Starting phenix.real_space_refine on Sat Aug 10 07:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/08_2024/6b2z_7036.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/08_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_7036/08_2024/6b2z_7036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/08_2024/6b2z_7036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/08_2024/6b2z_7036.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b2z_7036/08_2024/6b2z_7036.cif" } 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.43, per 1000 atoms: 0.53 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: 8.80 Conformation dependent library (CDL) restraints added in 3.6 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: 1.75 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: 6.52 Time building geometry restraints manager: 9.58 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 3.040 nonbonded pdb=" O SER 5 58 " pdb=" OG1 THR 5 61 " model vdw 2.290 3.040 nonbonded pdb=" O MET A 10 " pdb=" OG1 THR A 14 " model vdw 2.328 3.040 nonbonded pdb=" O MET L 10 " pdb=" OG1 THR L 14 " model vdw 2.328 3.040 nonbonded pdb=" OG SER M 1 " pdb=" OD2 ASP M 4 " model vdw 2.332 3.040 ... (remaining 170121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 2 through 73) selection = (chain '1' and resid 2 through 73) selection = (chain '2' and resid 2 through 73) selection = (chain '3' and resid 2 through 73) selection = (chain '4' and resid 2 through 73) selection = (chain '5' and resid 2 through 73) selection = (chain '6' and resid 2 through 73) selection = (chain '7' and resid 2 through 73) selection = (chain '8' and resid 2 through 73) selection = (chain '9' and resid 2 through 73) selection = (chain 'B' and resid 2 through 73) selection = (chain 'C' and resid 2 through 73) selection = (chain 'D' and resid 2 through 73) selection = (chain 'E' and resid 2 through 73) selection = (chain 'F' and resid 2 through 73) selection = (chain 'G' and resid 2 through 73) selection = (chain 'H' and resid 2 through 73) selection = (chain 'I' and resid 2 through 73) selection = (chain 'J' and resid 2 through 73) selection = (chain 'K' and resid 2 through 73) } ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } ncs_group { reference = chain 'O' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'e' } ncs_group { reference = chain 'Q' selection = chain 'f' } ncs_group { reference = chain 'R' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'i' } ncs_group { reference = chain 'T' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.070 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.070 ------------------------------------------------------------------------------- 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 : 2.819 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: 0.2950 time to fit residues: 471.0674 Evaluate side-chains 757 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 755 time to evaluate : 2.273 ------------------------------------------------------------------------------- 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: 0.8980 chunk 210 optimal weight: 0.3980 chunk 116 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 217 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 132 optimal weight: 0.2980 chunk 162 optimal weight: 0.5980 chunk 252 optimal weight: 20.0000 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21822 Z= 0.198 Angle : 0.715 11.487 29638 Z= 0.347 Chirality : 0.043 0.304 3678 Planarity : 0.005 0.061 3644 Dihedral : 4.917 25.168 3088 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.55 % Allowed : 16.83 % 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: -1.03 (0.15), residues: 2618 helix: -0.11 (0.11), residues: 2048 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 234 HIS 0.005 0.001 HIS f 68 PHE 0.029 0.002 PHE 7 55 TYR 0.017 0.002 TYR f 31 ARG 0.008 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 915 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 843 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 16 THR cc_start: 0.9239 (p) cc_final: 0.8961 (t) REVERT: 2 58 SER cc_start: 0.9002 (t) cc_final: 0.8701 (p) REVERT: 3 45 ASP cc_start: 0.8621 (m-30) cc_final: 0.8283 (t70) REVERT: 4 40 ASN cc_start: 0.8963 (t0) cc_final: 0.7870 (t0) REVERT: 4 43 ILE cc_start: 0.9087 (tp) cc_final: 0.8543 (tt) REVERT: 4 59 GLU cc_start: 0.8723 (tp30) cc_final: 0.8411 (tp30) REVERT: 4 61 THR cc_start: 0.9601 (p) cc_final: 0.9347 (t) REVERT: 5 2 GLN cc_start: 0.7647 (mt0) cc_final: 0.7314 (pm20) REVERT: 5 28 ILE cc_start: 0.9195 (mt) cc_final: 0.8954 (tp) REVERT: 6 35 ASN cc_start: 0.9334 (m-40) cc_final: 0.9046 (t0) REVERT: 6 72 LEU cc_start: 0.9186 (mt) cc_final: 0.8951 (tp) REVERT: 7 2 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7183 (pm20) REVERT: 7 9 TYR cc_start: 0.7379 (m-10) cc_final: 0.7167 (m-10) REVERT: 7 67 MET cc_start: 0.8770 (ptm) cc_final: 0.7941 (mtp) REVERT: 8 64 PHE cc_start: 0.9023 (m-10) cc_final: 0.8693 (m-10) REVERT: 8 67 MET cc_start: 0.8614 (ptm) cc_final: 0.8024 (mtp) REVERT: 9 35 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8518 (m-40) REVERT: 9 43 ILE cc_start: 0.8151 (tp) cc_final: 0.7815 (mt) REVERT: 9 46 THR cc_start: 0.7617 (m) cc_final: 0.7287 (p) REVERT: 0 5 LEU cc_start: 0.8729 (tp) cc_final: 0.8059 (pp) REVERT: 0 59 GLU cc_start: 0.8624 (tp30) cc_final: 0.8414 (tp30) REVERT: A 3 GLN cc_start: 0.7265 (tp-100) cc_final: 0.6384 (tp40) REVERT: A 8 TYR cc_start: 0.8431 (m-80) cc_final: 0.8071 (m-80) REVERT: a 68 THR cc_start: 0.9057 (t) cc_final: 0.8746 (m) REVERT: a 94 MET cc_start: 0.8939 (mmt) cc_final: 0.8701 (mmt) REVERT: a 186 LEU cc_start: 0.9169 (tp) cc_final: 0.8835 (tp) REVERT: b 72 TYR cc_start: 0.7942 (m-10) cc_final: 0.7528 (m-10) REVERT: b 82 ASP cc_start: 0.8808 (t70) cc_final: 0.8395 (m-30) REVERT: b 86 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8724 (ttpp) REVERT: i 1 MET cc_start: 0.6062 (ttp) cc_final: 0.4679 (tpt) REVERT: i 11 LYS cc_start: 0.8919 (pttt) cc_final: 0.8204 (mmtt) REVERT: i 42 ASN cc_start: 0.8695 (m-40) cc_final: 0.8421 (m-40) REVERT: i 57 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7866 (mp0) REVERT: C 39 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7740 (tpp80) REVERT: D 16 THR cc_start: 0.9233 (p) cc_final: 0.8949 (t) REVERT: D 58 SER cc_start: 0.8966 (t) cc_final: 0.8737 (p) REVERT: D 67 MET cc_start: 0.7943 (mmm) cc_final: 0.7293 (mmm) REVERT: E 45 ASP cc_start: 0.8640 (m-30) cc_final: 0.8306 (t70) REVERT: F 40 ASN cc_start: 0.8926 (t0) cc_final: 0.7855 (t0) REVERT: F 43 ILE cc_start: 0.9114 (tp) cc_final: 0.8559 (tt) REVERT: F 59 GLU cc_start: 0.8769 (tp30) cc_final: 0.8484 (tp30) REVERT: F 61 THR cc_start: 0.9587 (p) cc_final: 0.9348 (t) REVERT: F 69 SER cc_start: 0.8740 (t) cc_final: 0.8538 (p) REVERT: G 2 GLN cc_start: 0.7661 (mt0) cc_final: 0.7304 (pm20) REVERT: G 28 ILE cc_start: 0.9222 (mt) cc_final: 0.8985 (tp) REVERT: G 64 PHE cc_start: 0.8444 (m-10) cc_final: 0.8088 (m-80) REVERT: H 39 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7758 (ttm110) REVERT: H 46 THR cc_start: 0.8709 (m) cc_final: 0.8446 (p) REVERT: H 72 LEU cc_start: 0.9216 (mt) cc_final: 0.8938 (tp) REVERT: I 2 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7122 (pm20) REVERT: I 9 TYR cc_start: 0.7306 (m-10) cc_final: 0.7081 (m-10) REVERT: I 67 MET cc_start: 0.8732 (ptm) cc_final: 0.7922 (mtp) REVERT: I 72 LEU cc_start: 0.8084 (mp) cc_final: 0.7871 (tp) REVERT: J 1 MET cc_start: 0.8169 (mtm) cc_final: 0.7568 (tmm) REVERT: J 39 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7691 (ttm170) REVERT: J 59 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8666 (mm-30) REVERT: J 64 PHE cc_start: 0.9014 (m-10) cc_final: 0.8672 (m-10) REVERT: J 67 MET cc_start: 0.8629 (ptm) cc_final: 0.8058 (mtp) REVERT: K 35 ASN cc_start: 0.8898 (OUTLIER) cc_final: 0.8481 (m-40) REVERT: B 5 LEU cc_start: 0.8730 (tp) cc_final: 0.8019 (pp) REVERT: B 69 SER cc_start: 0.9208 (t) cc_final: 0.8938 (p) REVERT: L 3 GLN cc_start: 0.7255 (tp-100) cc_final: 0.6353 (tp40) REVERT: M 68 THR cc_start: 0.9034 (t) cc_final: 0.8715 (m) REVERT: M 186 LEU cc_start: 0.9186 (tp) cc_final: 0.8849 (tp) REVERT: M 199 MET cc_start: 0.8758 (mtm) cc_final: 0.8548 (mtt) REVERT: N 72 TYR cc_start: 0.7968 (m-10) cc_final: 0.7560 (m-10) REVERT: N 82 ASP cc_start: 0.8789 (t70) cc_final: 0.8387 (m-30) REVERT: N 86 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8746 (ttpp) REVERT: S 1 MET cc_start: 0.6006 (ttp) cc_final: 0.4655 (tpt) REVERT: S 11 LYS cc_start: 0.8925 (pttt) cc_final: 0.8188 (mmtt) REVERT: S 42 ASN cc_start: 0.8693 (m-40) cc_final: 0.8422 (m-40) REVERT: S 57 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7859 (mp0) outliers start: 72 outliers final: 33 residues processed: 873 average time/residue: 0.2684 time to fit residues: 379.3710 Evaluate side-chains 762 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 727 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 69 SER Chi-restraints excluded: chain 3 residue 55 PHE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 7 residue 46 THR Chi-restraints excluded: chain 7 residue 65 CYS Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 55 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 65 CYS Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 68 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 273 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 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 ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN K 2 GLN ** 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: 0.7821 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21822 Z= 0.214 Angle : 0.690 10.186 29638 Z= 0.335 Chirality : 0.042 0.240 3678 Planarity : 0.004 0.063 3644 Dihedral : 4.598 24.483 3084 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.70 % Allowed : 21.37 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.16), residues: 2618 helix: 0.55 (0.11), residues: 2048 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 570 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 0.035 0.002 PHE 7 55 TYR 0.019 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 839 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 764 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 33 LEU cc_start: 0.9154 (tp) cc_final: 0.8925 (tt) REVERT: 2 58 SER cc_start: 0.9169 (t) cc_final: 0.8821 (p) REVERT: 3 45 ASP cc_start: 0.8551 (m-30) cc_final: 0.8294 (t70) REVERT: 4 40 ASN cc_start: 0.8832 (t0) cc_final: 0.7786 (t0) REVERT: 4 43 ILE cc_start: 0.9078 (tp) cc_final: 0.8566 (tt) REVERT: 4 59 GLU cc_start: 0.8668 (tp30) cc_final: 0.8385 (tp30) REVERT: 4 61 THR cc_start: 0.9608 (p) cc_final: 0.9324 (t) REVERT: 4 72 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7862 (mm) REVERT: 5 2 GLN cc_start: 0.7588 (mt0) cc_final: 0.7352 (pm20) REVERT: 5 28 ILE cc_start: 0.9186 (mt) cc_final: 0.8965 (tp) REVERT: 6 35 ASN cc_start: 0.9369 (m-40) cc_final: 0.9042 (t0) REVERT: 6 43 ILE cc_start: 0.8624 (tp) cc_final: 0.8285 (tp) REVERT: 6 57 LEU cc_start: 0.8757 (tp) cc_final: 0.8426 (tp) REVERT: 6 72 LEU cc_start: 0.9180 (mt) cc_final: 0.8953 (tp) REVERT: 7 2 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7158 (pm20) REVERT: 7 14 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8206 (tp) REVERT: 7 67 MET cc_start: 0.8811 (ptm) cc_final: 0.7963 (mtp) REVERT: 8 43 ILE cc_start: 0.8032 (tp) cc_final: 0.7466 (tp) REVERT: 8 59 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8792 (mm-30) REVERT: 8 64 PHE cc_start: 0.9017 (m-10) cc_final: 0.8714 (m-10) REVERT: 8 67 MET cc_start: 0.8633 (ptm) cc_final: 0.8028 (mtp) REVERT: 8 72 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7864 (mm) REVERT: 9 35 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8450 (m-40) REVERT: 9 43 ILE cc_start: 0.8134 (tp) cc_final: 0.7839 (mt) REVERT: 9 46 THR cc_start: 0.7542 (m) cc_final: 0.7297 (p) REVERT: 9 59 GLU cc_start: 0.8443 (tp30) cc_final: 0.8169 (tp30) REVERT: 0 5 LEU cc_start: 0.8687 (tp) cc_final: 0.7776 (tp) REVERT: 0 9 TYR cc_start: 0.7816 (m-80) cc_final: 0.7103 (m-80) REVERT: 0 59 GLU cc_start: 0.8609 (tp30) cc_final: 0.8385 (tp30) REVERT: A 3 GLN cc_start: 0.7171 (tp-100) cc_final: 0.6851 (tp40) REVERT: A 8 TYR cc_start: 0.8455 (m-80) cc_final: 0.8063 (m-80) REVERT: a 68 THR cc_start: 0.9105 (t) cc_final: 0.8814 (m) REVERT: a 94 MET cc_start: 0.8997 (mmt) cc_final: 0.8785 (mmt) REVERT: a 186 LEU cc_start: 0.9206 (tp) cc_final: 0.8786 (tp) REVERT: b 72 TYR cc_start: 0.7939 (m-10) cc_final: 0.7512 (m-10) REVERT: b 82 ASP cc_start: 0.8806 (t70) cc_final: 0.8408 (m-30) REVERT: b 86 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8735 (ttpp) REVERT: i 1 MET cc_start: 0.6199 (ttp) cc_final: 0.4761 (tpt) REVERT: i 11 LYS cc_start: 0.8813 (pttt) cc_final: 0.8081 (mmtt) REVERT: C 39 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7721 (tpp80) REVERT: D 33 LEU cc_start: 0.9143 (tp) cc_final: 0.8928 (tt) REVERT: D 58 SER cc_start: 0.9155 (t) cc_final: 0.8805 (p) REVERT: D 67 MET cc_start: 0.8049 (mmm) cc_final: 0.7817 (mmm) REVERT: E 45 ASP cc_start: 0.8575 (m-30) cc_final: 0.8321 (t70) REVERT: E 67 MET cc_start: 0.8722 (tmm) cc_final: 0.8518 (tmm) REVERT: F 40 ASN cc_start: 0.8809 (t0) cc_final: 0.7772 (t0) REVERT: F 43 ILE cc_start: 0.9102 (tp) cc_final: 0.8592 (tt) REVERT: F 59 GLU cc_start: 0.8643 (tp30) cc_final: 0.8352 (tp30) REVERT: F 61 THR cc_start: 0.9604 (p) cc_final: 0.9371 (t) REVERT: F 72 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7792 (mm) REVERT: G 2 GLN cc_start: 0.7681 (mt0) cc_final: 0.7343 (pm20) REVERT: G 28 ILE cc_start: 0.9183 (mt) cc_final: 0.8971 (tp) REVERT: G 64 PHE cc_start: 0.8563 (m-10) cc_final: 0.8198 (m-80) REVERT: H 39 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7797 (ttm110) REVERT: H 57 LEU cc_start: 0.8752 (tp) cc_final: 0.8430 (tp) REVERT: H 72 LEU cc_start: 0.9152 (mt) cc_final: 0.8928 (tp) REVERT: I 2 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7163 (pm20) REVERT: I 8 LYS cc_start: 0.8019 (mttp) cc_final: 0.7805 (mtpp) REVERT: I 67 MET cc_start: 0.8704 (ptm) cc_final: 0.7880 (mtp) REVERT: J 1 MET cc_start: 0.8147 (mtm) cc_final: 0.7700 (tmm) REVERT: J 55 PHE cc_start: 0.9022 (t80) cc_final: 0.8729 (t80) REVERT: J 64 PHE cc_start: 0.9041 (m-10) cc_final: 0.8746 (m-10) REVERT: J 67 MET cc_start: 0.8599 (ptm) cc_final: 0.8017 (mtp) REVERT: K 35 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8415 (m-40) REVERT: B 5 LEU cc_start: 0.8644 (tp) cc_final: 0.7670 (tp) REVERT: B 9 TYR cc_start: 0.7843 (m-80) cc_final: 0.7031 (m-80) REVERT: B 69 SER cc_start: 0.9170 (t) cc_final: 0.8922 (p) REVERT: L 3 GLN cc_start: 0.7092 (tp-100) cc_final: 0.6735 (tp40) REVERT: M 68 THR cc_start: 0.9073 (t) cc_final: 0.8814 (m) REVERT: M 186 LEU cc_start: 0.9234 (tp) cc_final: 0.8814 (tp) REVERT: N 72 TYR cc_start: 0.7946 (m-10) cc_final: 0.7520 (m-10) REVERT: N 82 ASP cc_start: 0.8798 (t70) cc_final: 0.8408 (m-30) REVERT: N 86 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8735 (ttpp) REVERT: O 250 THR cc_start: 0.8878 (m) cc_final: 0.8615 (p) REVERT: S 1 MET cc_start: 0.6192 (ttp) cc_final: 0.4717 (tpt) REVERT: S 11 LYS cc_start: 0.8823 (pttt) cc_final: 0.8086 (mmtt) REVERT: S 57 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8067 (mp0) REVERT: T 8 MET cc_start: 0.6824 (tpt) cc_final: 0.6615 (tpt) outliers start: 75 outliers final: 40 residues processed: 795 average time/residue: 0.2648 time to fit residues: 342.6176 Evaluate side-chains 757 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 711 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 70 PHE Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 63 LEU Chi-restraints excluded: chain 7 residue 14 ILE Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 61 THR Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 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 55 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 206 LEU Chi-restraints excluded: chain N residue 51 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 268 optimal weight: 40.0000 chunk 132 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** K 2 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: 0.7847 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21822 Z= 0.233 Angle : 0.682 10.303 29638 Z= 0.331 Chirality : 0.042 0.229 3678 Planarity : 0.004 0.060 3644 Dihedral : 4.440 24.087 3084 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.08 % Allowed : 23.35 % Favored : 71.57 % 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: 0.30 (0.16), residues: 2618 helix: 0.83 (0.11), residues: 2070 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 234 HIS 0.006 0.001 HIS f 68 PHE 0.054 0.002 PHE I 55 TYR 0.020 0.002 TYR a 32 ARG 0.004 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 862 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 759 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9210 (t) cc_final: 0.8814 (p) REVERT: 2 67 MET cc_start: 0.7951 (mmm) cc_final: 0.7434 (mmm) REVERT: 3 45 ASP cc_start: 0.8628 (m-30) cc_final: 0.8330 (t0) REVERT: 4 40 ASN cc_start: 0.8793 (t0) cc_final: 0.7912 (t0) REVERT: 4 43 ILE cc_start: 0.9086 (tp) cc_final: 0.8659 (tt) REVERT: 4 59 GLU cc_start: 0.8707 (tp30) cc_final: 0.8215 (tp30) REVERT: 4 72 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7825 (mm) REVERT: 5 2 GLN cc_start: 0.7628 (mt0) cc_final: 0.7278 (pm20) REVERT: 5 55 PHE cc_start: 0.9226 (t80) cc_final: 0.9024 (t80) REVERT: 6 15 SER cc_start: 0.9264 (m) cc_final: 0.8980 (m) REVERT: 6 43 ILE cc_start: 0.8600 (tp) cc_final: 0.8220 (tp) REVERT: 6 72 LEU cc_start: 0.9075 (mt) cc_final: 0.8682 (mt) REVERT: 7 2 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7222 (pm20) REVERT: 7 14 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8237 (tp) REVERT: 7 67 MET cc_start: 0.8805 (ptm) cc_final: 0.7928 (mtp) REVERT: 8 43 ILE cc_start: 0.7941 (tp) cc_final: 0.7374 (tp) REVERT: 8 64 PHE cc_start: 0.8971 (m-10) cc_final: 0.8588 (m-10) REVERT: 8 67 MET cc_start: 0.8659 (ptm) cc_final: 0.8116 (mtp) REVERT: 8 72 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7871 (mm) REVERT: 0 5 LEU cc_start: 0.8700 (tp) cc_final: 0.7872 (tp) REVERT: 0 9 TYR cc_start: 0.7841 (m-80) cc_final: 0.7279 (m-80) REVERT: 0 59 GLU cc_start: 0.8648 (tp30) cc_final: 0.8446 (tp30) REVERT: A 3 GLN cc_start: 0.7309 (tp-100) cc_final: 0.6945 (tp40) REVERT: A 8 TYR cc_start: 0.8395 (m-80) cc_final: 0.7958 (m-80) REVERT: a 68 THR cc_start: 0.9170 (t) cc_final: 0.8944 (m) REVERT: a 186 LEU cc_start: 0.9220 (tp) cc_final: 0.8798 (tp) REVERT: b 72 TYR cc_start: 0.8012 (m-10) cc_final: 0.7619 (m-10) REVERT: b 82 ASP cc_start: 0.8811 (t70) cc_final: 0.8450 (m-30) REVERT: b 87 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8470 (ttmm) REVERT: i 1 MET cc_start: 0.6153 (ttp) cc_final: 0.4625 (tpt) REVERT: i 11 LYS cc_start: 0.8921 (pttt) cc_final: 0.8072 (mmpt) REVERT: C 39 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7803 (tpp80) REVERT: C 64 PHE cc_start: 0.8682 (m-10) cc_final: 0.8469 (m-10) REVERT: D 58 SER cc_start: 0.9207 (t) cc_final: 0.8821 (p) REVERT: D 67 MET cc_start: 0.7997 (mmm) cc_final: 0.7719 (mmm) REVERT: E 45 ASP cc_start: 0.8616 (m-30) cc_final: 0.8337 (t70) REVERT: F 40 ASN cc_start: 0.8781 (t0) cc_final: 0.7936 (t0) REVERT: F 43 ILE cc_start: 0.9086 (tp) cc_final: 0.8650 (tt) REVERT: F 59 GLU cc_start: 0.8632 (tp30) cc_final: 0.8352 (tp30) REVERT: F 72 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7864 (mm) REVERT: G 2 GLN cc_start: 0.7633 (mt0) cc_final: 0.7242 (pm20) REVERT: G 55 PHE cc_start: 0.9237 (t80) cc_final: 0.8924 (t80) REVERT: H 72 LEU cc_start: 0.9090 (mt) cc_final: 0.8838 (tp) REVERT: I 2 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7133 (pm20) REVERT: I 8 LYS cc_start: 0.7994 (mttp) cc_final: 0.7757 (mtpp) REVERT: I 14 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8328 (tp) REVERT: I 67 MET cc_start: 0.8698 (ptm) cc_final: 0.7860 (mtp) REVERT: J 1 MET cc_start: 0.8172 (mtm) cc_final: 0.7839 (tmm) REVERT: J 59 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8730 (mm-30) REVERT: J 64 PHE cc_start: 0.9019 (m-10) cc_final: 0.8584 (m-10) REVERT: J 67 MET cc_start: 0.8612 (ptm) cc_final: 0.8020 (mtp) REVERT: K 35 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8345 (m-40) REVERT: B 5 LEU cc_start: 0.8697 (tp) cc_final: 0.7796 (tp) REVERT: B 9 TYR cc_start: 0.7922 (m-80) cc_final: 0.7313 (m-80) REVERT: L 3 GLN cc_start: 0.7432 (tp-100) cc_final: 0.7145 (tp-100) REVERT: L 18 LEU cc_start: 0.9042 (mt) cc_final: 0.8728 (tt) REVERT: M 68 THR cc_start: 0.9154 (t) cc_final: 0.8896 (m) REVERT: M 94 MET cc_start: 0.9056 (mmt) cc_final: 0.8571 (mmt) REVERT: M 186 LEU cc_start: 0.9233 (tp) cc_final: 0.8823 (tp) REVERT: N 72 TYR cc_start: 0.8012 (m-10) cc_final: 0.7604 (m-10) REVERT: N 82 ASP cc_start: 0.8803 (t70) cc_final: 0.8453 (m-30) REVERT: N 87 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8464 (ttmm) REVERT: O 247 ASP cc_start: 0.8414 (m-30) cc_final: 0.8118 (m-30) REVERT: O 250 THR cc_start: 0.8834 (m) cc_final: 0.8580 (p) REVERT: S 1 MET cc_start: 0.6182 (ttp) cc_final: 0.4647 (tpt) REVERT: S 11 LYS cc_start: 0.8928 (pttt) cc_final: 0.8062 (mmpt) REVERT: S 25 TYR cc_start: 0.8140 (t80) cc_final: 0.7879 (t80) REVERT: S 57 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8023 (mp0) outliers start: 103 outliers final: 67 residues processed: 797 average time/residue: 0.2785 time to fit residues: 361.0410 Evaluate side-chains 778 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 705 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 52 ILE Chi-restraints excluded: chain 1 residue 61 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 2 residue 53 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 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 5 residue 50 MET Chi-restraints excluded: chain 6 residue 20 LEU Chi-restraints excluded: chain 6 residue 46 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 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 61 THR Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 188 MET Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 61 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 53 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR 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 206 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 93 ASN Chi-restraints excluded: chain O residue 271 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 0.0980 chunk 152 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 185 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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** K 2 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: 0.7813 moved from start: 0.3420 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= 0.191 Angle : 0.670 11.152 29638 Z= 0.324 Chirality : 0.041 0.253 3678 Planarity : 0.004 0.064 3644 Dihedral : 4.331 25.699 3084 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.29 % Allowed : 24.43 % Favored : 71.27 % 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: 0.57 (0.17), residues: 2618 helix: 1.01 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -1.93 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 234 HIS 0.005 0.001 HIS f 68 PHE 0.031 0.002 PHE 1 55 TYR 0.017 0.001 TYR S 24 ARG 0.005 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 844 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 757 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9206 (t) cc_final: 0.8783 (p) REVERT: 2 67 MET cc_start: 0.7927 (mmm) cc_final: 0.7345 (mmm) REVERT: 3 45 ASP cc_start: 0.8635 (m-30) cc_final: 0.8287 (t0) REVERT: 4 40 ASN cc_start: 0.8759 (t0) cc_final: 0.7939 (t0) REVERT: 4 43 ILE cc_start: 0.9067 (tp) cc_final: 0.8624 (tt) REVERT: 4 59 GLU cc_start: 0.8621 (tp30) cc_final: 0.8209 (tp30) REVERT: 4 72 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7824 (mm) REVERT: 5 2 GLN cc_start: 0.7637 (mt0) cc_final: 0.7178 (pm20) REVERT: 5 55 PHE cc_start: 0.9165 (t80) cc_final: 0.8911 (t80) REVERT: 6 43 ILE cc_start: 0.8551 (tp) cc_final: 0.8179 (tp) REVERT: 6 64 PHE cc_start: 0.8760 (m-80) cc_final: 0.8560 (m-80) REVERT: 6 72 LEU cc_start: 0.9045 (mt) cc_final: 0.8830 (tp) REVERT: 7 2 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7145 (pm20) REVERT: 7 14 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8262 (tp) REVERT: 7 67 MET cc_start: 0.8737 (ptm) cc_final: 0.7872 (mtp) REVERT: 8 43 ILE cc_start: 0.8052 (tp) cc_final: 0.7531 (tp) REVERT: 8 59 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8798 (mm-30) REVERT: 8 64 PHE cc_start: 0.8958 (m-10) cc_final: 0.8572 (m-10) REVERT: 8 67 MET cc_start: 0.8661 (ptm) cc_final: 0.8147 (mtp) REVERT: 8 72 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7920 (mm) REVERT: 9 59 GLU cc_start: 0.8438 (tp30) cc_final: 0.8139 (tp30) REVERT: 0 5 LEU cc_start: 0.8767 (tp) cc_final: 0.8071 (tp) REVERT: 0 9 TYR cc_start: 0.7768 (m-80) cc_final: 0.7313 (m-80) REVERT: 0 59 GLU cc_start: 0.8694 (tp30) cc_final: 0.8493 (tp30) REVERT: A 3 GLN cc_start: 0.7331 (tp-100) cc_final: 0.7073 (tp-100) REVERT: a 68 THR cc_start: 0.9143 (t) cc_final: 0.8908 (m) REVERT: a 94 MET cc_start: 0.9015 (mmt) cc_final: 0.8598 (mmt) REVERT: a 161 ILE cc_start: 0.8843 (tt) cc_final: 0.8521 (tt) REVERT: a 186 LEU cc_start: 0.9202 (tp) cc_final: 0.8779 (tp) REVERT: a 199 MET cc_start: 0.8484 (mtt) cc_final: 0.8221 (mtt) REVERT: b 72 TYR cc_start: 0.7997 (m-10) cc_final: 0.7582 (m-10) REVERT: b 82 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: b 87 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8340 (ttmm) REVERT: d 250 THR cc_start: 0.8799 (m) cc_final: 0.8533 (p) REVERT: f 76 PHE cc_start: 0.8557 (t80) cc_final: 0.8255 (t80) REVERT: i 1 MET cc_start: 0.6183 (ttp) cc_final: 0.4587 (tpt) REVERT: i 11 LYS cc_start: 0.8943 (pttt) cc_final: 0.8052 (mmpt) REVERT: C 39 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7806 (tpp80) REVERT: D 58 SER cc_start: 0.9209 (t) cc_final: 0.8792 (p) REVERT: D 67 MET cc_start: 0.7962 (mmm) cc_final: 0.7647 (mmm) REVERT: E 45 ASP cc_start: 0.8649 (m-30) cc_final: 0.8284 (t0) REVERT: F 40 ASN cc_start: 0.8732 (t0) cc_final: 0.7888 (t0) REVERT: F 43 ILE cc_start: 0.9063 (tp) cc_final: 0.8614 (tt) REVERT: F 59 GLU cc_start: 0.8537 (tp30) cc_final: 0.8144 (tp30) REVERT: F 72 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7788 (mm) REVERT: G 2 GLN cc_start: 0.7669 (mt0) cc_final: 0.7146 (pm20) REVERT: G 55 PHE cc_start: 0.9182 (t80) cc_final: 0.8848 (t80) REVERT: H 64 PHE cc_start: 0.8698 (m-80) cc_final: 0.8474 (m-80) REVERT: H 72 LEU cc_start: 0.9063 (mt) cc_final: 0.8709 (mt) REVERT: I 2 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7120 (pm20) REVERT: I 14 ILE cc_start: 0.8592 (mm) cc_final: 0.8342 (tp) REVERT: I 67 MET cc_start: 0.8622 (ptm) cc_final: 0.7755 (mtp) REVERT: J 1 MET cc_start: 0.8242 (mtm) cc_final: 0.7891 (tmm) REVERT: J 64 PHE cc_start: 0.8963 (m-10) cc_final: 0.8563 (m-10) REVERT: J 67 MET cc_start: 0.8630 (ptm) cc_final: 0.8074 (mtp) REVERT: K 59 GLU cc_start: 0.8518 (tp30) cc_final: 0.8193 (tp30) REVERT: B 5 LEU cc_start: 0.8765 (tp) cc_final: 0.7996 (tp) REVERT: B 9 TYR cc_start: 0.7848 (m-80) cc_final: 0.7327 (m-80) REVERT: L 3 GLN cc_start: 0.7482 (tp-100) cc_final: 0.7223 (tp-100) REVERT: L 18 LEU cc_start: 0.9070 (mt) cc_final: 0.8790 (tt) REVERT: M 68 THR cc_start: 0.9142 (t) cc_final: 0.8903 (m) REVERT: M 94 MET cc_start: 0.9003 (mmt) cc_final: 0.8612 (mmt) REVERT: M 161 ILE cc_start: 0.8841 (tt) cc_final: 0.8487 (mm) REVERT: M 186 LEU cc_start: 0.9234 (tp) cc_final: 0.8821 (tp) REVERT: M 199 MET cc_start: 0.8331 (mtt) cc_final: 0.8056 (mtt) REVERT: N 72 TYR cc_start: 0.7996 (m-10) cc_final: 0.7565 (m-10) REVERT: N 82 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8403 (m-30) REVERT: N 87 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8396 (ttmm) REVERT: O 247 ASP cc_start: 0.8366 (m-30) cc_final: 0.8106 (m-30) REVERT: O 250 THR cc_start: 0.8836 (m) cc_final: 0.8587 (p) REVERT: S 1 MET cc_start: 0.6221 (ttp) cc_final: 0.4647 (tpt) REVERT: S 11 LYS cc_start: 0.8933 (pttt) cc_final: 0.8000 (mmpt) REVERT: S 57 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7982 (mp0) outliers start: 87 outliers final: 52 residues processed: 784 average time/residue: 0.2699 time to fit residues: 344.9621 Evaluate side-chains 751 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 693 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 1 residue 70 PHE Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 7 residue 14 ILE Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 35 ASN Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 3 LEU Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 206 LEU 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 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 59 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain M residue 206 LEU 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 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 268 optimal weight: 30.0000 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN a 62 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN K 2 GLN M 62 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21822 Z= 0.332 Angle : 0.721 17.081 29638 Z= 0.354 Chirality : 0.044 0.295 3678 Planarity : 0.004 0.072 3644 Dihedral : 4.303 25.098 3084 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.23 % Allowed : 24.68 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.17), residues: 2618 helix: 1.08 (0.11), residues: 2060 sheet: None (None), residues: 0 loop : -1.48 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 234 HIS 0.006 0.002 HIS f 68 PHE 0.043 0.002 PHE 1 55 TYR 0.040 0.002 TYR a 241 ARG 0.009 0.001 ARG a 169 *********************** 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 815 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 709 time to evaluate : 2.382 Fit side-chains revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9193 (t) cc_final: 0.8820 (p) REVERT: 3 43 ILE cc_start: 0.8994 (tp) cc_final: 0.8786 (tt) REVERT: 3 45 ASP cc_start: 0.8647 (m-30) cc_final: 0.8260 (t0) REVERT: 4 40 ASN cc_start: 0.8815 (t0) cc_final: 0.8033 (t0) REVERT: 4 43 ILE cc_start: 0.9116 (tp) cc_final: 0.8783 (tt) REVERT: 4 59 GLU cc_start: 0.8650 (tp30) cc_final: 0.8296 (tp30) REVERT: 4 72 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7855 (mm) REVERT: 5 2 GLN cc_start: 0.7595 (mt0) cc_final: 0.7183 (pm20) REVERT: 5 55 PHE cc_start: 0.9194 (t80) cc_final: 0.8954 (t80) REVERT: 6 43 ILE cc_start: 0.8623 (tp) cc_final: 0.8246 (tp) REVERT: 6 72 LEU cc_start: 0.9051 (mt) cc_final: 0.8849 (tp) REVERT: 7 2 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7206 (pm20) REVERT: 7 14 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8384 (tp) REVERT: 7 67 MET cc_start: 0.8710 (ptm) cc_final: 0.7850 (mtp) REVERT: 8 43 ILE cc_start: 0.8100 (tp) cc_final: 0.7576 (tp) REVERT: 8 50 MET cc_start: 0.8462 (mtm) cc_final: 0.8193 (ptp) REVERT: 8 59 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8769 (mm-30) REVERT: 8 64 PHE cc_start: 0.8966 (m-10) cc_final: 0.8609 (m-10) REVERT: 8 67 MET cc_start: 0.8689 (ptm) cc_final: 0.8191 (mtp) REVERT: 9 59 GLU cc_start: 0.8492 (tp30) cc_final: 0.8125 (tp30) REVERT: 0 5 LEU cc_start: 0.8798 (tp) cc_final: 0.8068 (tp) REVERT: 0 9 TYR cc_start: 0.7711 (m-80) cc_final: 0.7308 (m-80) REVERT: a 161 ILE cc_start: 0.8924 (tt) cc_final: 0.8600 (tt) REVERT: a 186 LEU cc_start: 0.9259 (tp) cc_final: 0.8836 (tp) REVERT: a 199 MET cc_start: 0.8610 (mtt) cc_final: 0.8379 (mtt) REVERT: b 72 TYR cc_start: 0.8084 (m-10) cc_final: 0.7725 (m-10) REVERT: b 82 ASP cc_start: 0.8842 (t70) cc_final: 0.8504 (m-30) REVERT: b 87 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8393 (ttmm) REVERT: d 250 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8499 (p) REVERT: f 76 PHE cc_start: 0.8561 (t80) cc_final: 0.8307 (t80) REVERT: i 1 MET cc_start: 0.6245 (ttp) cc_final: 0.4529 (tpt) REVERT: i 11 LYS cc_start: 0.9062 (pttt) cc_final: 0.8105 (mmpt) REVERT: i 25 TYR cc_start: 0.8336 (t80) cc_final: 0.7903 (t80) REVERT: C 39 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7848 (tpp80) REVERT: D 58 SER cc_start: 0.9236 (t) cc_final: 0.8766 (p) REVERT: D 67 MET cc_start: 0.8067 (mmm) cc_final: 0.7558 (mmp) REVERT: E 45 ASP cc_start: 0.8714 (m-30) cc_final: 0.8304 (t0) REVERT: F 40 ASN cc_start: 0.8782 (t0) cc_final: 0.7965 (t0) REVERT: F 43 ILE cc_start: 0.9113 (tp) cc_final: 0.8770 (tt) REVERT: F 59 GLU cc_start: 0.8646 (tp30) cc_final: 0.8306 (tp30) REVERT: F 72 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7837 (mm) REVERT: G 2 GLN cc_start: 0.7723 (mt0) cc_final: 0.7241 (pm20) REVERT: G 55 PHE cc_start: 0.9232 (t80) cc_final: 0.8995 (t80) REVERT: G 59 GLU cc_start: 0.8523 (tp30) cc_final: 0.8273 (tp30) REVERT: H 35 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8832 (m-40) REVERT: I 2 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7181 (pm20) REVERT: I 67 MET cc_start: 0.8613 (ptm) cc_final: 0.7739 (mtp) REVERT: J 1 MET cc_start: 0.8323 (mtm) cc_final: 0.7939 (tmm) REVERT: J 8 LYS cc_start: 0.8930 (ptpp) cc_final: 0.8585 (mtmm) REVERT: J 55 PHE cc_start: 0.9111 (t80) cc_final: 0.8910 (t80) REVERT: J 64 PHE cc_start: 0.8995 (m-10) cc_final: 0.8585 (m-10) REVERT: J 67 MET cc_start: 0.8669 (ptm) cc_final: 0.8113 (mtp) REVERT: K 59 GLU cc_start: 0.8545 (tp30) cc_final: 0.8161 (tp30) REVERT: B 5 LEU cc_start: 0.8798 (tp) cc_final: 0.8017 (tp) REVERT: B 9 TYR cc_start: 0.7742 (m-80) cc_final: 0.7300 (m-80) REVERT: L 3 GLN cc_start: 0.7772 (tp-100) cc_final: 0.7463 (tp-100) REVERT: M 68 THR cc_start: 0.9193 (t) cc_final: 0.8988 (m) REVERT: M 161 ILE cc_start: 0.8904 (tt) cc_final: 0.8664 (mm) REVERT: M 186 LEU cc_start: 0.9282 (tp) cc_final: 0.8867 (tp) REVERT: M 199 MET cc_start: 0.8557 (mtt) cc_final: 0.8295 (mtt) REVERT: N 72 TYR cc_start: 0.8080 (m-10) cc_final: 0.7729 (m-10) REVERT: N 82 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8478 (m-30) REVERT: N 87 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8410 (ttmm) REVERT: O 247 ASP cc_start: 0.8437 (m-30) cc_final: 0.8109 (m-30) REVERT: O 250 THR cc_start: 0.8801 (m) cc_final: 0.8563 (p) REVERT: Q 76 PHE cc_start: 0.8661 (t80) cc_final: 0.8269 (t80) REVERT: S 1 MET cc_start: 0.6188 (ttp) cc_final: 0.4492 (tpt) REVERT: S 11 LYS cc_start: 0.9050 (pttt) cc_final: 0.8092 (mmpt) REVERT: S 25 TYR cc_start: 0.8313 (t80) cc_final: 0.7889 (t80) REVERT: S 57 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8064 (mp0) outliers start: 106 outliers final: 76 residues processed: 743 average time/residue: 0.2964 time to fit residues: 365.1223 Evaluate side-chains 767 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 685 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 67 MET Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 2 residue 55 PHE Chi-restraints excluded: chain 2 residue 69 SER Chi-restraints excluded: chain 3 residue 14 ILE Chi-restraints excluded: chain 3 residue 70 PHE Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 15 SER Chi-restraints excluded: chain 6 residue 20 LEU Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 6 residue 65 CYS Chi-restraints excluded: chain 7 residue 14 ILE Chi-restraints excluded: chain 7 residue 63 LEU Chi-restraints excluded: chain 7 residue 65 CYS Chi-restraints excluded: chain 9 residue 43 ILE Chi-restraints excluded: chain 0 residue 3 LEU Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain a residue 4 ASP Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 48 ASN Chi-restraints excluded: chain a residue 130 THR Chi-restraints excluded: chain a residue 152 LEU Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 250 THR 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 61 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 35 ASN 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 I residue 14 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 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 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: 4.9990 chunk 30 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 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: 0.9980 chunk 123 optimal weight: 30.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 2 GLN A 3 GLN ** k 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 GLN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21822 Z= 0.225 Angle : 0.708 17.690 29638 Z= 0.339 Chirality : 0.042 0.350 3678 Planarity : 0.004 0.074 3644 Dihedral : 4.277 27.543 3084 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.79 % Allowed : 25.91 % Favored : 69.30 % 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 (0.17), residues: 2618 helix: 1.15 (0.11), residues: 2074 sheet: None (None), residues: 0 loop : -1.71 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 234 HIS 0.005 0.001 HIS f 68 PHE 0.031 0.002 PHE 6 64 TYR 0.017 0.001 TYR i 24 ARG 0.004 0.000 ARG M 176 *********************** 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 812 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 715 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 58 SER cc_start: 0.9184 (t) cc_final: 0.8837 (p) REVERT: 3 45 ASP cc_start: 0.8668 (m-30) cc_final: 0.8297 (t0) REVERT: 4 40 ASN cc_start: 0.8757 (t0) cc_final: 0.7973 (t0) REVERT: 4 43 ILE cc_start: 0.9102 (tp) cc_final: 0.8766 (tt) REVERT: 4 59 GLU cc_start: 0.8555 (tp30) cc_final: 0.8228 (tp30) REVERT: 4 72 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7842 (mm) REVERT: 5 2 GLN cc_start: 0.7657 (mt0) cc_final: 0.7076 (pm20) REVERT: 6 43 ILE cc_start: 0.8611 (tp) cc_final: 0.8236 (tp) REVERT: 7 2 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7212 (pm20) REVERT: 7 14 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8358 (tp) REVERT: 7 67 MET cc_start: 0.8723 (ptm) cc_final: 0.7812 (mtp) REVERT: 8 1 MET cc_start: 0.8205 (mtm) cc_final: 0.7922 (tmm) REVERT: 8 43 ILE cc_start: 0.8058 (tp) cc_final: 0.7557 (tp) REVERT: 8 59 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8764 (mm-30) REVERT: 8 64 PHE cc_start: 0.8953 (m-10) cc_final: 0.8575 (m-10) REVERT: 8 67 MET cc_start: 0.8693 (ptm) cc_final: 0.8178 (mtp) REVERT: 9 59 GLU cc_start: 0.8467 (tp30) cc_final: 0.8096 (tp30) REVERT: 0 5 LEU cc_start: 0.8777 (tp) cc_final: 0.8162 (tp) REVERT: 0 9 TYR cc_start: 0.7556 (m-80) cc_final: 0.7254 (m-80) REVERT: A 3 GLN cc_start: 0.7542 (tp40) cc_final: 0.7259 (tp-100) REVERT: a 94 MET cc_start: 0.9090 (mmt) cc_final: 0.8659 (mmt) REVERT: a 161 ILE cc_start: 0.8933 (tt) cc_final: 0.8693 (mm) REVERT: a 186 LEU cc_start: 0.9232 (tp) cc_final: 0.8797 (tp) REVERT: a 199 MET cc_start: 0.8595 (mtt) cc_final: 0.8376 (mtt) REVERT: b 72 TYR cc_start: 0.8048 (m-10) cc_final: 0.7661 (m-10) REVERT: b 82 ASP cc_start: 0.8772 (t70) cc_final: 0.8434 (m-30) REVERT: b 87 LYS cc_start: 0.8630 (ttmt) cc_final: 0.8350 (ttmm) REVERT: d 250 THR cc_start: 0.8774 (m) cc_final: 0.8480 (p) REVERT: f 76 PHE cc_start: 0.8564 (t80) cc_final: 0.8245 (t80) REVERT: i 1 MET cc_start: 0.6159 (ttp) cc_final: 0.4426 (tpt) REVERT: i 11 LYS cc_start: 0.9047 (pttt) cc_final: 0.8051 (mmpt) REVERT: i 25 TYR cc_start: 0.8246 (t80) cc_final: 0.7899 (t80) REVERT: C 39 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7836 (tpp80) REVERT: D 58 SER cc_start: 0.9230 (t) cc_final: 0.8789 (p) REVERT: D 67 MET cc_start: 0.8034 (mmm) cc_final: 0.7569 (mmp) REVERT: E 45 ASP cc_start: 0.8693 (m-30) cc_final: 0.8328 (t0) REVERT: F 40 ASN cc_start: 0.8723 (t0) cc_final: 0.7928 (t0) REVERT: F 43 ILE cc_start: 0.9097 (tp) cc_final: 0.8766 (tt) REVERT: F 59 GLU cc_start: 0.8559 (tp30) cc_final: 0.8227 (tp30) REVERT: F 72 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7802 (mm) REVERT: G 55 PHE cc_start: 0.9207 (t80) cc_final: 0.8963 (t80) REVERT: H 64 PHE cc_start: 0.8772 (m-80) cc_final: 0.8553 (m-80) REVERT: I 2 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7092 (pm20) REVERT: I 67 MET cc_start: 0.8534 (ptm) cc_final: 0.7555 (mtp) REVERT: J 1 MET cc_start: 0.8304 (mtm) cc_final: 0.7952 (tmm) REVERT: J 8 LYS cc_start: 0.8929 (ptpp) cc_final: 0.8581 (mtmm) REVERT: J 64 PHE cc_start: 0.8949 (m-10) cc_final: 0.8537 (m-10) REVERT: J 67 MET cc_start: 0.8654 (ptm) cc_final: 0.8091 (mtp) REVERT: K 59 GLU cc_start: 0.8507 (tp30) cc_final: 0.8147 (tp30) REVERT: B 5 LEU cc_start: 0.8778 (tp) cc_final: 0.8088 (tp) REVERT: B 9 TYR cc_start: 0.7673 (m-80) cc_final: 0.7335 (m-80) REVERT: L 3 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7392 (tp-100) REVERT: M 161 ILE cc_start: 0.8939 (tt) cc_final: 0.8694 (mm) REVERT: M 186 LEU cc_start: 0.9237 (tp) cc_final: 0.8802 (tp) REVERT: M 199 MET cc_start: 0.8514 (mtt) cc_final: 0.8269 (mtt) REVERT: N 72 TYR cc_start: 0.8047 (m-10) cc_final: 0.7667 (m-10) REVERT: N 82 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: N 87 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8369 (ttmm) REVERT: O 247 ASP cc_start: 0.8430 (m-30) cc_final: 0.8106 (m-30) REVERT: O 250 THR cc_start: 0.8826 (m) cc_final: 0.8570 (p) REVERT: Q 76 PHE cc_start: 0.8570 (t80) cc_final: 0.8200 (t80) REVERT: S 1 MET cc_start: 0.6179 (ttp) cc_final: 0.4479 (tpt) REVERT: S 11 LYS cc_start: 0.9057 (pttt) cc_final: 0.8048 (mmpt) REVERT: S 25 TYR cc_start: 0.8273 (t80) cc_final: 0.7944 (t80) REVERT: S 57 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8033 (mp0) outliers start: 97 outliers final: 58 residues processed: 748 average time/residue: 0.2666 time to fit residues: 325.9350 Evaluate side-chains 746 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 684 time to evaluate : 2.483 ------------------------------------------------------------------------------- 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 70 PHE Chi-restraints excluded: chain 4 residue 72 LEU Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 55 PHE Chi-restraints excluded: chain 7 residue 14 ILE 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 43 ILE Chi-restraints excluded: chain 0 residue 3 LEU Chi-restraints excluded: chain 0 residue 14 ILE Chi-restraints excluded: chain 0 residue 61 THR Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain a residue 10 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain d residue 257 ASP Chi-restraints excluded: chain d residue 271 VAL Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 29 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 140 VAL 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 263 MET Chi-restraints excluded: chain O residue 271 VAL Chi-restraints excluded: chain S residue 29 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1336 > 50: distance: 66 - 67: 4.192 distance: 67 - 68: 4.075 distance: 67 - 70: 3.389 distance: 68 - 69: 7.976 distance: 68 - 74: 5.090 distance: 70 - 71: 3.094 distance: 74 - 75: 7.061 distance: 75 - 76: 7.908 distance: 75 - 78: 16.373 distance: 76 - 77: 6.913 distance: 76 - 82: 11.402 distance: 78 - 79: 7.034 distance: 79 - 80: 17.048 distance: 79 - 81: 11.342 distance: 82 - 83: 15.283 distance: 83 - 84: 10.219 distance: 83 - 86: 15.905 distance: 84 - 85: 19.124 distance: 84 - 91: 7.561 distance: 86 - 87: 11.520 distance: 87 - 88: 7.984 distance: 88 - 89: 4.764 distance: 91 - 92: 6.152 distance: 92 - 93: 20.776 distance: 92 - 95: 8.266 distance: 93 - 94: 26.598 distance: 93 - 102: 4.104 distance: 95 - 96: 12.203 distance: 96 - 97: 8.996 distance: 97 - 98: 11.130 distance: 98 - 99: 5.324 distance: 102 - 103: 9.587 distance: 103 - 104: 21.549 distance: 103 - 106: 25.576 distance: 104 - 105: 17.766 distance: 104 - 113: 19.135 distance: 106 - 107: 9.063 distance: 107 - 108: 11.455 distance: 107 - 109: 11.741 distance: 108 - 110: 14.655 distance: 109 - 111: 14.676 distance: 110 - 112: 7.074 distance: 111 - 112: 9.198 distance: 113 - 114: 8.293 distance: 113 - 119: 10.046 distance: 114 - 115: 13.485 distance: 114 - 117: 7.748 distance: 115 - 116: 11.783 distance: 115 - 120: 42.086 distance: 117 - 118: 5.099 distance: 118 - 119: 21.463 distance: 120 - 121: 21.354 distance: 121 - 122: 5.419 distance: 121 - 124: 11.694 distance: 122 - 123: 20.610 distance: 122 - 127: 11.337 distance: 124 - 125: 6.898 distance: 124 - 126: 8.987 distance: 127 - 128: 21.608 distance: 127 - 133: 10.850 distance: 128 - 129: 11.667 distance: 128 - 131: 23.722 distance: 129 - 130: 9.919 distance: 129 - 134: 18.354 distance: 131 - 132: 18.540 distance: 132 - 133: 42.303 distance: 134 - 135: 16.505 distance: 135 - 136: 18.169 distance: 135 - 138: 19.971 distance: 136 - 137: 20.467 distance: 136 - 142: 24.737 distance: 138 - 139: 25.508 distance: 138 - 140: 7.438 distance: 139 - 141: 8.224