN cc_start: 0.8744 (t0) cc_final: 0.7937 (t0) REVERT: F 43 ILE cc_start: 0.9082 (tp) cc_final: 0.8807 (tt) REVERT: F 59 GLU cc_start: 0.8541 (tp30) cc_final: 0.8145 (tp30) REVERT: F 72 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8001 (mm) REVERT: G 2 GLN cc_start: 0.7717 (mt0) cc_final: 0.7199 (pm20) REVERT: G 55 PHE cc_start: 0.9189 (t80) cc_final: 0.8788 (t80) REVERT: H 72 LEU cc_start: 0.9114 (mt) cc_final: 0.8774 (mt) REVERT: I 2 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7138 (pm20) REVERT: I 57 LEU cc_start: 0.8915 (mt) cc_final: 0.8615 (mt) REVERT: I 67 MET cc_start: 0.8654 (ptm) cc_final: 0.7812 (mtp) REVERT: J 1 MET cc_start: 0.8325 (mtm) cc_final: 0.7892 (tmm) REVERT: J 8 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8331 (mtmm) REVERT: J 55 PHE cc_start: 0.8871 (t80) cc_final: 0.8587 (t80) REVERT: J 64 PHE cc_start: 0.8997 (m-10) cc_final: 0.8740 (m-10) REVERT: J 67 MET cc_start: 0.8633 (ptm) cc_final: 0.8138 (mtp) REVERT: K 59 GLU cc_start: 0.8553 (tp30) cc_final: 0.8189 (tp30) REVERT: B 5 LEU cc_start: 0.8714 (tp) cc_final: 0.7890 (tp) REVERT: B 9 TYR cc_start: 0.7758 (m-80) cc_final: 0.7245 (m-80) REVERT: M 68 THR cc_start: 0.9218 (t) cc_final: 0.9002 (m) REVERT: M 186 LEU cc_start: 0.9227 (tp) cc_final: 0.8801 (tp) REVERT: M 199 MET cc_start: 0.8377 (mtt) cc_final: 0.8133 (mtt) REVERT: N 72 TYR cc_start: 0.8035 (m-10) cc_final: 0.7670 (m-10) REVERT: N 87 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8551 (ttmm) REVERT: O 247 ASP cc_start: 0.8416 (m-30) cc_final: 0.8132 (m-30) REVERT: O 250 THR cc_start: 0.8856 (m) cc_final: 0.8590 (p) REVERT: S 1 MET cc_start: 0.6170 (ttp) cc_final: 0.4559 (tpt) REVERT: S 11 LYS cc_start: 0.8986 (pttt) cc_final: 0.8099 (mmpt) REVERT: S 25 TYR cc_start: 0.8126 (t80) cc_final: 0.7880 (t80) outliers start: 100 outliers final: 64 residues processed: 779 average time/residue: 0.1269 time to fit residues: 164.3661 Evaluate side-chains 760 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 694 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain 0 residue 66 LEU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 182 optimal weight: 0.3980 chunk 274 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 191 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 2 GLN a 62 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN M 62 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.141240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110356 restraints weight = 38672.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109766 restraints weight = 19370.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110167 restraints weight = 20936.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.111140 restraints weight = 14728.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112257 restraints weight = 12480.693| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21822 Z= 0.139 Angle : 0.684 16.639 29638 Z= 0.332 Chirality : 0.041 0.350 3678 Planarity : 0.004 0.069 3644 Dihedral : 4.307 30.980 3084 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.99 % Allowed : 25.02 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2618 helix: 1.13 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG a 176 TYR 0.023 0.001 TYR M 32 PHE 0.037 0.002 PHE 1 55 TRP 0.008 0.001 TRP M 126 HIS 0.005 0.001 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00312 (21822) covalent geometry : angle 0.68425 (29638) hydrogen bonds : bond 0.03827 ( 1673) hydrogen bonds : angle 3.92937 ( 4965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 748 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 40 ASN cc_start: 0.8655 (t0) cc_final: 0.7868 (t0) REVERT: 4 43 ILE cc_start: 0.9042 (tp) cc_final: 0.8675 (tt) REVERT: 4 59 GLU cc_start: 0.8454 (tp30) cc_final: 0.8095 (tp30) REVERT: 4 72 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7899 (mm) REVERT: 5 2 GLN cc_start: 0.7770 (mt0) cc_final: 0.7264 (pm20) REVERT: 6 64 PHE cc_start: 0.8720 (m-80) cc_final: 0.8490 (m-80) REVERT: 7 2 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7179 (pm20) REVERT: 7 14 ILE cc_start: 0.8658 (mm) cc_final: 0.8442 (tp) REVERT: 7 67 MET cc_start: 0.8686 (ptm) cc_final: 0.7844 (mtp) REVERT: 8 1 MET cc_start: 0.8216 (mtm) cc_final: 0.7879 (tmm) REVERT: 8 43 ILE cc_start: 0.8072 (tp) cc_final: 0.7550 (tp) REVERT: 8 64 PHE cc_start: 0.8913 (m-10) cc_final: 0.8543 (m-10) REVERT: 8 67 MET cc_start: 0.8563 (ptm) cc_final: 0.8137 (mtp) REVERT: 0 5 LEU cc_start: 0.8757 (tp) cc_final: 0.7973 (tp) REVERT: 0 9 TYR cc_start: 0.7624 (m-80) cc_final: 0.7241 (m-80) REVERT: a 68 THR cc_start: 0.9200 (t) cc_final: 0.8962 (m) REVERT: a 94 MET cc_start: 0.9007 (mmt) cc_final: 0.8586 (mmt) REVERT: a 186 LEU cc_start: 0.9228 (tp) cc_final: 0.8840 (tp) REVERT: a 199 MET cc_start: 0.8387 (mtt) cc_final: 0.8142 (mtt) REVERT: b 72 TYR cc_start: 0.8011 (m-10) cc_final: 0.7616 (m-10) REVERT: b 87 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8390 (ttmm) REVERT: d 250 THR cc_start: 0.8816 (m) cc_final: 0.8551 (p) REVERT: i 1 MET cc_start: 0.6180 (ttp) cc_final: 0.4500 (tpt) REVERT: i 11 LYS cc_start: 0.9002 (pttt) cc_final: 0.8044 (mmpt) REVERT: i 25 TYR cc_start: 0.8142 (t80) cc_final: 0.7789 (t80) REVERT: C 39 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7809 (tpp80) REVERT: D 67 MET cc_start: 0.8129 (mmm) cc_final: 0.7914 (mmm) REVERT: F 40 ASN cc_start: 0.8669 (t0) cc_final: 0.7904 (t0) REVERT: F 43 ILE cc_start: 0.9055 (tp) cc_final: 0.8796 (tt) REVERT: F 59 GLU cc_start: 0.8510 (tp30) cc_final: 0.8149 (tp30) REVERT: F 72 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8077 (mm) REVERT: G 2 GLN cc_start: 0.7797 (mt0) cc_final: 0.7203 (pm20) REVERT: G 55 PHE cc_start: 0.9178 (t80) cc_final: 0.8935 (t80) REVERT: I 2 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7158 (pm20) REVERT: I 67 MET cc_start: 0.8586 (ptm) cc_final: 0.7715 (mtp) REVERT: J 1 MET cc_start: 0.8341 (mtm) cc_final: 0.7884 (tmm) REVERT: J 8 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8346 (mtmm) REVERT: J 50 MET cc_start: 0.8461 (mtm) cc_final: 0.8218 (ptp) REVERT: J 64 PHE cc_start: 0.8953 (m-10) cc_final: 0.8667 (m-10) REVERT: J 67 MET cc_start: 0.8590 (ptm) cc_final: 0.8138 (mtp) REVERT: K 59 GLU cc_start: 0.8532 (tp30) cc_final: 0.8214 (tp30) REVERT: B 5 LEU cc_start: 0.8776 (tp) cc_final: 0.8039 (tp) REVERT: B 9 TYR cc_start: 0.7660 (m-80) cc_final: 0.7273 (m-80) REVERT: L 3 GLN cc_start: 0.7469 (tp-100) cc_final: 0.7197 (tp-100) REVERT: M 68 THR cc_start: 0.9202 (t) cc_final: 0.8996 (m) REVERT: M 94 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8493 (mmt) REVERT: M 186 LEU cc_start: 0.9230 (tp) cc_final: 0.8814 (tp) REVERT: M 199 MET cc_start: 0.8345 (mtt) cc_final: 0.8112 (mtt) REVERT: N 72 TYR cc_start: 0.8017 (m-10) cc_final: 0.7622 (m-10) REVERT: O 247 ASP cc_start: 0.8379 (m-30) cc_final: 0.8089 (m-30) REVERT: O 250 THR cc_start: 0.8832 (m) cc_final: 0.8582 (p) REVERT: S 1 MET cc_start: 0.6112 (ttp) cc_final: 0.4462 (tpt) REVERT: S 11 LYS cc_start: 0.9002 (pttt) cc_final: 0.8068 (mmpt) REVERT: S 25 TYR cc_start: 0.8057 (t80) cc_final: 0.7821 (t80) outliers start: 101 outliers final: 58 residues processed: 783 average time/residue: 0.1289 time to fit residues: 167.3821 Evaluate side-chains 757 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 696 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 70 PHE Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 8 residue 37 VAL Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain 0 residue 66 LEU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 10 LEU Chi-restraints excluded: chain S residue 29 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 167 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 262 optimal weight: 30.0000 chunk 246 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 2 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103070 restraints weight = 38416.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107516 restraints weight = 19300.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108151 restraints weight = 11098.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108559 restraints weight = 9713.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108782 restraints weight = 9765.460| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21822 Z= 0.144 Angle : 0.706 17.522 29638 Z= 0.339 Chirality : 0.043 0.349 3678 Planarity : 0.004 0.072 3644 Dihedral : 4.258 32.332 3084 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.84 % Allowed : 25.91 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2618 helix: 1.21 (0.11), residues: 2080 sheet: None (None), residues: 0 loop : -1.71 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 39 TYR 0.025 0.001 TYR a 32 PHE 0.040 0.002 PHE C 55 TRP 0.008 0.001 TRP M 234 HIS 0.005 0.001 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00330 (21822) covalent geometry : angle 0.70577 (29638) hydrogen bonds : bond 0.03816 ( 1673) hydrogen bonds : angle 3.94913 ( 4965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 728 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 40 ASN cc_start: 0.8629 (t0) cc_final: 0.7899 (t0) REVERT: 4 43 ILE cc_start: 0.9075 (tp) cc_final: 0.8751 (tt) REVERT: 4 59 GLU cc_start: 0.8544 (tp30) cc_final: 0.8184 (tp30) REVERT: 4 72 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7788 (mm) REVERT: 7 2 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7184 (pm20) REVERT: 7 14 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8345 (tp) REVERT: 7 35 ASN cc_start: 0.9128 (m-40) cc_final: 0.8908 (m110) REVERT: 7 67 MET cc_start: 0.8739 (ptm) cc_final: 0.7839 (mtp) REVERT: 8 1 MET cc_start: 0.8409 (mtm) cc_final: 0.7912 (tmm) REVERT: 8 43 ILE cc_start: 0.7990 (tp) cc_final: 0.7492 (tp) REVERT: 8 64 PHE cc_start: 0.8951 (m-10) cc_final: 0.8529 (m-10) REVERT: 8 67 MET cc_start: 0.8656 (ptm) cc_final: 0.8165 (mtp) REVERT: 0 5 LEU cc_start: 0.8799 (tp) cc_final: 0.8065 (tp) REVERT: 0 9 TYR cc_start: 0.7598 (m-80) cc_final: 0.7228 (m-80) REVERT: A 3 GLN cc_start: 0.7598 (tp-100) cc_final: 0.7356 (tp-100) REVERT: a 68 THR cc_start: 0.9184 (t) cc_final: 0.8968 (m) REVERT: a 94 MET cc_start: 0.9111 (mmt) cc_final: 0.8695 (mmt) REVERT: a 186 LEU cc_start: 0.9185 (tp) cc_final: 0.8746 (tp) REVERT: a 199 MET cc_start: 0.8404 (mtt) cc_final: 0.8126 (mtt) REVERT: b 72 TYR cc_start: 0.8017 (m-10) cc_final: 0.7611 (m-10) REVERT: b 87 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8337 (ttmm) REVERT: d 250 THR cc_start: 0.8761 (m) cc_final: 0.8490 (p) REVERT: i 1 MET cc_start: 0.6191 (ttp) cc_final: 0.4509 (tpt) REVERT: i 11 LYS cc_start: 0.9036 (pttt) cc_final: 0.8009 (mmpt) REVERT: i 25 TYR cc_start: 0.8197 (t80) cc_final: 0.7826 (t80) REVERT: C 39 ARG cc_start: 0.8218 (tpp80) cc_final: 0.7787 (tpp80) REVERT: D 67 MET cc_start: 0.8075 (mmm) cc_final: 0.7815 (mmm) REVERT: F 40 ASN cc_start: 0.8655 (t0) cc_final: 0.7910 (t0) REVERT: F 43 ILE cc_start: 0.9073 (tp) cc_final: 0.8771 (tt) REVERT: F 59 GLU cc_start: 0.8558 (tp30) cc_final: 0.8205 (tp30) REVERT: F 72 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7864 (mm) REVERT: G 55 PHE cc_start: 0.9162 (t80) cc_final: 0.8931 (t80) REVERT: G 57 LEU cc_start: 0.8566 (mp) cc_final: 0.8304 (tp) REVERT: H 19 LEU cc_start: 0.9099 (mt) cc_final: 0.8719 (tt) REVERT: H 64 PHE cc_start: 0.8927 (m-80) cc_final: 0.8667 (m-80) REVERT: I 2 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7067 (pm20) REVERT: I 14 ILE cc_start: 0.8742 (tp) cc_final: 0.8452 (tp) REVERT: I 67 MET cc_start: 0.8666 (ptm) cc_final: 0.7763 (mtp) REVERT: J 1 MET cc_start: 0.8453 (mtm) cc_final: 0.7893 (tmm) REVERT: J 8 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8227 (mtmm) REVERT: J 64 PHE cc_start: 0.8988 (m-10) cc_final: 0.8662 (m-10) REVERT: J 67 MET cc_start: 0.8660 (ptm) cc_final: 0.8182 (mtp) REVERT: K 59 GLU cc_start: 0.8658 (tp30) cc_final: 0.8274 (tp30) REVERT: B 5 LEU cc_start: 0.8794 (tp) cc_final: 0.8102 (tp) REVERT: B 9 TYR cc_start: 0.7639 (m-80) cc_final: 0.7260 (m-80) REVERT: M 68 THR cc_start: 0.9190 (t) cc_final: 0.8978 (m) REVERT: M 94 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: M 186 LEU cc_start: 0.9199 (tp) cc_final: 0.8775 (tp) REVERT: N 72 TYR cc_start: 0.8012 (m-10) cc_final: 0.7618 (m-10) REVERT: O 247 ASP cc_start: 0.8388 (m-30) cc_final: 0.8079 (m-30) REVERT: O 250 THR cc_start: 0.8798 (m) cc_final: 0.8555 (p) REVERT: S 1 MET cc_start: 0.6126 (ttp) cc_final: 0.4471 (tpt) REVERT: S 11 LYS cc_start: 0.9039 (pttt) cc_final: 0.8027 (mmpt) REVERT: S 25 TYR cc_start: 0.8130 (t80) cc_final: 0.7832 (t80) outliers start: 98 outliers final: 67 residues processed: 759 average time/residue: 0.1274 time to fit residues: 161.5482 Evaluate side-chains 764 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 693 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 1 residue 70 PHE Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 61 THR Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 7 residue 14 ILE Chi-restraints excluded: chain 7 residue 48 PHE Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 3 LEU Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain 0 residue 66 LEU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 29 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 222 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 2 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN L 3 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100471 restraints weight = 38537.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104082 restraints weight = 20317.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104943 restraints weight = 12295.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105650 restraints weight = 10404.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105608 restraints weight = 9897.566| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21822 Z= 0.192 Angle : 0.726 16.730 29638 Z= 0.355 Chirality : 0.044 0.295 3678 Planarity : 0.004 0.080 3644 Dihedral : 4.261 30.769 3084 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.84 % Allowed : 26.70 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.05 (0.17), residues: 2618 helix: 1.25 (0.11), residues: 2058 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 176 TYR 0.012 0.002 TYR M 166 PHE 0.035 0.002 PHE C 55 TRP 0.014 0.001 TRP M 234 HIS 0.006 0.001 HIS f 68 Details of bonding type rmsd covalent geometry : bond 0.00457 (21822) covalent geometry : angle 0.72587 (29638) hydrogen bonds : bond 0.03999 ( 1673) hydrogen bonds : angle 4.06572 ( 4965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 703 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: 4 40 ASN cc_start: 0.8670 (t0) cc_final: 0.7964 (t0) REVERT: 4 43 ILE cc_start: 0.9070 (tp) cc_final: 0.8762 (tt) REVERT: 4 59 GLU cc_start: 0.8554 (tp30) cc_final: 0.8221 (tp30) REVERT: 4 72 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7803 (mm) REVERT: 6 59 GLU cc_start: 0.8635 (tp30) cc_final: 0.8161 (mt-10) REVERT: 7 2 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7117 (pm20) REVERT: 7 67 MET cc_start: 0.8741 (ptm) cc_final: 0.7818 (mtp) REVERT: 8 43 ILE cc_start: 0.7929 (tp) cc_final: 0.7467 (tp) REVERT: 8 64 PHE cc_start: 0.8954 (m-10) cc_final: 0.8537 (m-10) REVERT: 8 67 MET cc_start: 0.8694 (ptm) cc_final: 0.8175 (mtp) REVERT: 0 5 LEU cc_start: 0.8820 (tp) cc_final: 0.8072 (tp) REVERT: 0 9 TYR cc_start: 0.7645 (m-80) cc_final: 0.7314 (m-80) REVERT: A 18 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8783 (tt) REVERT: a 68 THR cc_start: 0.9252 (t) cc_final: 0.9052 (m) REVERT: a 186 LEU cc_start: 0.9193 (tp) cc_final: 0.8789 (tp) REVERT: a 199 MET cc_start: 0.8577 (mtt) cc_final: 0.8336 (mtt) REVERT: b 72 TYR cc_start: 0.8053 (m-10) cc_final: 0.7683 (m-10) REVERT: b 87 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8400 (ttmm) REVERT: d 250 THR cc_start: 0.8751 (m) cc_final: 0.8468 (p) REVERT: i 1 MET cc_start: 0.6296 (ttp) cc_final: 0.4471 (tpt) REVERT: i 11 LYS cc_start: 0.9102 (pttt) cc_final: 0.8045 (mmpt) REVERT: i 25 TYR cc_start: 0.8251 (t80) cc_final: 0.7962 (t80) REVERT: C 39 ARG cc_start: 0.8276 (tpp80) cc_final: 0.7852 (tpp80) REVERT: D 67 MET cc_start: 0.8035 (mmm) cc_final: 0.7586 (mmp) REVERT: F 40 ASN cc_start: 0.8676 (t0) cc_final: 0.7947 (t0) REVERT: F 43 ILE cc_start: 0.9064 (tp) cc_final: 0.8763 (tt) REVERT: F 59 GLU cc_start: 0.8668 (tp30) cc_final: 0.8291 (tp30) REVERT: F 72 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7847 (mm) REVERT: G 55 PHE cc_start: 0.9201 (t80) cc_final: 0.8945 (t80) REVERT: H 19 LEU cc_start: 0.9113 (mt) cc_final: 0.8736 (tt) REVERT: H 64 PHE cc_start: 0.8915 (m-80) cc_final: 0.8592 (m-80) REVERT: I 2 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7120 (pm20) REVERT: I 14 ILE cc_start: 0.8738 (tp) cc_final: 0.8444 (tp) REVERT: I 67 MET cc_start: 0.8697 (ptm) cc_final: 0.7781 (mtp) REVERT: J 8 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8283 (mtmm) REVERT: J 64 PHE cc_start: 0.8974 (m-10) cc_final: 0.8629 (m-10) REVERT: J 67 MET cc_start: 0.8705 (ptm) cc_final: 0.8210 (mtp) REVERT: J 72 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7837 (mm) REVERT: B 5 LEU cc_start: 0.8781 (tp) cc_final: 0.8011 (tp) REVERT: B 9 TYR cc_start: 0.7627 (m-80) cc_final: 0.7278 (m-80) REVERT: L 3 GLN cc_start: 0.7555 (tp40) cc_final: 0.7341 (tp-100) REVERT: M 94 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8587 (mmt) REVERT: M 186 LEU cc_start: 0.9201 (tp) cc_final: 0.8769 (tp) REVERT: M 199 MET cc_start: 0.8540 (mtt) cc_final: 0.8291 (mtt) REVERT: N 72 TYR cc_start: 0.8056 (m-10) cc_final: 0.7692 (m-10) REVERT: O 247 ASP cc_start: 0.8422 (m-30) cc_final: 0.8108 (m-30) REVERT: O 250 THR cc_start: 0.8752 (m) cc_final: 0.8507 (p) REVERT: S 1 MET cc_start: 0.6308 (ttp) cc_final: 0.4492 (tpt) REVERT: S 11 LYS cc_start: 0.9116 (pttt) cc_final: 0.8075 (mmtt) REVERT: S 25 TYR cc_start: 0.8207 (t80) cc_final: 0.7985 (t80) outliers start: 98 outliers final: 76 residues processed: 737 average time/residue: 0.1302 time to fit residues: 158.6413 Evaluate side-chains 763 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 682 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 20 LEU Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 61 THR Chi-restraints excluded: chain 7 residue 48 PHE Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 8 residue 37 VAL Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 3 LEU Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain 0 residue 66 LEU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 152 LEU Chi-restraints excluded: chain a residue 180 ASN Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 268 optimal weight: 30.0000 chunk 170 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 193 optimal weight: 0.9990 chunk 229 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 2 GLN A 3 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.141655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.105991 restraints weight = 38150.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107627 restraints weight = 20175.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107790 restraints weight = 13124.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108550 restraints weight = 13709.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108445 restraints weight = 11225.674| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 21822 Z= 0.147 Angle : 0.728 16.536 29638 Z= 0.350 Chirality : 0.043 0.362 3678 Planarity : 0.004 0.079 3644 Dihedral : 4.236 31.065 3084 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.54 % Allowed : 27.99 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.16 (0.17), residues: 2618 helix: 1.33 (0.11), residues: 2056 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 176 TYR 0.017 0.001 TYR i 24 PHE 0.035 0.002 PHE 5 55 TRP 0.009 0.001 TRP a 126 HIS 0.005 0.001 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00339 (21822) covalent geometry : angle 0.72833 (29638) hydrogen bonds : bond 0.03876 ( 1673) hydrogen bonds : angle 4.00628 ( 4965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 710 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: 4 40 ASN cc_start: 0.8599 (t0) cc_final: 0.7943 (t0) REVERT: 4 43 ILE cc_start: 0.9060 (tp) cc_final: 0.8750 (tt) REVERT: 4 59 GLU cc_start: 0.8485 (tp30) cc_final: 0.8175 (tp30) REVERT: 4 72 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7736 (mm) REVERT: 5 67 MET cc_start: 0.8705 (ptm) cc_final: 0.7814 (mmt) REVERT: 6 19 LEU cc_start: 0.9080 (mt) cc_final: 0.8684 (tt) REVERT: 7 2 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7099 (pm20) REVERT: 7 67 MET cc_start: 0.8689 (ptm) cc_final: 0.7693 (mtp) REVERT: 8 64 PHE cc_start: 0.8904 (m-10) cc_final: 0.8519 (m-10) REVERT: 8 67 MET cc_start: 0.8680 (ptm) cc_final: 0.8087 (mtp) REVERT: 9 59 GLU cc_start: 0.8899 (tp30) cc_final: 0.8619 (tp30) REVERT: 0 5 LEU cc_start: 0.8827 (tp) cc_final: 0.8059 (pp) REVERT: a 50 ASN cc_start: 0.8598 (p0) cc_final: 0.8360 (p0) REVERT: a 68 THR cc_start: 0.9215 (t) cc_final: 0.9011 (m) REVERT: a 94 MET cc_start: 0.8995 (mmt) cc_final: 0.8555 (mmt) REVERT: a 186 LEU cc_start: 0.9159 (tp) cc_final: 0.8747 (tp) REVERT: a 199 MET cc_start: 0.8545 (mtt) cc_final: 0.8267 (mtt) REVERT: b 87 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8342 (ttmm) REVERT: d 250 THR cc_start: 0.8718 (m) cc_final: 0.8437 (p) REVERT: i 1 MET cc_start: 0.6223 (ttp) cc_final: 0.4331 (tpt) REVERT: i 11 LYS cc_start: 0.9040 (pttt) cc_final: 0.7938 (mmpt) REVERT: i 25 TYR cc_start: 0.8251 (t80) cc_final: 0.7942 (t80) REVERT: C 39 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7830 (tpp80) REVERT: D 67 MET cc_start: 0.8021 (mmm) cc_final: 0.7758 (mmm) REVERT: F 40 ASN cc_start: 0.8599 (t0) cc_final: 0.7906 (t0) REVERT: F 43 ILE cc_start: 0.9040 (tp) cc_final: 0.8714 (tt) REVERT: F 59 GLU cc_start: 0.8594 (tp30) cc_final: 0.8095 (tp30) REVERT: F 72 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7811 (mm) REVERT: G 55 PHE cc_start: 0.9191 (t80) cc_final: 0.8991 (t80) REVERT: G 67 MET cc_start: 0.8689 (ptm) cc_final: 0.7763 (mmt) REVERT: H 64 PHE cc_start: 0.8836 (m-80) cc_final: 0.8491 (m-80) REVERT: I 2 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7028 (pm20) REVERT: I 67 MET cc_start: 0.8687 (ptm) cc_final: 0.7750 (mtp) REVERT: J 8 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8222 (mtmm) REVERT: J 64 PHE cc_start: 0.8925 (m-10) cc_final: 0.8564 (m-10) REVERT: J 67 MET cc_start: 0.8683 (ptm) cc_final: 0.8177 (mtp) REVERT: J 72 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7834 (mm) REVERT: K 59 GLU cc_start: 0.8935 (tp30) cc_final: 0.8698 (tp30) REVERT: B 5 LEU cc_start: 0.8822 (tp) cc_final: 0.8064 (pp) REVERT: M 94 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8568 (mmt) REVERT: M 186 LEU cc_start: 0.9189 (tp) cc_final: 0.8758 (tp) REVERT: M 199 MET cc_start: 0.8506 (mtt) cc_final: 0.8260 (mtt) REVERT: N 85 MET cc_start: 0.8251 (mmm) cc_final: 0.8013 (mmt) REVERT: O 247 ASP cc_start: 0.8383 (m-30) cc_final: 0.8058 (m-30) REVERT: O 250 THR cc_start: 0.8776 (m) cc_final: 0.8504 (p) REVERT: S 1 MET cc_start: 0.6252 (ttp) cc_final: 0.4202 (tpt) REVERT: S 11 LYS cc_start: 0.9058 (pttt) cc_final: 0.7950 (mmpt) REVERT: S 25 TYR cc_start: 0.8154 (t80) cc_final: 0.7873 (t80) outliers start: 92 outliers final: 74 residues processed: 741 average time/residue: 0.1284 time to fit residues: 157.1629 Evaluate side-chains 760 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 682 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 61 THR Chi-restraints excluded: chain 7 residue 48 PHE Chi-restraints excluded: chain 7 residue 65 CYS Chi-restraints excluded: chain 8 residue 37 VAL Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 3 LEU Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain 0 residue 66 LEU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 152 LEU Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 29 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 180 ASN Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 172 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 258 optimal weight: 0.0870 chunk 179 optimal weight: 0.5980 chunk 224 optimal weight: 0.7980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 35 ASN 9 2 GLN k 15 HIS K 2 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110607 restraints weight = 38344.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108914 restraints weight = 21426.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110140 restraints weight = 17718.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110587 restraints weight = 13732.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110941 restraints weight = 12362.361| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21822 Z= 0.146 Angle : 0.748 16.080 29638 Z= 0.359 Chirality : 0.044 0.360 3678 Planarity : 0.004 0.083 3644 Dihedral : 4.208 30.588 3084 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.15 % Allowed : 28.87 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.14 (0.17), residues: 2618 helix: 1.31 (0.11), residues: 2068 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 176 TYR 0.023 0.001 TYR 0 9 PHE 0.035 0.002 PHE 6 64 TRP 0.007 0.001 TRP M 234 HIS 0.004 0.001 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00331 (21822) covalent geometry : angle 0.74777 (29638) hydrogen bonds : bond 0.03828 ( 1673) hydrogen bonds : angle 4.05656 ( 4965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 693 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 40 ASN cc_start: 0.8583 (t0) cc_final: 0.7895 (t0) REVERT: 4 43 ILE cc_start: 0.9056 (tp) cc_final: 0.8756 (tt) REVERT: 4 59 GLU cc_start: 0.8324 (tp30) cc_final: 0.8058 (tp30) REVERT: 4 72 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7813 (mm) REVERT: 5 67 MET cc_start: 0.8531 (ptm) cc_final: 0.7746 (mmt) REVERT: 6 19 LEU cc_start: 0.9070 (mt) cc_final: 0.8670 (tt) REVERT: 7 2 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7092 (pm20) REVERT: 7 67 MET cc_start: 0.8668 (ptm) cc_final: 0.7685 (mtp) REVERT: 8 64 PHE cc_start: 0.8901 (m-10) cc_final: 0.8458 (m-10) REVERT: 8 67 MET cc_start: 0.8623 (ptm) cc_final: 0.8126 (mtp) REVERT: 9 59 GLU cc_start: 0.8861 (tp30) cc_final: 0.8602 (tp30) REVERT: 0 5 LEU cc_start: 0.8764 (tp) cc_final: 0.7729 (pp) REVERT: 0 9 TYR cc_start: 0.7863 (m-80) cc_final: 0.7195 (m-80) REVERT: a 47 THR cc_start: 0.9008 (m) cc_final: 0.8762 (m) REVERT: a 68 THR cc_start: 0.9213 (t) cc_final: 0.9009 (m) REVERT: a 94 MET cc_start: 0.8853 (mmt) cc_final: 0.8498 (mmt) REVERT: a 186 LEU cc_start: 0.9202 (tp) cc_final: 0.8819 (tp) REVERT: a 199 MET cc_start: 0.8484 (mtt) cc_final: 0.8226 (mtt) REVERT: b 72 TYR cc_start: 0.7813 (m-10) cc_final: 0.7563 (m-10) REVERT: b 87 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8325 (ttmm) REVERT: d 250 THR cc_start: 0.8721 (m) cc_final: 0.8446 (p) REVERT: d 276 ASP cc_start: 0.8616 (p0) cc_final: 0.8335 (p0) REVERT: i 1 MET cc_start: 0.6181 (ttp) cc_final: 0.4302 (tpt) REVERT: i 11 LYS cc_start: 0.9023 (pttt) cc_final: 0.7876 (mmpt) REVERT: i 25 TYR cc_start: 0.8250 (t80) cc_final: 0.7936 (t80) REVERT: C 39 ARG cc_start: 0.8240 (tpp80) cc_final: 0.7821 (tpp80) REVERT: D 67 MET cc_start: 0.8045 (mmm) cc_final: 0.7816 (mmm) REVERT: F 40 ASN cc_start: 0.8570 (t0) cc_final: 0.7883 (t0) REVERT: F 43 ILE cc_start: 0.9034 (tp) cc_final: 0.8734 (tt) REVERT: F 59 GLU cc_start: 0.8445 (tp30) cc_final: 0.8105 (tp30) REVERT: F 72 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7895 (mm) REVERT: G 67 MET cc_start: 0.8534 (ptm) cc_final: 0.7735 (mmt) REVERT: I 2 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7002 (pm20) REVERT: I 67 MET cc_start: 0.8657 (ptm) cc_final: 0.7668 (mtp) REVERT: J 8 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8202 (mtmm) REVERT: J 64 PHE cc_start: 0.8910 (m-10) cc_final: 0.8577 (m-10) REVERT: J 67 MET cc_start: 0.8668 (ptm) cc_final: 0.8185 (mtp) REVERT: J 72 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7920 (mm) REVERT: K 59 GLU cc_start: 0.8868 (tp30) cc_final: 0.8642 (tp30) REVERT: B 5 LEU cc_start: 0.8719 (tp) cc_final: 0.7978 (pp) REVERT: L 3 GLN cc_start: 0.8014 (tp40) cc_final: 0.7415 (tp-100) REVERT: M 94 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8533 (mmt) REVERT: M 186 LEU cc_start: 0.9209 (tp) cc_final: 0.8784 (tp) REVERT: M 199 MET cc_start: 0.8454 (mtt) cc_final: 0.8204 (mtt) REVERT: N 72 TYR cc_start: 0.7814 (m-10) cc_final: 0.7572 (m-10) REVERT: O 250 THR cc_start: 0.8791 (m) cc_final: 0.8532 (p) REVERT: O 276 ASP cc_start: 0.8628 (p0) cc_final: 0.8403 (p0) REVERT: S 1 MET cc_start: 0.6189 (ttp) cc_final: 0.4113 (tpt) REVERT: S 11 LYS cc_start: 0.9046 (pttt) cc_final: 0.7906 (mmpt) REVERT: S 25 TYR cc_start: 0.8092 (t80) cc_final: 0.7801 (t80) outliers start: 84 outliers final: 69 residues processed: 721 average time/residue: 0.1312 time to fit residues: 156.4144 Evaluate side-chains 754 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 681 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 59 GLU Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 61 THR Chi-restraints excluded: chain 7 residue 48 PHE Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 7 residue 65 CYS Chi-restraints excluded: chain 8 residue 37 VAL Chi-restraints excluded: chain 8 residue 52 ILE Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 57 LEU Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain 0 residue 66 LEU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 152 LEU Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 94 MET Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 180 ASN Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 222 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 192 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 2 GLN K 2 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.142677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111124 restraints weight = 38009.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109576 restraints weight = 21722.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110546 restraints weight = 17941.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111095 restraints weight = 13859.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.111601 restraints weight = 12551.725| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21822 Z= 0.148 Angle : 0.747 16.630 29638 Z= 0.356 Chirality : 0.044 0.371 3678 Planarity : 0.004 0.079 3644 Dihedral : 4.195 29.777 3084 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.95 % Allowed : 29.32 % Favored : 66.73 % 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: 1.10 (0.17), residues: 2618 helix: 1.29 (0.11), residues: 2064 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 176 TYR 0.027 0.001 TYR 0 9 PHE 0.043 0.002 PHE 5 55 TRP 0.008 0.001 TRP M 234 HIS 0.005 0.001 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00342 (21822) covalent geometry : angle 0.74679 (29638) hydrogen bonds : bond 0.03798 ( 1673) hydrogen bonds : angle 4.04273 ( 4965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4720.04 seconds wall clock time: 81 minutes 46.05 seconds (4906.05 seconds total)