Starting phenix.real_space_refine on Thu Aug 8 02:53:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/08_2024/7mqb_23941.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/08_2024/7mqb_23941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/08_2024/7mqb_23941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/08_2024/7mqb_23941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/08_2024/7mqb_23941.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mqb_23941/08_2024/7mqb_23941.cif" } resolution = 3.25 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= 0.002 sd= 0.012 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 11544 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 48 5.16 5 C 8064 2.51 5 N 2328 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 84": "OD1" <-> "OD2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G ASP 193": "OD1" <-> "OD2" Residue "I ASP 25": "OD1" <-> "OD2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 84": "OD1" <-> "OD2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I ASP 193": "OD1" <-> "OD2" Residue "K ASP 25": "OD1" <-> "OD2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 84": "OD1" <-> "OD2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K ASP 193": "OD1" <-> "OD2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M GLU 124": "OE1" <-> "OE2" Residue "M ASP 155": "OD1" <-> "OD2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "M ASP 193": "OD1" <-> "OD2" Residue "O ASP 25": "OD1" <-> "OD2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O GLU 167": "OE1" <-> "OE2" Residue "O GLU 173": "OE1" <-> "OE2" Residue "O ASP 193": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12760 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "E" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "I" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "K" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "M" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "N" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "O" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 7.12, per 1000 atoms: 0.56 Number of scatterers: 12760 At special positions: 0 Unit cell: (105.4, 105.4, 88.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 16 15.00 O 2304 8.00 N 2328 7.00 C 8064 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: 4.65 Conformation dependent library (CDL) restraints added in 2.4 seconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 45.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.887A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 71 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 145 through 155 Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 155 Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 155 Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU A 3 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL A 52 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 23 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU C 3 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL C 52 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA C 23 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU E 3 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL E 52 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU G 3 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL G 52 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.484A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU K 3 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL K 52 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA K 23 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA M 23 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4216 1.34 - 1.46: 2302 1.46 - 1.57: 6418 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 13024 Sorted by residual: bond pdb=" CG LYS C 103 " pdb=" CD LYS C 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CG LYS E 103 " pdb=" CD LYS E 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS O 103 " pdb=" CD LYS O 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS I 103 " pdb=" CD LYS I 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS A 103 " pdb=" CD LYS A 103 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 13019 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 376 106.97 - 113.73: 7665 113.73 - 120.49: 5167 120.49 - 127.25: 4392 127.25 - 134.01: 176 Bond angle restraints: 17776 Sorted by residual: angle pdb=" C SER E 61 " pdb=" N ALA E 62 " pdb=" CA ALA E 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.55e+01 angle pdb=" C SER C 61 " pdb=" N ALA C 62 " pdb=" CA ALA C 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.55e+01 angle pdb=" C SER A 61 " pdb=" N ALA A 62 " pdb=" CA ALA A 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.54e+01 angle pdb=" C SER G 61 " pdb=" N ALA G 62 " pdb=" CA ALA G 62 " ideal model delta sigma weight residual 122.28 125.73 -3.45 8.80e-01 1.29e+00 1.54e+01 angle pdb=" C SER I 61 " pdb=" N ALA I 62 " pdb=" CA ALA I 62 " ideal model delta sigma weight residual 122.28 125.72 -3.44 8.80e-01 1.29e+00 1.53e+01 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7169 17.25 - 34.50: 459 34.50 - 51.75: 116 51.75 - 69.00: 48 69.00 - 86.25: 16 Dihedral angle restraints: 7808 sinusoidal: 3024 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE M 78 " pdb=" C PHE M 78 " pdb=" N HIS M 79 " pdb=" CA HIS M 79 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 79 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 978 0.030 - 0.061: 617 0.061 - 0.091: 339 0.091 - 0.121: 157 0.121 - 0.152: 37 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA VAL E 40 " pdb=" N VAL E 40 " pdb=" C VAL E 40 " pdb=" CB VAL E 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA VAL I 40 " pdb=" N VAL I 40 " pdb=" C VAL I 40 " pdb=" CB VAL I 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA VAL O 40 " pdb=" N VAL O 40 " pdb=" C VAL O 40 " pdb=" CB VAL O 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2125 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 83 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C PHE K 83 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE K 83 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP K 84 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 83 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE O 83 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE O 83 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP O 84 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE C 83 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE C 83 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP C 84 " 0.009 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3579 2.82 - 3.34: 11494 3.34 - 3.86: 21299 3.86 - 4.38: 25619 4.38 - 4.90: 43455 Nonbonded interactions: 105446 Sorted by model distance: nonbonded pdb=" NE2 HIS K 79 " pdb=" OP1 G L 603 " model vdw 2.302 3.120 nonbonded pdb=" NE2 HIS A 79 " pdb=" OP1 G B 603 " model vdw 2.341 3.120 nonbonded pdb=" OH TYR M 17 " pdb=" OD2 ASP M 51 " model vdw 2.341 3.040 nonbonded pdb=" OH TYR O 17 " pdb=" OD2 ASP O 51 " model vdw 2.341 3.040 nonbonded pdb=" OH TYR C 17 " pdb=" OD2 ASP C 51 " model vdw 2.341 3.040 ... (remaining 105441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.460 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 13024 Z= 0.436 Angle : 0.721 4.752 17776 Z= 0.456 Chirality : 0.052 0.152 2128 Planarity : 0.004 0.021 2200 Dihedral : 14.343 86.249 4688 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.66 % Allowed : 1.32 % Favored : 98.03 % 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: 1.28 (0.20), residues: 1624 helix: 0.73 (0.19), residues: 704 sheet: 0.72 (0.23), residues: 248 loop : 1.33 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP G 197 HIS 0.004 0.001 HIS G 79 PHE 0.018 0.002 PHE E 78 TYR 0.006 0.002 TYR M 17 ARG 0.009 0.001 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 1.454 Fit side-chains REVERT: A 51 ASP cc_start: 0.7822 (m-30) cc_final: 0.7490 (m-30) REVERT: A 119 LYS cc_start: 0.8624 (tttm) cc_final: 0.8314 (tttp) REVERT: C 119 LYS cc_start: 0.8704 (tttm) cc_final: 0.8405 (tttp) REVERT: I 51 ASP cc_start: 0.7900 (m-30) cc_final: 0.7616 (m-30) REVERT: K 51 ASP cc_start: 0.7863 (m-30) cc_final: 0.7541 (m-30) REVERT: K 119 LYS cc_start: 0.8611 (tttm) cc_final: 0.8295 (tttp) REVERT: K 138 ASP cc_start: 0.8546 (t0) cc_final: 0.8340 (t0) REVERT: O 119 LYS cc_start: 0.8787 (tttm) cc_final: 0.8481 (tttt) outliers start: 8 outliers final: 0 residues processed: 241 average time/residue: 0.2463 time to fit residues: 85.6110 Evaluate side-chains 193 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 41 optimal weight: 0.0980 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN C 59 GLN E 8 GLN E 16 ASN E 59 GLN G 8 GLN G 16 ASN G 59 GLN I 16 ASN I 59 GLN K 16 ASN M 16 ASN O 8 GLN O 16 ASN O 59 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13024 Z= 0.212 Angle : 0.461 4.845 17776 Z= 0.251 Chirality : 0.046 0.125 2128 Planarity : 0.003 0.026 2200 Dihedral : 9.996 63.788 2040 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.40 % Allowed : 6.99 % Favored : 91.61 % 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: 2.03 (0.21), residues: 1624 helix: 2.00 (0.20), residues: 704 sheet: 1.05 (0.24), residues: 248 loop : 0.91 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 197 HIS 0.002 0.001 HIS K 116 PHE 0.012 0.001 PHE K 78 TYR 0.006 0.001 TYR I 158 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 1.416 Fit side-chains REVERT: A 51 ASP cc_start: 0.8157 (m-30) cc_final: 0.7771 (m-30) REVERT: A 119 LYS cc_start: 0.8794 (tttm) cc_final: 0.8457 (tttp) REVERT: C 17 TYR cc_start: 0.9026 (m-80) cc_final: 0.8713 (m-80) REVERT: C 115 ARG cc_start: 0.8389 (mtm180) cc_final: 0.8117 (mtm180) REVERT: C 119 LYS cc_start: 0.8865 (tttm) cc_final: 0.8530 (tttp) REVERT: E 51 ASP cc_start: 0.8428 (m-30) cc_final: 0.8028 (m-30) REVERT: E 115 ARG cc_start: 0.8435 (mtm180) cc_final: 0.8149 (mtm180) REVERT: G 51 ASP cc_start: 0.8427 (m-30) cc_final: 0.7962 (m-30) REVERT: I 51 ASP cc_start: 0.8291 (m-30) cc_final: 0.8090 (m-30) REVERT: K 17 TYR cc_start: 0.8976 (m-80) cc_final: 0.8748 (m-80) REVERT: K 51 ASP cc_start: 0.8168 (m-30) cc_final: 0.7692 (m-30) REVERT: K 119 LYS cc_start: 0.8804 (tttm) cc_final: 0.8448 (tttp) REVERT: M 17 TYR cc_start: 0.9018 (m-80) cc_final: 0.8783 (m-80) REVERT: O 51 ASP cc_start: 0.8394 (m-30) cc_final: 0.8104 (m-30) REVERT: O 115 ARG cc_start: 0.8405 (mtm180) cc_final: 0.8127 (mtm180) REVERT: O 119 LYS cc_start: 0.8889 (tttm) cc_final: 0.8549 (tttp) outliers start: 17 outliers final: 9 residues processed: 214 average time/residue: 0.2403 time to fit residues: 74.3260 Evaluate side-chains 205 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 196 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 13024 Z= 0.489 Angle : 0.550 4.772 17776 Z= 0.294 Chirality : 0.050 0.139 2128 Planarity : 0.004 0.032 2200 Dihedral : 10.168 63.896 2040 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.14 % Allowed : 6.91 % Favored : 90.95 % 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: 1.32 (0.20), residues: 1624 helix: 1.53 (0.19), residues: 704 sheet: 0.84 (0.27), residues: 240 loop : 0.33 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 197 HIS 0.005 0.002 HIS M 116 PHE 0.014 0.002 PHE C 78 TYR 0.009 0.001 TYR C 17 ARG 0.003 0.001 ARG O 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 1.473 Fit side-chains REVERT: A 119 LYS cc_start: 0.8915 (tttm) cc_final: 0.8612 (tttt) REVERT: C 119 LYS cc_start: 0.8918 (tttm) cc_final: 0.8611 (tttt) REVERT: E 51 ASP cc_start: 0.8382 (m-30) cc_final: 0.8061 (m-30) REVERT: G 51 ASP cc_start: 0.8313 (m-30) cc_final: 0.8027 (m-30) REVERT: K 164 ASP cc_start: 0.7070 (m-30) cc_final: 0.6704 (m-30) REVERT: O 17 TYR cc_start: 0.9171 (m-80) cc_final: 0.8920 (m-80) REVERT: O 51 ASP cc_start: 0.8438 (m-30) cc_final: 0.8000 (m-30) REVERT: O 119 LYS cc_start: 0.8916 (tttm) cc_final: 0.8608 (tttt) outliers start: 26 outliers final: 15 residues processed: 200 average time/residue: 0.2195 time to fit residues: 65.5579 Evaluate side-chains 198 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 59 GLN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN M 59 GLN O 16 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13024 Z= 0.268 Angle : 0.445 4.516 17776 Z= 0.241 Chirality : 0.045 0.126 2128 Planarity : 0.003 0.029 2200 Dihedral : 9.954 63.819 2040 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.97 % Allowed : 8.72 % Favored : 89.31 % 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: 1.28 (0.21), residues: 1624 helix: 1.58 (0.20), residues: 704 sheet: 1.08 (0.28), residues: 240 loop : 0.07 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP O 197 HIS 0.003 0.001 HIS G 79 PHE 0.011 0.001 PHE K 78 TYR 0.006 0.001 TYR C 17 ARG 0.002 0.000 ARG E 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.498 Fit side-chains REVERT: A 119 LYS cc_start: 0.8928 (tttm) cc_final: 0.8607 (tttt) REVERT: C 51 ASP cc_start: 0.8383 (m-30) cc_final: 0.8044 (m-30) REVERT: C 119 LYS cc_start: 0.8925 (tttm) cc_final: 0.8604 (tttt) REVERT: E 51 ASP cc_start: 0.8340 (m-30) cc_final: 0.8006 (m-30) REVERT: G 17 TYR cc_start: 0.9171 (m-80) cc_final: 0.8783 (m-80) REVERT: G 51 ASP cc_start: 0.8301 (m-30) cc_final: 0.8045 (m-30) REVERT: K 51 ASP cc_start: 0.8337 (m-30) cc_final: 0.8065 (m-30) REVERT: O 17 TYR cc_start: 0.9073 (m-80) cc_final: 0.8535 (m-80) REVERT: O 51 ASP cc_start: 0.8411 (m-30) cc_final: 0.7840 (m-30) REVERT: O 119 LYS cc_start: 0.8930 (tttm) cc_final: 0.8609 (tttt) outliers start: 24 outliers final: 16 residues processed: 204 average time/residue: 0.2199 time to fit residues: 67.0130 Evaluate side-chains 199 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN K 59 GLN M 16 ASN O 16 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 13024 Z= 0.348 Angle : 0.467 4.554 17776 Z= 0.252 Chirality : 0.046 0.130 2128 Planarity : 0.003 0.030 2200 Dihedral : 10.003 63.850 2040 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.06 % Allowed : 10.53 % Favored : 87.42 % 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: 1.10 (0.21), residues: 1624 helix: 1.49 (0.20), residues: 704 sheet: 1.03 (0.28), residues: 240 loop : -0.11 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 197 HIS 0.004 0.001 HIS O 79 PHE 0.012 0.002 PHE M 78 TYR 0.007 0.001 TYR K 17 ARG 0.002 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 1.483 Fit side-chains REVERT: A 119 LYS cc_start: 0.8888 (tttm) cc_final: 0.8593 (tttt) REVERT: C 119 LYS cc_start: 0.8891 (tttm) cc_final: 0.8598 (tttt) REVERT: G 17 TYR cc_start: 0.9120 (m-80) cc_final: 0.8807 (m-80) REVERT: G 51 ASP cc_start: 0.8352 (m-30) cc_final: 0.8075 (m-30) REVERT: O 51 ASP cc_start: 0.8410 (m-30) cc_final: 0.8082 (m-30) REVERT: O 119 LYS cc_start: 0.8889 (tttm) cc_final: 0.8595 (tttt) outliers start: 25 outliers final: 16 residues processed: 204 average time/residue: 0.2192 time to fit residues: 67.0091 Evaluate side-chains 199 residues out of total 1424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 72.3336 > 50: distance: 28 - 37: 34.986 distance: 37 - 38: 5.257 distance: 38 - 39: 41.131 distance: 38 - 41: 18.728 distance: 39 - 40: 19.306 distance: 39 - 43: 59.992 distance: 41 - 42: 43.276 distance: 43 - 44: 30.621 distance: 44 - 45: 8.603 distance: 44 - 47: 51.830 distance: 45 - 46: 10.055 distance: 45 - 50: 39.070 distance: 46 - 72: 40.016 distance: 47 - 49: 15.320 distance: 50 - 51: 6.826 distance: 51 - 52: 4.641 distance: 51 - 54: 18.326 distance: 52 - 53: 19.534 distance: 52 - 59: 40.611 distance: 53 - 78: 30.683 distance: 54 - 55: 33.537 distance: 55 - 56: 13.075 distance: 56 - 57: 25.656 distance: 57 - 58: 14.599 distance: 59 - 60: 3.681 distance: 61 - 62: 11.478 distance: 61 - 67: 56.448 distance: 62 - 87: 40.496 distance: 63 - 64: 21.459 distance: 63 - 65: 14.564 distance: 64 - 66: 7.487 distance: 67 - 68: 47.633 distance: 68 - 69: 49.093 distance: 68 - 71: 8.064 distance: 69 - 70: 56.211 distance: 69 - 72: 39.092 distance: 70 - 95: 52.108 distance: 72 - 73: 56.789 distance: 73 - 74: 42.419 distance: 73 - 76: 3.541 distance: 74 - 75: 19.008 distance: 74 - 78: 35.640 distance: 75 - 102: 56.625 distance: 76 - 77: 38.715 distance: 78 - 79: 33.726 distance: 79 - 80: 55.986 distance: 79 - 82: 60.345 distance: 80 - 81: 32.255 distance: 80 - 87: 65.666 distance: 82 - 83: 40.960 distance: 83 - 84: 14.459 distance: 84 - 85: 30.193 distance: 85 - 86: 27.702 distance: 88 - 89: 40.010 distance: 88 - 91: 39.921 distance: 89 - 90: 57.298 distance: 89 - 95: 5.039 distance: 91 - 92: 38.901 distance: 92 - 94: 38.601 distance: 95 - 96: 32.209 distance: 96 - 97: 55.860 distance: 96 - 99: 48.097 distance: 97 - 98: 40.949 distance: 97 - 102: 44.207 distance: 99 - 100: 42.230 distance: 99 - 101: 14.373 distance: 102 - 103: 49.243 distance: 103 - 104: 40.686 distance: 103 - 106: 8.465 distance: 104 - 105: 37.268 distance: 104 - 113: 25.595 distance: 106 - 107: 22.897 distance: 107 - 108: 24.183 distance: 108 - 109: 7.152 distance: 109 - 110: 19.639 distance: 110 - 111: 15.193 distance: 110 - 112: 15.104