Starting phenix.real_space_refine on Wed Feb 21 15:07:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/02_2024/6b2z_7036.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/02_2024/6b2z_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/02_2024/6b2z_7036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/02_2024/6b2z_7036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/02_2024/6b2z_7036.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/02_2024/6b2z_7036.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "a ARG 57": "NH1" <-> "NH2" Residue "a PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 57": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 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, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 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: 10.92, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 8.25 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 1.86 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: 6.73 Time building geometry restraints manager: 8.84 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: 96.03 - 103.74: 276 103.74 - 111.45: 9262 111.45 - 119.16: 8469 119.16 - 126.87: 11471 126.87 - 134.58: 160 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 2.440 nonbonded pdb=" O SER 5 58 " pdb=" OG1 THR 5 61 " model vdw 2.290 2.440 nonbonded pdb=" O MET A 10 " pdb=" OG1 THR A 14 " model vdw 2.328 2.440 nonbonded pdb=" O MET L 10 " pdb=" OG1 THR L 14 " model vdw 2.328 2.440 nonbonded pdb=" OG SER M 1 " pdb=" OD2 ASP M 4 " model vdw 2.332 2.440 ... (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 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 8.110 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 53.540 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.520 ------------------------------------------------------------------------------- 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= 0.484 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.003 TRP M 234 HIS 0.010 0.002 HIS f 68 PHE 0.044 0.004 PHE M 224 TYR 0.039 0.003 TYR M 32 ARG 0.011 0.001 ARG N 84 *********************** 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 fitting. rotamer outliers: 14 poor density : 1011 time to evaluate : 2.394 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: 0.8827 (t) REVERT: 2 58 SER cc_start: 0.8981 (t) cc_final: 0.8618 (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: 0.8511 (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: 0.8811 (tp) REVERT: 5 64 PHE cc_start: 0.8460 (m-10) cc_final: 0.8163 (m-80) REVERT: 6 39 ARG cc_start: 0.8247 (ttm170) cc_final: 0.7917 (ttm110) REVERT: 6 46 THR cc_start: 0.8705 (m) cc_final: 0.8320 (p) REVERT: 6 65 CYS cc_start: 0.8960 (m) cc_final: 0.8439 (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: 0.8156 (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: 0.7865 (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: 0.7370 (p) REVERT: 0 5 LEU cc_start: 0.8725 (tp) cc_final: 0.8186 (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: 0.8697 (pp) REVERT: 0 47 VAL cc_start: 0.8682 (t) cc_final: 0.8310 (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: 0.8500 (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: 0.7599 (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: 0.7656 (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: 0.8402 (mmtt) REVERT: D 16 THR cc_start: 0.9144 (p) cc_final: 0.8839 (t) REVERT: D 58 SER cc_start: 0.8962 (t) cc_final: 0.8624 (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: 0.8538 (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: 0.8461 (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: 0.8763 (tp) REVERT: G 64 PHE cc_start: 0.8405 (m-10) cc_final: 0.8113 (m-80) REVERT: H 39 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7898 (ttm110) REVERT: H 46 THR cc_start: 0.8639 (m) cc_final: 0.8319 (p) REVERT: H 65 CYS cc_start: 0.8989 (m) cc_final: 0.8415 (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: 0.6960 (pm20) REVERT: I 9 TYR cc_start: 0.7409 (m-10) cc_final: 0.7120 (m-10) REVERT: I 35 ASN cc_start: 0.8966 (m-40) cc_final: 0.8115 (t0) REVERT: I 44 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8456 (tptm) REVERT: I 67 MET cc_start: 0.8673 (ptm) cc_final: 0.7865 (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: 0.7569 (tp) REVERT: J 67 MET cc_start: 0.8599 (ptm) cc_final: 0.8061 (mtp) REVERT: K 39 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8474 (mtp180) REVERT: K 43 ILE cc_start: 0.7978 (tp) cc_final: 0.7688 (mt) REVERT: K 46 THR cc_start: 0.7579 (m) cc_final: 0.7228 (p) REVERT: B 5 LEU cc_start: 0.8698 (tp) cc_final: 0.8187 (tp) REVERT: B 9 TYR cc_start: 0.7922 (m-80) cc_final: 0.7700 (m-80) REVERT: B 69 SER cc_start: 0.9255 (t) cc_final: 0.9007 (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: 0.8680 (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: 0.7583 (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: 0.7694 (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: 0.4833 (tpt) REVERT: S 11 LYS cc_start: 0.8928 (pttt) cc_final: 0.8289 (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: 0.2883 time to fit residues: 460.6942 Evaluate side-chains 757 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 755 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 234 optimal weight: 0.9980 chunk 210 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 252 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21822 Z= 0.206 Angle : 0.705 11.580 29638 Z= 0.342 Chirality : 0.042 0.262 3678 Planarity : 0.005 0.060 3644 Dihedral : 4.844 25.201 3088 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.15 % Allowed : 16.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 2618 helix: 0.02 (0.11), residues: 2036 sheet: None (None), residues: 0 loop : -2.25 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 234 HIS 0.005 0.001 HIS f 68 PHE 0.032 0.002 PHE 7 55 TYR 0.016 0.002 TYR f 31 ARG 0.004 0.001 ARG K 39 *********************** 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 919 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 835 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 16 THR cc_start: 0.9193 (p) cc_final: 0.8926 (t) REVERT: 2 58 SER cc_start: 0.9018 (t) cc_final: 0.8697 (p) REVERT: 3 43 ILE cc_start: 0.8874 (tp) cc_final: 0.8673 (tt) REVERT: 3 45 ASP cc_start: 0.8580 (m-30) cc_final: 0.8270 (t70) REVERT: 4 40 ASN cc_start: 0.8982 (t0) cc_final: 0.7884 (t0) REVERT: 4 43 ILE cc_start: 0.9105 (tp) cc_final: 0.8552 (tt) REVERT: 4 59 GLU cc_start: 0.8730 (tp30) cc_final: 0.8431 (tp30) REVERT: 4 61 THR cc_start: 0.9606 (p) cc_final: 0.9353 (t) REVERT: 5 2 GLN cc_start: 0.7665 (mt0) cc_final: 0.7315 (pm20) REVERT: 5 28 ILE cc_start: 0.9211 (mt) cc_final: 0.8991 (tp) REVERT: 6 39 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7824 (ttm110) REVERT: 6 72 LEU cc_start: 0.9186 (mt) cc_final: 0.8950 (tp) REVERT: 7 2 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7126 (pm20) REVERT: 7 9 TYR cc_start: 0.7442 (m-10) cc_final: 0.7232 (m-10) REVERT: 7 67 MET cc_start: 0.8778 (ptm) cc_final: 0.7974 (mtp) REVERT: 8 55 PHE cc_start: 0.9040 (t80) cc_final: 0.8553 (t80) REVERT: 8 59 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8565 (mm-30) REVERT: 8 64 PHE cc_start: 0.9032 (m-10) cc_final: 0.8697 (m-10) REVERT: 8 67 MET cc_start: 0.8609 (ptm) cc_final: 0.8021 (mtp) REVERT: 9 35 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: 9 43 ILE cc_start: 0.8162 (tp) cc_final: 0.7797 (mt) REVERT: 9 46 THR cc_start: 0.7632 (m) cc_final: 0.7294 (p) REVERT: 0 5 LEU cc_start: 0.8728 (tp) cc_final: 0.8041 (pp) REVERT: 0 59 GLU cc_start: 0.8644 (tp30) cc_final: 0.8431 (tp30) REVERT: A 3 GLN cc_start: 0.7344 (tp-100) cc_final: 0.6344 (tp-100) REVERT: a 68 THR cc_start: 0.9052 (t) cc_final: 0.8709 (m) REVERT: a 85 TYR cc_start: 0.8528 (m-80) cc_final: 0.8262 (m-80) REVERT: a 89 ILE cc_start: 0.9190 (tp) cc_final: 0.8980 (tp) REVERT: a 94 MET cc_start: 0.8939 (mmt) cc_final: 0.8636 (mmt) REVERT: a 179 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8139 (t) REVERT: a 186 LEU cc_start: 0.9143 (tp) cc_final: 0.8799 (tp) REVERT: a 199 MET cc_start: 0.8898 (mtm) cc_final: 0.8689 (mtt) REVERT: b 72 TYR cc_start: 0.7964 (m-10) cc_final: 0.7560 (m-10) REVERT: b 82 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: i 1 MET cc_start: 0.6096 (ttp) cc_final: 0.4587 (tpt) REVERT: i 11 LYS cc_start: 0.8947 (pttt) cc_final: 0.8198 (mmtt) REVERT: C 39 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7722 (tpp80) REVERT: D 16 THR cc_start: 0.9214 (p) cc_final: 0.8941 (t) REVERT: D 58 SER cc_start: 0.9001 (t) cc_final: 0.8718 (p) REVERT: E 45 ASP cc_start: 0.8656 (m-30) cc_final: 0.8329 (t70) REVERT: F 40 ASN cc_start: 0.8949 (t0) cc_final: 0.7854 (t0) REVERT: F 43 ILE cc_start: 0.9109 (tp) cc_final: 0.8563 (tt) REVERT: F 59 GLU cc_start: 0.8693 (tp30) cc_final: 0.8396 (tp30) REVERT: F 61 THR cc_start: 0.9599 (p) cc_final: 0.9361 (t) REVERT: F 69 SER cc_start: 0.8738 (t) cc_final: 0.8534 (p) REVERT: G 28 ILE cc_start: 0.9220 (mt) cc_final: 0.9006 (tp) REVERT: G 64 PHE cc_start: 0.8417 (m-10) cc_final: 0.8039 (m-80) REVERT: H 39 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7748 (ttm110) REVERT: H 46 THR cc_start: 0.8731 (m) cc_final: 0.8471 (p) REVERT: H 72 LEU cc_start: 0.9209 (mt) cc_final: 0.8958 (tp) REVERT: I 2 GLN cc_start: 0.7570 (tp-100) cc_final: 0.7121 (pm20) REVERT: I 8 LYS cc_start: 0.8115 (mttp) cc_final: 0.7555 (mtmm) REVERT: I 9 TYR cc_start: 0.7357 (m-10) cc_final: 0.7128 (m-10) REVERT: I 19 LEU cc_start: 0.9481 (mt) cc_final: 0.9280 (mt) REVERT: I 67 MET cc_start: 0.8737 (ptm) cc_final: 0.7939 (mtp) REVERT: J 8 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8384 (mtmm) REVERT: J 39 ARG cc_start: 0.7953 (ttm170) cc_final: 0.7705 (ttm170) REVERT: J 59 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8649 (mm-30) REVERT: J 64 PHE cc_start: 0.9026 (m-10) cc_final: 0.8684 (m-10) REVERT: J 67 MET cc_start: 0.8605 (ptm) cc_final: 0.8023 (mtp) REVERT: K 35 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8493 (m-40) REVERT: K 59 GLU cc_start: 0.8505 (tp30) cc_final: 0.8271 (tp30) REVERT: B 5 LEU cc_start: 0.8725 (tp) cc_final: 0.8006 (pp) REVERT: B 19 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8918 (mp) REVERT: B 59 GLU cc_start: 0.8670 (tp30) cc_final: 0.8465 (tp30) REVERT: B 69 SER cc_start: 0.9206 (t) cc_final: 0.8934 (p) REVERT: L 3 GLN cc_start: 0.7302 (tp-100) cc_final: 0.6275 (tp-100) REVERT: M 68 THR cc_start: 0.9044 (t) cc_final: 0.8738 (m) REVERT: M 89 ILE cc_start: 0.9226 (tp) cc_final: 0.9020 (tp) REVERT: M 186 LEU cc_start: 0.9172 (tp) cc_final: 0.8823 (tp) REVERT: M 199 MET cc_start: 0.8849 (mtm) cc_final: 0.8647 (mtt) REVERT: N 72 TYR cc_start: 0.7980 (m-10) cc_final: 0.7587 (m-10) REVERT: N 82 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: O 276 ASP cc_start: 0.8378 (p0) cc_final: 0.7958 (p0) REVERT: S 1 MET cc_start: 0.6061 (ttp) cc_final: 0.4590 (tpt) REVERT: S 11 LYS cc_start: 0.8955 (pttt) cc_final: 0.8197 (mmtt) REVERT: S 57 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7939 (mp0) outliers start: 84 outliers final: 47 residues processed: 870 average time/residue: 0.2679 time to fit residues: 377.5173 Evaluate side-chains 770 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 717 time to evaluate : 2.175 ------------------------------------------------------------------------------- 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 16 THR Chi-restraints excluded: chain 3 residue 55 PHE Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 5 residue 58 SER 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 16 THR Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain a residue 179 SER 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 82 ASP 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 16 THR Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 58 SER 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 2 GLN Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 58 SER 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 L residue 41 SER Chi-restraints excluded: chain M residue 45 THR 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 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 252 optimal weight: 20.0000 chunk 273 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 250 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21822 Z= 0.231 Angle : 0.694 10.470 29638 Z= 0.336 Chirality : 0.042 0.250 3678 Planarity : 0.004 0.065 3644 Dihedral : 4.567 24.925 3084 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.89 % Allowed : 20.93 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2618 helix: 0.66 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.04 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 234 HIS 0.006 0.001 HIS f 68 PHE 0.034 0.002 PHE 7 55 TYR 0.022 0.002 TYR a 32 ARG 0.002 0.000 ARG b 84 *********************** 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 845 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 746 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 33 LEU cc_start: 0.9175 (tp) cc_final: 0.8953 (tt) REVERT: 2 58 SER cc_start: 0.9189 (t) cc_final: 0.8808 (p) REVERT: 3 45 ASP cc_start: 0.8576 (m-30) cc_final: 0.8294 (t70) REVERT: 4 40 ASN cc_start: 0.8864 (t0) cc_final: 0.7813 (t0) REVERT: 4 43 ILE cc_start: 0.9087 (tp) cc_final: 0.8579 (tt) REVERT: 4 59 GLU cc_start: 0.8681 (tp30) cc_final: 0.8422 (tp30) REVERT: 4 72 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7836 (mm) REVERT: 5 2 GLN cc_start: 0.7517 (mt0) cc_final: 0.7253 (pm20) REVERT: 5 28 ILE cc_start: 0.9199 (mt) cc_final: 0.8996 (tp) REVERT: 6 39 ARG cc_start: 0.8077 (ttm170) cc_final: 0.7850 (ttm110) REVERT: 6 57 LEU cc_start: 0.8758 (tp) cc_final: 0.8553 (tp) REVERT: 6 72 LEU cc_start: 0.9175 (mt) cc_final: 0.8941 (tp) REVERT: 7 2 GLN cc_start: 0.7929 (tp-100) cc_final: 0.7158 (pm20) REVERT: 7 57 LEU cc_start: 0.8907 (mt) cc_final: 0.8703 (mt) REVERT: 7 67 MET cc_start: 0.8820 (ptm) cc_final: 0.7969 (mtp) REVERT: 8 43 ILE cc_start: 0.8091 (tp) cc_final: 0.7543 (tp) REVERT: 8 55 PHE cc_start: 0.8992 (t80) cc_final: 0.8660 (t80) REVERT: 8 59 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8736 (mm-30) REVERT: 8 64 PHE cc_start: 0.9015 (m-10) cc_final: 0.8715 (m-10) REVERT: 8 67 MET cc_start: 0.8667 (ptm) cc_final: 0.8051 (mtp) REVERT: 8 72 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7829 (mm) REVERT: 9 35 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8454 (m-40) REVERT: 9 43 ILE cc_start: 0.8183 (tp) cc_final: 0.7873 (mt) REVERT: 9 46 THR cc_start: 0.7561 (m) cc_final: 0.7313 (p) REVERT: 0 5 LEU cc_start: 0.8644 (tp) cc_final: 0.7764 (tp) REVERT: 0 9 TYR cc_start: 0.7890 (m-80) cc_final: 0.7219 (m-80) REVERT: 0 59 GLU cc_start: 0.8667 (tp30) cc_final: 0.8439 (tp30) REVERT: A 3 GLN cc_start: 0.7240 (tp-100) cc_final: 0.6877 (tp40) REVERT: a 68 THR cc_start: 0.9145 (t) cc_final: 0.8878 (m) REVERT: a 94 MET cc_start: 0.9026 (mmt) cc_final: 0.8691 (mmt) REVERT: a 186 LEU cc_start: 0.9188 (tp) cc_final: 0.8799 (tp) REVERT: a 199 MET cc_start: 0.8903 (mtm) cc_final: 0.8688 (mtt) REVERT: b 72 TYR cc_start: 0.8007 (m-10) cc_final: 0.7598 (m-10) REVERT: b 82 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: f 76 PHE cc_start: 0.8619 (t80) cc_final: 0.8136 (t80) REVERT: i 1 MET cc_start: 0.6218 (ttp) cc_final: 0.4715 (tpt) REVERT: i 11 LYS cc_start: 0.8878 (pttt) cc_final: 0.8099 (mmpt) REVERT: C 1 MET cc_start: 0.6792 (mmm) cc_final: 0.6495 (mmm) REVERT: C 39 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7734 (tpp80) REVERT: D 33 LEU cc_start: 0.9173 (tp) cc_final: 0.8956 (tt) REVERT: D 58 SER cc_start: 0.9185 (t) cc_final: 0.8802 (p) REVERT: E 45 ASP cc_start: 0.8599 (m-30) cc_final: 0.8331 (t70) REVERT: F 40 ASN cc_start: 0.8847 (t0) cc_final: 0.7805 (t0) REVERT: F 43 ILE cc_start: 0.9097 (tp) cc_final: 0.8575 (tt) REVERT: F 59 GLU cc_start: 0.8663 (tp30) cc_final: 0.8391 (tp30) REVERT: F 72 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7974 (mm) REVERT: H 39 ARG cc_start: 0.8067 (ttm170) cc_final: 0.7788 (ttm110) REVERT: H 72 LEU cc_start: 0.9113 (mt) cc_final: 0.8825 (tp) REVERT: I 2 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7145 (pm20) REVERT: I 8 LYS cc_start: 0.8046 (mttp) cc_final: 0.7756 (mtpp) REVERT: I 19 LEU cc_start: 0.9463 (mt) cc_final: 0.9262 (mt) REVERT: I 67 MET cc_start: 0.8711 (ptm) cc_final: 0.7874 (mtp) REVERT: J 55 PHE cc_start: 0.9016 (t80) cc_final: 0.8721 (t80) REVERT: J 64 PHE cc_start: 0.9064 (m-10) cc_final: 0.8798 (m-10) REVERT: J 67 MET cc_start: 0.8631 (ptm) cc_final: 0.8038 (mtp) REVERT: K 35 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8510 (m-40) REVERT: B 5 LEU cc_start: 0.8632 (tp) cc_final: 0.7747 (tp) REVERT: B 9 TYR cc_start: 0.7923 (m-80) cc_final: 0.7172 (m-80) REVERT: B 59 GLU cc_start: 0.8665 (tp30) cc_final: 0.8451 (tp30) REVERT: B 69 SER cc_start: 0.9184 (t) cc_final: 0.8947 (p) REVERT: L 3 GLN cc_start: 0.7245 (tp-100) cc_final: 0.6892 (tp40) REVERT: M 68 THR cc_start: 0.9125 (t) cc_final: 0.8887 (m) REVERT: M 186 LEU cc_start: 0.9217 (tp) cc_final: 0.8802 (tp) REVERT: M 199 MET cc_start: 0.8881 (mtm) cc_final: 0.8679 (mtt) REVERT: N 72 TYR cc_start: 0.7964 (m-10) cc_final: 0.7553 (m-10) REVERT: N 82 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: N 87 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8538 (ttmm) REVERT: S 1 MET cc_start: 0.6180 (ttp) cc_final: 0.4680 (tpt) REVERT: S 11 LYS cc_start: 0.8900 (pttt) cc_final: 0.8095 (mmtt) outliers start: 99 outliers final: 57 residues processed: 786 average time/residue: 0.2642 time to fit residues: 337.1766 Evaluate side-chains 758 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 694 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 46 THR Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 69 SER Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 16 THR Chi-restraints excluded: chain 5 residue 58 SER Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 65 CYS Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 58 SER Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 179 SER 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 82 ASP 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 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 16 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 70 PHE 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 58 SER Chi-restraints excluded: chain B residue 15 SER 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 45 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain M residue 188 MET 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 82 ASP Chi-restraints excluded: chain N residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 253 optimal weight: 20.0000 chunk 268 optimal weight: 40.0000 chunk 132 optimal weight: 0.9990 chunk 240 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3156 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= 0.207 Angle : 0.670 10.345 29638 Z= 0.323 Chirality : 0.041 0.216 3678 Planarity : 0.004 0.059 3644 Dihedral : 4.412 24.680 3084 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.38 % Allowed : 23.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2618 helix: 0.90 (0.11), residues: 2070 sheet: None (None), residues: 0 loop : -2.19 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 234 HIS 0.005 0.001 HIS f 68 PHE 0.043 0.002 PHE 7 55 TYR 0.015 0.001 TYR Q 83 ARG 0.003 0.000 ARG f 23 *********************** 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 875 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 766 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9199 (t) cc_final: 0.8810 (p) REVERT: 3 45 ASP cc_start: 0.8598 (m-30) cc_final: 0.8327 (t0) REVERT: 4 40 ASN cc_start: 0.8784 (t0) cc_final: 0.7867 (t0) REVERT: 4 43 ILE cc_start: 0.9075 (tp) cc_final: 0.8607 (tt) REVERT: 4 59 GLU cc_start: 0.8625 (tp30) cc_final: 0.8234 (tp30) REVERT: 4 72 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7827 (mm) REVERT: 5 2 GLN cc_start: 0.7482 (mt0) cc_final: 0.7176 (pm20) REVERT: 6 15 SER cc_start: 0.9115 (m) cc_final: 0.8839 (m) REVERT: 6 39 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7884 (ttm110) REVERT: 6 72 LEU cc_start: 0.9105 (mt) cc_final: 0.8733 (mt) REVERT: 7 2 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7202 (pm20) REVERT: 7 67 MET cc_start: 0.8809 (ptm) cc_final: 0.7923 (mtp) REVERT: 8 1 MET cc_start: 0.8359 (mtm) cc_final: 0.7944 (tmm) REVERT: 8 43 ILE cc_start: 0.8032 (tp) cc_final: 0.7483 (tp) REVERT: 8 64 PHE cc_start: 0.8961 (m-10) cc_final: 0.8651 (m-10) REVERT: 8 67 MET cc_start: 0.8664 (ptm) cc_final: 0.8071 (mtp) REVERT: 9 59 GLU cc_start: 0.8467 (tp30) cc_final: 0.8133 (tp30) REVERT: 0 5 LEU cc_start: 0.8678 (tp) cc_final: 0.7737 (tp) REVERT: 0 9 TYR cc_start: 0.7863 (m-80) cc_final: 0.7237 (m-80) REVERT: 0 59 GLU cc_start: 0.8656 (tp30) cc_final: 0.8436 (tp30) REVERT: A 8 TYR cc_start: 0.8393 (m-80) cc_final: 0.8177 (m-80) REVERT: a 68 THR cc_start: 0.9160 (t) cc_final: 0.8935 (m) REVERT: a 186 LEU cc_start: 0.9199 (tp) cc_final: 0.8808 (tp) REVERT: a 199 MET cc_start: 0.8914 (mtm) cc_final: 0.8712 (mtt) REVERT: b 72 TYR cc_start: 0.8009 (m-10) cc_final: 0.7598 (m-10) REVERT: b 82 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: b 87 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8447 (ttmm) REVERT: d 284 MET cc_start: 0.8259 (pmm) cc_final: 0.6882 (pmm) REVERT: f 76 PHE cc_start: 0.8631 (t80) cc_final: 0.8114 (t80) REVERT: i 1 MET cc_start: 0.6142 (ttp) cc_final: 0.4637 (tpt) REVERT: i 11 LYS cc_start: 0.8917 (pttt) cc_final: 0.8064 (mmpt) REVERT: i 25 TYR cc_start: 0.8125 (t80) cc_final: 0.7862 (t80) REVERT: C 39 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7805 (tpp80) REVERT: D 58 SER cc_start: 0.9211 (t) cc_final: 0.8866 (p) REVERT: E 45 ASP cc_start: 0.8609 (m-30) cc_final: 0.8335 (t70) REVERT: E 67 MET cc_start: 0.8717 (tmm) cc_final: 0.8480 (tmm) REVERT: F 40 ASN cc_start: 0.8805 (t0) cc_final: 0.7902 (t0) REVERT: F 43 ILE cc_start: 0.9081 (tp) cc_final: 0.8617 (tt) REVERT: F 59 GLU cc_start: 0.8533 (tp30) cc_final: 0.8262 (tp30) REVERT: F 72 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7828 (mm) REVERT: G 16 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8814 (t) REVERT: G 55 PHE cc_start: 0.9240 (t80) cc_final: 0.9038 (t80) REVERT: H 15 SER cc_start: 0.9106 (m) cc_final: 0.8822 (m) REVERT: H 72 LEU cc_start: 0.9074 (mt) cc_final: 0.8685 (mt) REVERT: I 2 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7117 (pm20) REVERT: I 8 LYS cc_start: 0.8014 (mttp) cc_final: 0.7741 (mtpp) REVERT: I 67 MET cc_start: 0.8705 (ptm) cc_final: 0.7888 (mtp) REVERT: J 1 MET cc_start: 0.8356 (mtm) cc_final: 0.7908 (tmm) REVERT: J 59 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8742 (mm-30) REVERT: J 64 PHE cc_start: 0.9015 (m-10) cc_final: 0.8713 (m-10) REVERT: J 67 MET cc_start: 0.8638 (ptm) cc_final: 0.8042 (mtp) REVERT: K 35 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8394 (m-40) REVERT: K 59 GLU cc_start: 0.8469 (tp30) cc_final: 0.8122 (tp30) REVERT: B 5 LEU cc_start: 0.8670 (tp) cc_final: 0.7664 (tp) REVERT: B 9 TYR cc_start: 0.7922 (m-80) cc_final: 0.7260 (m-80) REVERT: B 59 GLU cc_start: 0.8631 (tp30) cc_final: 0.8428 (tp30) REVERT: B 69 SER cc_start: 0.9134 (t) cc_final: 0.8911 (p) REVERT: M 62 GLN cc_start: 0.8566 (mp10) cc_final: 0.8247 (mp10) REVERT: M 68 THR cc_start: 0.9154 (t) cc_final: 0.8904 (m) REVERT: M 94 MET cc_start: 0.9054 (mmt) cc_final: 0.8589 (mmt) REVERT: M 186 LEU cc_start: 0.9217 (tp) cc_final: 0.8817 (tp) REVERT: N 72 TYR cc_start: 0.8006 (m-10) cc_final: 0.7582 (m-10) REVERT: N 82 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: N 87 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8436 (ttmm) REVERT: O 276 ASP cc_start: 0.8410 (p0) cc_final: 0.8004 (p0) REVERT: O 284 MET cc_start: 0.8445 (pmm) cc_final: 0.7068 (pmm) REVERT: S 1 MET cc_start: 0.6163 (ttp) cc_final: 0.4627 (tpt) REVERT: S 11 LYS cc_start: 0.8912 (pttt) cc_final: 0.8045 (mmpt) REVERT: S 25 TYR cc_start: 0.8150 (t80) cc_final: 0.7906 (t80) REVERT: T 8 MET cc_start: 0.6874 (tpt) cc_final: 0.6672 (tpt) outliers start: 109 outliers final: 70 residues processed: 802 average time/residue: 0.2768 time to fit residues: 362.8190 Evaluate side-chains 783 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 707 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 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 46 THR Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 16 THR Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 7 residue 14 ILE Chi-restraints excluded: chain 9 residue 58 SER 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 41 SER Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 179 SER 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 82 ASP 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 29 LYS 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 14 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 SER 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 18 LEU Chi-restraints excluded: chain L residue 41 SER 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 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 82 ASP Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 229 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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** ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21822 Z= 0.198 Angle : 0.669 11.004 29638 Z= 0.322 Chirality : 0.041 0.286 3678 Planarity : 0.004 0.064 3644 Dihedral : 4.300 23.496 3084 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.28 % Allowed : 25.02 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2618 helix: 1.08 (0.11), residues: 2072 sheet: None (None), residues: 0 loop : -2.07 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 234 HIS 0.005 0.001 HIS f 68 PHE 0.027 0.002 PHE C 55 TYR 0.022 0.001 TYR a 166 ARG 0.004 0.000 ARG f 23 *********************** 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 856 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 749 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9198 (t) cc_final: 0.8789 (p) REVERT: 3 45 ASP cc_start: 0.8577 (m-30) cc_final: 0.8251 (t0) REVERT: 4 40 ASN cc_start: 0.8724 (t0) cc_final: 0.7889 (t0) REVERT: 4 43 ILE cc_start: 0.9079 (tp) cc_final: 0.8725 (tt) REVERT: 4 59 GLU cc_start: 0.8549 (tp30) cc_final: 0.8183 (tp30) REVERT: 4 72 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7851 (mm) REVERT: 6 15 SER cc_start: 0.9108 (m) cc_final: 0.8823 (m) REVERT: 6 64 PHE cc_start: 0.8886 (m-80) cc_final: 0.8598 (m-80) REVERT: 6 72 LEU cc_start: 0.9062 (mt) cc_final: 0.8684 (mt) REVERT: 7 2 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7313 (pm20) REVERT: 7 67 MET cc_start: 0.8754 (ptm) cc_final: 0.7936 (mtp) REVERT: 8 1 MET cc_start: 0.8333 (mtm) cc_final: 0.7933 (tmm) REVERT: 8 43 ILE cc_start: 0.8125 (tp) cc_final: 0.7609 (tp) REVERT: 8 50 MET cc_start: 0.8426 (mtm) cc_final: 0.8169 (ptp) REVERT: 8 59 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8771 (mm-30) REVERT: 8 64 PHE cc_start: 0.8998 (m-10) cc_final: 0.8631 (m-10) REVERT: 8 67 MET cc_start: 0.8686 (ptm) cc_final: 0.8108 (mtp) REVERT: 8 72 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7820 (mm) REVERT: 9 59 GLU cc_start: 0.8481 (tp30) cc_final: 0.8140 (tp30) REVERT: 0 5 LEU cc_start: 0.8735 (tp) cc_final: 0.7932 (tp) REVERT: 0 9 TYR cc_start: 0.7785 (m-80) cc_final: 0.7241 (m-80) REVERT: 0 59 GLU cc_start: 0.8671 (tp30) cc_final: 0.8464 (tp30) REVERT: A 8 TYR cc_start: 0.8349 (m-80) cc_final: 0.8146 (m-80) REVERT: a 68 THR cc_start: 0.9161 (t) cc_final: 0.8928 (m) REVERT: a 94 MET cc_start: 0.9077 (mmt) cc_final: 0.8624 (mmt) REVERT: a 161 ILE cc_start: 0.8815 (tt) cc_final: 0.8436 (mm) REVERT: a 186 LEU cc_start: 0.9216 (tp) cc_final: 0.8815 (tp) REVERT: b 72 TYR cc_start: 0.8008 (m-10) cc_final: 0.7579 (m-10) REVERT: b 82 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: b 87 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8416 (ttmm) REVERT: d 250 THR cc_start: 0.8822 (m) cc_final: 0.8532 (p) REVERT: d 284 MET cc_start: 0.8285 (pmm) cc_final: 0.6864 (pmm) REVERT: f 76 PHE cc_start: 0.8547 (t80) cc_final: 0.8042 (t80) REVERT: i 1 MET cc_start: 0.6160 (ttp) cc_final: 0.4619 (tpt) REVERT: i 9 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8630 (mp) REVERT: i 11 LYS cc_start: 0.8958 (pttt) cc_final: 0.8053 (mmpt) REVERT: i 25 TYR cc_start: 0.8152 (t80) cc_final: 0.7910 (t80) REVERT: i 54 LYS cc_start: 0.8193 (tppt) cc_final: 0.7704 (pttp) REVERT: C 39 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7838 (tpp80) REVERT: D 58 SER cc_start: 0.9208 (t) cc_final: 0.8838 (p) REVERT: E 45 ASP cc_start: 0.8665 (m-30) cc_final: 0.8273 (t0) REVERT: E 67 MET cc_start: 0.8725 (tmm) cc_final: 0.8468 (tmm) REVERT: F 40 ASN cc_start: 0.8785 (t0) cc_final: 0.7960 (t0) REVERT: F 43 ILE cc_start: 0.9088 (tp) cc_final: 0.8738 (tt) REVERT: F 59 GLU cc_start: 0.8501 (tp30) cc_final: 0.8190 (tp30) REVERT: F 72 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7850 (mm) REVERT: G 16 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8833 (t) REVERT: H 64 PHE cc_start: 0.8859 (m-80) cc_final: 0.8574 (m-80) REVERT: H 72 LEU cc_start: 0.9051 (mt) cc_final: 0.8802 (tp) REVERT: I 2 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7167 (pm20) REVERT: I 67 MET cc_start: 0.8667 (ptm) cc_final: 0.7847 (mtp) REVERT: J 1 MET cc_start: 0.8362 (mtm) cc_final: 0.7898 (tmm) REVERT: J 55 PHE cc_start: 0.9105 (t80) cc_final: 0.8819 (t80) REVERT: J 64 PHE cc_start: 0.9010 (m-10) cc_final: 0.8664 (m-10) REVERT: J 67 MET cc_start: 0.8659 (ptm) cc_final: 0.8091 (mtp) REVERT: K 59 GLU cc_start: 0.8489 (tp30) cc_final: 0.8154 (tp30) REVERT: B 5 LEU cc_start: 0.8706 (tp) cc_final: 0.7852 (tp) REVERT: B 9 TYR cc_start: 0.7808 (m-80) cc_final: 0.7285 (m-80) REVERT: B 59 GLU cc_start: 0.8656 (tp30) cc_final: 0.8455 (tp30) REVERT: B 69 SER cc_start: 0.9126 (t) cc_final: 0.8915 (p) REVERT: L 18 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8598 (tt) REVERT: M 68 THR cc_start: 0.9163 (t) cc_final: 0.8913 (m) REVERT: M 94 MET cc_start: 0.9047 (mmt) cc_final: 0.8632 (mmt) REVERT: M 161 ILE cc_start: 0.8829 (tt) cc_final: 0.8460 (mm) REVERT: M 186 LEU cc_start: 0.9233 (tp) cc_final: 0.8843 (tp) REVERT: N 72 TYR cc_start: 0.8007 (m-10) cc_final: 0.7577 (m-10) REVERT: N 82 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: N 87 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8425 (ttmm) REVERT: O 250 THR cc_start: 0.8828 (m) cc_final: 0.8566 (p) REVERT: O 276 ASP cc_start: 0.8440 (p0) cc_final: 0.8149 (p0) REVERT: O 284 MET cc_start: 0.8415 (pmm) cc_final: 0.7026 (pmm) REVERT: S 1 MET cc_start: 0.6177 (ttp) cc_final: 0.4614 (tpt) REVERT: S 9 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8574 (mp) REVERT: S 11 LYS cc_start: 0.8938 (pttt) cc_final: 0.8031 (mmpt) REVERT: S 25 TYR cc_start: 0.8201 (t80) cc_final: 0.7879 (t80) outliers start: 107 outliers final: 68 residues processed: 786 average time/residue: 0.2663 time to fit residues: 341.2814 Evaluate side-chains 779 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 702 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 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 14 ILE Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 16 THR Chi-restraints excluded: chain 5 residue 58 SER Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 6 residue 65 CYS Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 9 residue 58 SER 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 41 SER Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 111 LEU Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 179 SER 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 82 ASP 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 i residue 29 LYS 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 46 THR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 SER 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 18 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR 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 82 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 268 optimal weight: 40.0000 chunk 223 optimal weight: 0.3980 chunk 124 optimal weight: 30.0000 chunk 22 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 f 29 HIS ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21822 Z= 0.238 Angle : 0.678 17.084 29638 Z= 0.326 Chirality : 0.041 0.255 3678 Planarity : 0.004 0.071 3644 Dihedral : 4.238 23.847 3084 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 6.02 % Allowed : 25.07 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2618 helix: 1.19 (0.12), residues: 2072 sheet: None (None), residues: 0 loop : -1.96 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 234 HIS 0.005 0.001 HIS Q 68 PHE 0.035 0.002 PHE C 55 TYR 0.025 0.002 TYR a 32 ARG 0.004 0.000 ARG Q 23 *********************** 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 856 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 734 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 2 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8106 (mm110) REVERT: 2 58 SER cc_start: 0.9221 (t) cc_final: 0.8780 (p) REVERT: 3 45 ASP cc_start: 0.8619 (m-30) cc_final: 0.8272 (t0) REVERT: 4 40 ASN cc_start: 0.8693 (t0) cc_final: 0.7932 (t0) REVERT: 4 43 ILE cc_start: 0.9086 (tp) cc_final: 0.8746 (tt) REVERT: 4 59 GLU cc_start: 0.8466 (tp30) cc_final: 0.8172 (tp30) REVERT: 4 72 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7844 (mm) REVERT: 5 16 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8864 (t) REVERT: 6 72 LEU cc_start: 0.9043 (mt) cc_final: 0.8833 (tp) REVERT: 7 2 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7284 (pm20) REVERT: 7 67 MET cc_start: 0.8728 (ptm) cc_final: 0.7890 (mtp) REVERT: 8 1 MET cc_start: 0.8343 (mtm) cc_final: 0.7940 (tmm) REVERT: 8 43 ILE cc_start: 0.8113 (tp) cc_final: 0.7639 (tp) REVERT: 8 55 PHE cc_start: 0.9091 (t80) cc_final: 0.8778 (t80) REVERT: 8 59 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8870 (mm-30) REVERT: 8 64 PHE cc_start: 0.9005 (m-10) cc_final: 0.8631 (m-10) REVERT: 8 67 MET cc_start: 0.8695 (ptm) cc_final: 0.8184 (mtp) REVERT: 9 59 GLU cc_start: 0.8492 (tp30) cc_final: 0.8151 (tp30) REVERT: 0 5 LEU cc_start: 0.8759 (tp) cc_final: 0.8018 (tp) REVERT: 0 9 TYR cc_start: 0.7707 (m-80) cc_final: 0.7287 (m-80) REVERT: a 68 THR cc_start: 0.9183 (t) cc_final: 0.8953 (m) REVERT: a 94 MET cc_start: 0.9123 (mmt) cc_final: 0.8648 (mmt) REVERT: a 161 ILE cc_start: 0.8881 (tt) cc_final: 0.8519 (mm) REVERT: a 186 LEU cc_start: 0.9222 (tp) cc_final: 0.8805 (tp) REVERT: b 72 TYR cc_start: 0.8039 (m-10) cc_final: 0.7625 (m-10) REVERT: b 82 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: b 87 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8394 (ttmm) REVERT: d 250 THR cc_start: 0.8782 (m) cc_final: 0.8496 (p) REVERT: d 276 ASP cc_start: 0.8450 (p0) cc_final: 0.8167 (p0) REVERT: d 284 MET cc_start: 0.8297 (pmm) cc_final: 0.6944 (pmm) REVERT: f 76 PHE cc_start: 0.8544 (t80) cc_final: 0.8051 (t80) REVERT: i 1 MET cc_start: 0.6194 (ttp) cc_final: 0.4547 (tpt) REVERT: i 9 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8613 (mp) REVERT: i 11 LYS cc_start: 0.9011 (pttt) cc_final: 0.8086 (mmpt) REVERT: i 25 TYR cc_start: 0.8234 (t80) cc_final: 0.7910 (t80) REVERT: i 54 LYS cc_start: 0.8165 (tppt) cc_final: 0.7778 (pttp) REVERT: C 39 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7821 (tpp80) REVERT: D 58 SER cc_start: 0.9228 (t) cc_final: 0.8799 (p) REVERT: E 45 ASP cc_start: 0.8713 (m-30) cc_final: 0.8335 (t0) REVERT: E 67 MET cc_start: 0.8735 (tmm) cc_final: 0.8463 (tmm) REVERT: F 40 ASN cc_start: 0.8741 (t0) cc_final: 0.7940 (t0) REVERT: F 43 ILE cc_start: 0.9092 (tp) cc_final: 0.8753 (tt) REVERT: F 59 GLU cc_start: 0.8500 (tp30) cc_final: 0.8207 (tp30) REVERT: F 72 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7933 (mm) REVERT: G 16 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8889 (t) REVERT: G 55 PHE cc_start: 0.9154 (t80) cc_final: 0.8742 (t80) REVERT: H 15 SER cc_start: 0.8788 (m) cc_final: 0.8516 (m) REVERT: H 72 LEU cc_start: 0.9037 (mt) cc_final: 0.8704 (mt) REVERT: I 2 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7205 (pm20) REVERT: I 67 MET cc_start: 0.8653 (ptm) cc_final: 0.7788 (mtp) REVERT: J 1 MET cc_start: 0.8480 (mtm) cc_final: 0.7987 (tmm) REVERT: J 55 PHE cc_start: 0.9008 (t80) cc_final: 0.8777 (t80) REVERT: J 59 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8791 (mm-30) REVERT: J 64 PHE cc_start: 0.8993 (m-10) cc_final: 0.8627 (m-10) REVERT: J 67 MET cc_start: 0.8684 (ptm) cc_final: 0.8156 (mtp) REVERT: B 5 LEU cc_start: 0.8780 (tp) cc_final: 0.7984 (tp) REVERT: B 9 TYR cc_start: 0.7717 (m-80) cc_final: 0.7248 (m-80) REVERT: B 69 SER cc_start: 0.9129 (t) cc_final: 0.8915 (p) REVERT: M 68 THR cc_start: 0.9181 (t) cc_final: 0.8957 (m) REVERT: M 94 MET cc_start: 0.9084 (mmt) cc_final: 0.8661 (mmt) REVERT: M 161 ILE cc_start: 0.8917 (tt) cc_final: 0.8654 (mm) REVERT: M 186 LEU cc_start: 0.9215 (tp) cc_final: 0.8799 (tp) REVERT: N 72 TYR cc_start: 0.8039 (m-10) cc_final: 0.7626 (m-10) REVERT: N 82 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8342 (m-30) REVERT: N 87 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8367 (ttmm) REVERT: O 250 THR cc_start: 0.8841 (m) cc_final: 0.8566 (p) REVERT: O 276 ASP cc_start: 0.8470 (p0) cc_final: 0.8193 (p0) REVERT: S 1 MET cc_start: 0.6149 (ttp) cc_final: 0.4499 (tpt) REVERT: S 9 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8600 (mp) REVERT: S 11 LYS cc_start: 0.9011 (pttt) cc_final: 0.8075 (mmpt) REVERT: S 13 TYR cc_start: 0.9036 (m-80) cc_final: 0.8797 (m-80) REVERT: S 25 TYR cc_start: 0.8199 (t80) cc_final: 0.7887 (t80) outliers start: 122 outliers final: 78 residues processed: 780 average time/residue: 0.2735 time to fit residues: 347.2988 Evaluate side-chains 792 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 705 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 2 residue 2 GLN 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 14 ILE Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 16 THR 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 63 LEU Chi-restraints excluded: chain 6 residue 65 CYS Chi-restraints excluded: chain 7 residue 14 ILE Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 9 residue 58 SER 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 41 SER Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 130 THR 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 82 ASP 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 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 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 SER 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 36 LEU Chi-restraints excluded: chain L residue 41 SER 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 130 THR 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 82 ASP Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain Q residue 79 SER Chi-restraints excluded: chain S residue 9 ILE 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 259 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 226 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 267 optimal weight: 40.0000 chunk 167 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21822 Z= 0.244 Angle : 0.699 17.245 29638 Z= 0.334 Chirality : 0.042 0.347 3678 Planarity : 0.004 0.074 3644 Dihedral : 4.238 25.698 3084 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.73 % Allowed : 26.46 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2618 helix: 1.26 (0.11), residues: 2072 sheet: None (None), residues: 0 loop : -1.92 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 234 HIS 0.005 0.001 HIS Q 68 PHE 0.040 0.002 PHE 1 55 TYR 0.016 0.001 TYR S 24 ARG 0.004 0.000 ARG f 23 *********************** 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 846 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 730 time to evaluate : 2.228 Fit side-chains revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9166 (t) cc_final: 0.8751 (p) REVERT: 3 45 ASP cc_start: 0.8650 (m-30) cc_final: 0.8305 (t0) REVERT: 4 40 ASN cc_start: 0.8683 (t0) cc_final: 0.8008 (t0) REVERT: 4 43 ILE cc_start: 0.9085 (tp) cc_final: 0.8758 (tt) REVERT: 4 59 GLU cc_start: 0.8446 (tp30) cc_final: 0.8192 (tp30) REVERT: 4 72 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7824 (mm) REVERT: 5 16 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8898 (t) REVERT: 6 64 PHE cc_start: 0.8869 (m-80) cc_final: 0.8599 (m-80) REVERT: 6 72 LEU cc_start: 0.9037 (mt) cc_final: 0.8826 (tp) REVERT: 7 2 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7282 (pm20) REVERT: 7 67 MET cc_start: 0.8709 (ptm) cc_final: 0.7867 (mtp) REVERT: 8 1 MET cc_start: 0.8377 (mtm) cc_final: 0.7946 (tmm) REVERT: 8 43 ILE cc_start: 0.8002 (tp) cc_final: 0.7507 (tp) REVERT: 8 55 PHE cc_start: 0.9025 (t80) cc_final: 0.8791 (t80) REVERT: 8 59 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8785 (mm-30) REVERT: 8 64 PHE cc_start: 0.8939 (m-10) cc_final: 0.8541 (m-10) REVERT: 8 67 MET cc_start: 0.8693 (ptm) cc_final: 0.8121 (mtp) REVERT: 0 5 LEU cc_start: 0.8769 (tp) cc_final: 0.8090 (tp) REVERT: 0 9 TYR cc_start: 0.7658 (m-80) cc_final: 0.7277 (m-80) REVERT: 0 59 GLU cc_start: 0.8602 (tp30) cc_final: 0.8376 (tp30) REVERT: A 18 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8337 (mt) REVERT: a 68 THR cc_start: 0.9188 (t) cc_final: 0.8966 (m) REVERT: a 94 MET cc_start: 0.9133 (mmt) cc_final: 0.8688 (mmt) REVERT: a 161 ILE cc_start: 0.8928 (tt) cc_final: 0.8681 (mm) REVERT: a 186 LEU cc_start: 0.9217 (tp) cc_final: 0.8810 (tp) REVERT: b 72 TYR cc_start: 0.8041 (m-10) cc_final: 0.7633 (m-10) REVERT: b 82 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: b 87 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8356 (ttmm) REVERT: d 276 ASP cc_start: 0.8474 (p0) cc_final: 0.8179 (p0) REVERT: d 284 MET cc_start: 0.8315 (pmm) cc_final: 0.7002 (pmm) REVERT: f 76 PHE cc_start: 0.8594 (t80) cc_final: 0.8127 (t80) REVERT: i 1 MET cc_start: 0.6147 (ttp) cc_final: 0.4452 (tpt) REVERT: i 11 LYS cc_start: 0.9059 (pttt) cc_final: 0.8075 (mmpt) REVERT: i 25 TYR cc_start: 0.8159 (t80) cc_final: 0.7861 (t80) REVERT: i 54 LYS cc_start: 0.8116 (tppt) cc_final: 0.7709 (pttp) REVERT: C 39 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7818 (tpp80) REVERT: D 58 SER cc_start: 0.9177 (t) cc_final: 0.8853 (p) REVERT: E 43 ILE cc_start: 0.8837 (tp) cc_final: 0.8635 (tt) REVERT: E 45 ASP cc_start: 0.8746 (m-30) cc_final: 0.8386 (t0) REVERT: E 67 MET cc_start: 0.8706 (tmm) cc_final: 0.8401 (tmm) REVERT: F 40 ASN cc_start: 0.8727 (t0) cc_final: 0.7959 (t0) REVERT: F 43 ILE cc_start: 0.9085 (tp) cc_final: 0.8743 (tt) REVERT: F 59 GLU cc_start: 0.8552 (tp30) cc_final: 0.8288 (tp30) REVERT: F 72 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7925 (mm) REVERT: H 15 SER cc_start: 0.8786 (m) cc_final: 0.8527 (m) REVERT: H 64 PHE cc_start: 0.8859 (m-80) cc_final: 0.8595 (m-80) REVERT: H 72 LEU cc_start: 0.9028 (mt) cc_final: 0.8692 (mt) REVERT: I 2 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7209 (pm20) REVERT: I 67 MET cc_start: 0.8640 (ptm) cc_final: 0.7668 (mtp) REVERT: J 59 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8791 (mm-30) REVERT: J 64 PHE cc_start: 0.8979 (m-10) cc_final: 0.8612 (m-10) REVERT: J 67 MET cc_start: 0.8691 (ptm) cc_final: 0.8153 (mtp) REVERT: B 5 LEU cc_start: 0.8778 (tp) cc_final: 0.8014 (tp) REVERT: B 9 TYR cc_start: 0.7714 (m-80) cc_final: 0.7304 (m-80) REVERT: B 59 GLU cc_start: 0.8622 (tp30) cc_final: 0.8345 (tp30) REVERT: L 3 GLN cc_start: 0.7480 (tp40) cc_final: 0.7270 (tp-100) REVERT: M 68 THR cc_start: 0.9185 (t) cc_final: 0.8980 (m) REVERT: M 94 MET cc_start: 0.9088 (mmt) cc_final: 0.8679 (mmt) REVERT: M 161 ILE cc_start: 0.8926 (tt) cc_final: 0.8675 (mm) REVERT: M 186 LEU cc_start: 0.9215 (tp) cc_final: 0.8791 (tp) REVERT: M 199 MET cc_start: 0.8541 (mtt) cc_final: 0.8285 (mtt) REVERT: N 72 TYR cc_start: 0.8037 (m-10) cc_final: 0.7628 (m-10) REVERT: N 82 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8353 (m-30) REVERT: N 87 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8361 (ttmm) REVERT: O 250 THR cc_start: 0.8812 (m) cc_final: 0.8571 (p) REVERT: O 276 ASP cc_start: 0.8478 (p0) cc_final: 0.8202 (p0) REVERT: S 1 MET cc_start: 0.6167 (ttp) cc_final: 0.4476 (tpt) REVERT: S 11 LYS cc_start: 0.9048 (pttt) cc_final: 0.8053 (mmpt) REVERT: S 25 TYR cc_start: 0.8245 (t80) cc_final: 0.7963 (t80) outliers start: 116 outliers final: 88 residues processed: 768 average time/residue: 0.2692 time to fit residues: 337.5843 Evaluate side-chains 794 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 700 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 52 ILE 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 14 ILE Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 16 THR 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 6 residue 65 CYS 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 7 residue 65 CYS 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 9 residue 58 SER 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 41 SER Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 130 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 82 ASP 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 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 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 58 SER 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 36 LEU Chi-restraints excluded: chain L residue 41 SER 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 130 THR Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 188 MET 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 82 ASP Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain Q residue 79 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21822 Z= 0.262 Angle : 0.708 17.303 29638 Z= 0.342 Chirality : 0.042 0.249 3678 Planarity : 0.004 0.080 3644 Dihedral : 4.251 25.799 3084 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.02 % Allowed : 26.36 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2618 helix: 1.27 (0.11), residues: 2084 sheet: None (None), residues: 0 loop : -1.88 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 234 HIS 0.005 0.001 HIS f 68 PHE 0.053 0.002 PHE G 55 TYR 0.012 0.001 TYR A 8 ARG 0.004 0.000 ARG f 23 *********************** 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 834 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 712 time to evaluate : 2.370 Fit side-chains revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9189 (t) cc_final: 0.8885 (p) REVERT: 2 67 MET cc_start: 0.8350 (mmm) cc_final: 0.7951 (mmm) REVERT: 3 45 ASP cc_start: 0.8664 (m-30) cc_final: 0.8341 (t0) REVERT: 4 40 ASN cc_start: 0.8686 (t0) cc_final: 0.8000 (t0) REVERT: 4 43 ILE cc_start: 0.9103 (tp) cc_final: 0.8766 (tt) REVERT: 4 59 GLU cc_start: 0.8426 (tp30) cc_final: 0.8205 (tp30) REVERT: 4 72 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7817 (mm) REVERT: 6 64 PHE cc_start: 0.8845 (m-80) cc_final: 0.8546 (m-80) REVERT: 7 2 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7252 (pm20) REVERT: 7 67 MET cc_start: 0.8716 (ptm) cc_final: 0.7768 (mtp) REVERT: 8 43 ILE cc_start: 0.8008 (tp) cc_final: 0.7517 (tp) REVERT: 8 59 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8738 (mm-30) REVERT: 8 64 PHE cc_start: 0.8908 (m-10) cc_final: 0.8560 (m-10) REVERT: 8 67 MET cc_start: 0.8712 (ptm) cc_final: 0.8130 (mtp) REVERT: 0 5 LEU cc_start: 0.8807 (tp) cc_final: 0.8116 (pp) REVERT: 0 59 GLU cc_start: 0.8623 (tp30) cc_final: 0.8322 (tp30) REVERT: A 3 GLN cc_start: 0.7508 (tp40) cc_final: 0.7076 (tp40) REVERT: A 18 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8347 (mt) REVERT: a 94 MET cc_start: 0.9147 (mmt) cc_final: 0.8705 (mmt) REVERT: a 186 LEU cc_start: 0.9223 (tp) cc_final: 0.8812 (tp) REVERT: b 82 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: b 87 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8352 (ttmm) REVERT: d 250 THR cc_start: 0.8730 (m) cc_final: 0.8467 (p) REVERT: d 276 ASP cc_start: 0.8499 (p0) cc_final: 0.8227 (p0) REVERT: f 76 PHE cc_start: 0.8549 (t80) cc_final: 0.8103 (t80) REVERT: i 1 MET cc_start: 0.6258 (ttp) cc_final: 0.4485 (tpt) REVERT: i 11 LYS cc_start: 0.9074 (pttt) cc_final: 0.8052 (mmpt) REVERT: i 25 TYR cc_start: 0.8199 (t80) cc_final: 0.7892 (t80) REVERT: i 54 LYS cc_start: 0.8179 (tppt) cc_final: 0.7817 (pttp) REVERT: C 39 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7839 (tpp80) REVERT: D 58 SER cc_start: 0.9177 (t) cc_final: 0.8825 (p) REVERT: E 45 ASP cc_start: 0.8733 (m-30) cc_final: 0.8358 (t0) REVERT: E 67 MET cc_start: 0.8711 (tmm) cc_final: 0.8415 (tmm) REVERT: F 40 ASN cc_start: 0.8744 (t0) cc_final: 0.8018 (t0) REVERT: F 43 ILE cc_start: 0.9071 (tp) cc_final: 0.8751 (tt) REVERT: F 59 GLU cc_start: 0.8533 (tp30) cc_final: 0.8321 (tp30) REVERT: F 72 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7900 (mm) REVERT: H 64 PHE cc_start: 0.8830 (m-80) cc_final: 0.8537 (m-80) REVERT: H 72 LEU cc_start: 0.9030 (mt) cc_final: 0.8806 (tp) REVERT: I 2 GLN cc_start: 0.7836 (tp-100) cc_final: 0.7143 (pm20) REVERT: I 67 MET cc_start: 0.8588 (ptm) cc_final: 0.7688 (mtp) REVERT: J 59 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8821 (mm-30) REVERT: J 64 PHE cc_start: 0.8897 (m-10) cc_final: 0.8583 (m-10) REVERT: J 67 MET cc_start: 0.8668 (ptm) cc_final: 0.8113 (mtp) REVERT: B 5 LEU cc_start: 0.8802 (tp) cc_final: 0.8061 (pp) REVERT: B 50 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8059 (ptm) REVERT: B 59 GLU cc_start: 0.8630 (tp30) cc_final: 0.8309 (tp30) REVERT: M 186 LEU cc_start: 0.9225 (tp) cc_final: 0.8804 (tp) REVERT: M 199 MET cc_start: 0.8558 (mtt) cc_final: 0.8285 (mtt) REVERT: N 72 TYR cc_start: 0.8041 (m-10) cc_final: 0.7646 (m-10) REVERT: N 82 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: N 87 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8366 (ttmm) REVERT: O 250 THR cc_start: 0.8824 (m) cc_final: 0.8553 (p) REVERT: O 276 ASP cc_start: 0.8524 (p0) cc_final: 0.8257 (p0) REVERT: S 1 MET cc_start: 0.6284 (ttp) cc_final: 0.4504 (tpt) REVERT: S 11 LYS cc_start: 0.9067 (pttt) cc_final: 0.8044 (mmpt) REVERT: S 25 TYR cc_start: 0.8245 (t80) cc_final: 0.7959 (t80) REVERT: S 57 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7545 (mp0) outliers start: 122 outliers final: 93 residues processed: 753 average time/residue: 0.2704 time to fit residues: 332.6847 Evaluate side-chains 795 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 696 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 52 ILE 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 16 THR Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 65 CYS 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 6 residue 65 CYS 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 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 9 residue 58 SER 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 18 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 152 LEU Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 211 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 82 ASP 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 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 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 CYS 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 K residue 58 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 50 MET 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 36 LEU Chi-restraints excluded: chain L residue 41 SER 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 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 180 ASN Chi-restraints excluded: chain M residue 188 MET 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 82 ASP Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain Q residue 79 SER 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 243 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21822 Z= 0.218 Angle : 0.715 16.227 29638 Z= 0.341 Chirality : 0.042 0.298 3678 Planarity : 0.004 0.080 3644 Dihedral : 4.234 27.081 3084 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.99 % Allowed : 27.94 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2618 helix: 1.33 (0.11), residues: 2080 sheet: None (None), residues: 0 loop : -1.86 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 126 HIS 0.005 0.001 HIS Q 68 PHE 0.057 0.002 PHE 8 55 TYR 0.027 0.001 TYR B 9 ARG 0.004 0.000 ARG f 23 *********************** 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 817 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 716 time to evaluate : 2.115 Fit side-chains revert: symmetry clash REVERT: 1 16 THR cc_start: 0.9242 (OUTLIER) cc_final: 0.8826 (t) REVERT: 2 58 SER cc_start: 0.9169 (t) cc_final: 0.8858 (p) REVERT: 3 45 ASP cc_start: 0.8662 (m-30) cc_final: 0.8336 (t0) REVERT: 4 40 ASN cc_start: 0.8646 (t0) cc_final: 0.7883 (t0) REVERT: 4 43 ILE cc_start: 0.9060 (tp) cc_final: 0.8726 (tt) REVERT: 4 59 GLU cc_start: 0.8352 (tp30) cc_final: 0.8125 (tp30) REVERT: 4 72 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7805 (mm) REVERT: 6 64 PHE cc_start: 0.8807 (m-80) cc_final: 0.8532 (m-80) REVERT: 7 2 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7205 (pm20) REVERT: 7 39 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7991 (ttm-80) REVERT: 7 67 MET cc_start: 0.8692 (ptm) cc_final: 0.7706 (mtp) REVERT: 8 43 ILE cc_start: 0.7975 (tp) cc_final: 0.7501 (tp) REVERT: 8 59 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8702 (mm-30) REVERT: 8 64 PHE cc_start: 0.8861 (m-10) cc_final: 0.8550 (m-10) REVERT: 8 67 MET cc_start: 0.8707 (ptm) cc_final: 0.8120 (mtp) REVERT: 0 5 LEU cc_start: 0.8688 (tp) cc_final: 0.7651 (pp) REVERT: 0 9 TYR cc_start: 0.7789 (m-80) cc_final: 0.7423 (m-80) REVERT: 0 59 GLU cc_start: 0.8633 (tp30) cc_final: 0.8348 (tp30) REVERT: A 3 GLN cc_start: 0.7526 (tp40) cc_final: 0.7148 (tp-100) REVERT: A 18 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8675 (tt) REVERT: a 94 MET cc_start: 0.9121 (mmt) cc_final: 0.8713 (mmt) REVERT: a 186 LEU cc_start: 0.9198 (tp) cc_final: 0.8791 (tp) REVERT: a 199 MET cc_start: 0.8546 (mtt) cc_final: 0.8280 (mtt) REVERT: b 72 TYR cc_start: 0.7839 (m-10) cc_final: 0.7545 (m-10) REVERT: b 82 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8352 (m-30) REVERT: b 87 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8331 (ttmm) REVERT: d 250 THR cc_start: 0.8714 (m) cc_final: 0.8462 (p) REVERT: d 276 ASP cc_start: 0.8501 (p0) cc_final: 0.8230 (p0) REVERT: f 76 PHE cc_start: 0.8528 (t80) cc_final: 0.8257 (t80) REVERT: i 1 MET cc_start: 0.6231 (ttp) cc_final: 0.4458 (tpt) REVERT: i 11 LYS cc_start: 0.9055 (pttt) cc_final: 0.8027 (mmpt) REVERT: i 25 TYR cc_start: 0.8195 (t80) cc_final: 0.7892 (t80) REVERT: i 54 LYS cc_start: 0.8111 (tppt) cc_final: 0.7812 (pttp) REVERT: C 39 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7863 (tpp80) REVERT: D 58 SER cc_start: 0.9197 (t) cc_final: 0.8974 (p) REVERT: E 45 ASP cc_start: 0.8717 (m-30) cc_final: 0.8388 (t0) REVERT: F 40 ASN cc_start: 0.8649 (t0) cc_final: 0.7922 (t0) REVERT: F 43 ILE cc_start: 0.9050 (tp) cc_final: 0.8716 (tt) REVERT: F 59 GLU cc_start: 0.8457 (tp30) cc_final: 0.8100 (tp30) REVERT: F 72 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7896 (mm) REVERT: H 64 PHE cc_start: 0.8791 (m-80) cc_final: 0.8507 (m-80) REVERT: H 72 LEU cc_start: 0.9037 (mt) cc_final: 0.8695 (mt) REVERT: I 2 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7100 (pm20) REVERT: I 67 MET cc_start: 0.8576 (ptm) cc_final: 0.7670 (mtp) REVERT: J 59 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8804 (mm-30) REVERT: J 64 PHE cc_start: 0.8902 (m-10) cc_final: 0.8533 (m-10) REVERT: J 67 MET cc_start: 0.8675 (ptm) cc_final: 0.8117 (mtp) REVERT: B 5 LEU cc_start: 0.8669 (tp) cc_final: 0.7558 (pp) REVERT: B 9 TYR cc_start: 0.7845 (m-80) cc_final: 0.7310 (m-80) REVERT: B 59 GLU cc_start: 0.8662 (tp30) cc_final: 0.8325 (tp30) REVERT: M 94 MET cc_start: 0.9079 (mmt) cc_final: 0.8717 (mmt) REVERT: M 186 LEU cc_start: 0.9213 (tp) cc_final: 0.8800 (tp) REVERT: M 199 MET cc_start: 0.8545 (mtt) cc_final: 0.8266 (mtt) REVERT: N 82 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: N 87 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8357 (ttmm) REVERT: O 250 THR cc_start: 0.8813 (m) cc_final: 0.8545 (p) REVERT: O 276 ASP cc_start: 0.8520 (p0) cc_final: 0.8257 (p0) REVERT: S 1 MET cc_start: 0.6260 (ttp) cc_final: 0.4474 (tpt) REVERT: S 11 LYS cc_start: 0.9022 (pttt) cc_final: 0.7944 (mmpt) REVERT: S 25 TYR cc_start: 0.8149 (t80) cc_final: 0.7886 (t80) outliers start: 101 outliers final: 80 residues processed: 748 average time/residue: 0.2778 time to fit residues: 340.7009 Evaluate side-chains 772 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 686 time to evaluate : 2.223 ------------------------------------------------------------------------------- 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 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 65 CYS 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 6 residue 65 CYS 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 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 18 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 45 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 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 82 ASP Chi-restraints excluded: chain b residue 93 ASN 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 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 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 16 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain K residue 58 SER 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 41 SER 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 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 180 ASN Chi-restraints excluded: chain M residue 188 MET 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 82 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 0.7980 chunk 264 optimal weight: 30.0000 chunk 161 optimal weight: 8.9990 chunk 125 optimal weight: 30.0000 chunk 183 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN k 15 HIS T 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21822 Z= 0.285 Angle : 0.738 16.423 29638 Z= 0.356 Chirality : 0.044 0.343 3678 Planarity : 0.004 0.085 3644 Dihedral : 4.254 28.719 3084 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.49 % Allowed : 28.97 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2618 helix: 1.30 (0.11), residues: 2070 sheet: None (None), residues: 0 loop : -1.55 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 234 HIS 0.005 0.001 HIS Q 68 PHE 0.057 0.002 PHE 8 55 TYR 0.027 0.002 TYR a 32 ARG 0.004 0.000 ARG f 23 ********************** 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 787 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 696 time to evaluate : 2.116 Fit side-chains revert: symmetry clash REVERT: 1 16 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8845 (t) REVERT: 2 58 SER cc_start: 0.9168 (t) cc_final: 0.8932 (p) REVERT: 2 67 MET cc_start: 0.8322 (mmm) cc_final: 0.7607 (mmm) REVERT: 3 45 ASP cc_start: 0.8674 (m-30) cc_final: 0.8293 (t0) REVERT: 4 40 ASN cc_start: 0.8684 (t0) cc_final: 0.7935 (t0) REVERT: 4 43 ILE cc_start: 0.9077 (tp) cc_final: 0.8734 (tt) REVERT: 4 59 GLU cc_start: 0.8400 (tp30) cc_final: 0.8181 (tp30) REVERT: 4 72 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7911 (mm) REVERT: 7 2 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7221 (pm20) REVERT: 7 67 MET cc_start: 0.8700 (ptm) cc_final: 0.7776 (mtp) REVERT: 8 64 PHE cc_start: 0.8939 (m-10) cc_final: 0.8543 (m-10) REVERT: 8 67 MET cc_start: 0.8721 (ptm) cc_final: 0.8134 (mtp) REVERT: 0 5 LEU cc_start: 0.8677 (tp) cc_final: 0.7595 (tp) REVERT: 0 9 TYR cc_start: 0.7898 (m-80) cc_final: 0.7390 (m-80) REVERT: A 3 GLN cc_start: 0.7551 (tp40) cc_final: 0.7274 (tp-100) REVERT: a 186 LEU cc_start: 0.9232 (tp) cc_final: 0.8826 (tp) REVERT: a 199 MET cc_start: 0.8586 (mtt) cc_final: 0.8310 (mtt) REVERT: b 82 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: d 250 THR cc_start: 0.8720 (m) cc_final: 0.8479 (p) REVERT: d 276 ASP cc_start: 0.8550 (p0) cc_final: 0.8300 (p0) REVERT: i 1 MET cc_start: 0.6242 (ttp) cc_final: 0.4167 (tpt) REVERT: i 11 LYS cc_start: 0.9075 (pttt) cc_final: 0.7959 (mmpt) REVERT: i 25 TYR cc_start: 0.8236 (t80) cc_final: 0.7920 (t80) REVERT: i 54 LYS cc_start: 0.8065 (tppt) cc_final: 0.7788 (pttp) REVERT: C 16 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.8854 (t) REVERT: C 39 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7846 (tpp80) REVERT: D 58 SER cc_start: 0.9257 (t) cc_final: 0.9036 (p) REVERT: E 45 ASP cc_start: 0.8718 (m-30) cc_final: 0.8391 (t0) REVERT: F 40 ASN cc_start: 0.8670 (t0) cc_final: 0.7966 (t0) REVERT: F 43 ILE cc_start: 0.9091 (tp) cc_final: 0.8760 (tt) REVERT: F 72 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8111 (mm) REVERT: H 72 LEU cc_start: 0.9039 (mt) cc_final: 0.8694 (mt) REVERT: I 2 GLN cc_start: 0.7761 (tp-100) cc_final: 0.7116 (pm20) REVERT: I 67 MET cc_start: 0.8578 (ptm) cc_final: 0.7677 (mtp) REVERT: J 64 PHE cc_start: 0.8915 (m-10) cc_final: 0.8546 (m-10) REVERT: J 67 MET cc_start: 0.8689 (ptm) cc_final: 0.8123 (mtp) REVERT: B 5 LEU cc_start: 0.8700 (tp) cc_final: 0.7695 (tp) REVERT: B 9 TYR cc_start: 0.7866 (m-80) cc_final: 0.7342 (m-80) REVERT: M 186 LEU cc_start: 0.9250 (tp) cc_final: 0.8831 (tp) REVERT: M 199 MET cc_start: 0.8583 (mtt) cc_final: 0.8316 (mtt) REVERT: N 82 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: N 87 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8370 (ttmm) REVERT: O 250 THR cc_start: 0.8818 (m) cc_final: 0.8560 (p) REVERT: O 276 ASP cc_start: 0.8552 (p0) cc_final: 0.8299 (p0) REVERT: S 1 MET cc_start: 0.6273 (ttp) cc_final: 0.4176 (tpt) REVERT: S 11 LYS cc_start: 0.9064 (pttt) cc_final: 0.7958 (mmpt) REVERT: S 25 TYR cc_start: 0.8250 (t80) cc_final: 0.7971 (t80) outliers start: 91 outliers final: 79 residues processed: 725 average time/residue: 0.2656 time to fit residues: 313.7664 Evaluate side-chains 767 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 682 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 58 SER Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 65 CYS 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 6 residue 65 CYS Chi-restraints excluded: chain 7 residue 48 PHE Chi-restraints excluded: chain 7 residue 65 CYS 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 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 41 SER Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 45 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 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 82 ASP Chi-restraints excluded: chain b residue 93 ASN 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 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 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 16 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 CYS Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain K residue 58 SER 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 41 SER 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 140 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 180 ASN Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 82 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109460 restraints weight = 38814.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109022 restraints weight = 19902.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109670 restraints weight = 20809.601| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21822 Z= 0.225 Angle : 0.736 16.494 29638 Z= 0.351 Chirality : 0.043 0.344 3678 Planarity : 0.004 0.084 3644 Dihedral : 4.254 27.911 3084 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.49 % Allowed : 28.97 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2618 helix: 1.35 (0.11), residues: 2070 sheet: None (None), residues: 0 loop : -1.57 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 126 HIS 0.005 0.001 HIS Q 68 PHE 0.051 0.002 PHE 8 55 TYR 0.019 0.001 TYR B 9 ARG 0.003 0.000 ARG 5 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5780.44 seconds wall clock time: 104 minutes 22.76 seconds (6262.76 seconds total)