Starting phenix.real_space_refine on Sun Dec 10 22:11:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnb_34159/12_2023/8gnb_34159.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnb_34159/12_2023/8gnb_34159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnb_34159/12_2023/8gnb_34159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnb_34159/12_2023/8gnb_34159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnb_34159/12_2023/8gnb_34159.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gnb_34159/12_2023/8gnb_34159.pdb" } resolution = 3.9 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 10410 2.51 5 N 2670 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 193": "OE1" <-> "OE2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 193": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15770 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "B" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "C" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "F" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "G" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "H" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "I" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Time building chain proxies: 7.80, per 1000 atoms: 0.49 Number of scatterers: 15770 At special positions: 0 Unit cell: (148.12, 122.36, 100.28, 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 140 16.00 O 2550 8.00 N 2670 7.00 C 10410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 186 " distance=2.05 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 186 " distance=2.05 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 186 " distance=2.05 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 186 " distance=2.05 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 186 " distance=2.04 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 186 " distance=2.05 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 175 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 186 " distance=2.05 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 180 " distance=2.04 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 175 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 186 " distance=2.04 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 180 " distance=2.04 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 175 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 186 " distance=2.05 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 180 " distance=2.04 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 175 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 186 " distance=2.04 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 175 " distance=2.03 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: 5.99 Conformation dependent library (CDL) restraints added in 3.2 seconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 72.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 38 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Proline residue: D 43 - end of helix Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.946A pdb=" N GLN D 49 " --> pdb=" O GLN D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Proline residue: D 88 - end of helix removed outlier: 4.064A pdb=" N LEU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 106 " --> pdb=" O THR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS D 194 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Proline residue: A 43 - end of helix Processing helix chain 'A' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN A 49 " --> pdb=" O GLN A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 4.063A pdb=" N LEU A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 166 " --> pdb=" O TYR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 38 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN B 49 " --> pdb=" O GLN B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 107 removed outlier: 3.541A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 4.064A pdb=" N LEU B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS B 194 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 16 Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Proline residue: C 43 - end of helix Processing helix chain 'C' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN C 49 " --> pdb=" O GLN C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 4.063A pdb=" N LEU C 103 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 106 " --> pdb=" O THR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 166 " --> pdb=" O TYR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 16 Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL E 38 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN E 49 " --> pdb=" O GLN E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 49' Processing helix chain 'E' and resid 60 through 70 removed outlier: 4.170A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 107 removed outlier: 3.541A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Proline residue: E 88 - end of helix removed outlier: 4.064A pdb=" N LEU E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 106 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY E 166 " --> pdb=" O TYR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS E 194 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG E 221 " --> pdb=" O VAL E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE F 37 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL F 38 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Proline residue: F 43 - end of helix Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.946A pdb=" N GLN F 49 " --> pdb=" O GLN F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Proline residue: F 88 - end of helix removed outlier: 4.064A pdb=" N LEU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU F 106 " --> pdb=" O THR F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 155 " --> pdb=" O THR F 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG F 221 " --> pdb=" O VAL F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 16 Processing helix chain 'G' and resid 19 through 32 Processing helix chain 'G' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE G 37 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN G 49 " --> pdb=" O GLN G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Proline residue: G 88 - end of helix removed outlier: 4.063A pdb=" N LEU G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU G 106 " --> pdb=" O THR G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA G 155 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY G 166 " --> pdb=" O TYR G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG G 221 " --> pdb=" O VAL G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 19 through 32 Processing helix chain 'H' and resid 33 through 45 removed outlier: 3.876A pdb=" N ILE H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL H 38 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Proline residue: H 43 - end of helix Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN H 49 " --> pdb=" O GLN H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) Proline residue: H 88 - end of helix removed outlier: 4.063A pdb=" N LEU H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU H 106 " --> pdb=" O THR H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE H 144 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA H 155 " --> pdb=" O THR H 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA H 156 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE H 157 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 166 " --> pdb=" O TYR H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS H 194 " --> pdb=" O ARG H 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG H 221 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 16 Processing helix chain 'I' and resid 19 through 32 Processing helix chain 'I' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE I 37 " --> pdb=" O ARG I 33 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL I 38 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Proline residue: I 43 - end of helix Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.948A pdb=" N GLN I 49 " --> pdb=" O GLN I 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 49' Processing helix chain 'I' and resid 60 through 70 removed outlier: 4.169A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 107 removed outlier: 3.542A pdb=" N PHE I 77 " --> pdb=" O SER I 73 " (cutoff:3.500A) Proline residue: I 88 - end of helix removed outlier: 4.063A pdb=" N LEU I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA I 104 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU I 106 " --> pdb=" O THR I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 166 removed outlier: 3.530A pdb=" N ILE I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE I 157 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 166 " --> pdb=" O TYR I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS I 194 " --> pdb=" O ARG I 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG I 221 " --> pdb=" O VAL I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 16 Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 33 through 45 removed outlier: 3.875A pdb=" N ILE J 37 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL J 38 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Proline residue: J 43 - end of helix Processing helix chain 'J' and resid 46 through 49 removed outlier: 3.947A pdb=" N GLN J 49 " --> pdb=" O GLN J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 46 through 49' Processing helix chain 'J' and resid 60 through 70 removed outlier: 4.170A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 107 removed outlier: 3.541A pdb=" N PHE J 77 " --> pdb=" O SER J 73 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 4.064A pdb=" N LEU J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA J 105 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU J 106 " --> pdb=" O THR J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 166 removed outlier: 3.529A pdb=" N ILE J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY J 166 " --> pdb=" O TYR J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 225 removed outlier: 4.060A pdb=" N LYS J 194 " --> pdb=" O ARG J 190 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG J 221 " --> pdb=" O VAL J 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 172 through 175 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AA4, first strand: chain 'C' and resid 172 through 175 Processing sheet with id=AA5, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'F' and resid 172 through 175 Processing sheet with id=AA7, first strand: chain 'G' and resid 172 through 175 Processing sheet with id=AA8, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AA9, first strand: chain 'I' and resid 172 through 175 Processing sheet with id=AB1, first strand: chain 'J' and resid 172 through 175 950 hydrogen bonds defined for protein. 2820 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: 4.39 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4880 1.35 - 1.47: 3922 1.47 - 1.59: 7168 1.59 - 1.71: 0 1.71 - 1.83: 190 Bond restraints: 16160 Sorted by residual: bond pdb=" CB GLN I 46 " pdb=" CG GLN I 46 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN F 46 " pdb=" CG GLN F 46 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLN D 46 " pdb=" CG GLN D 46 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLN H 46 " pdb=" CG GLN H 46 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CB GLN J 46 " pdb=" CG GLN J 46 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 16155 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.17: 585 107.17 - 113.87: 8980 113.87 - 120.57: 6866 120.57 - 127.27: 5391 127.27 - 133.97: 158 Bond angle restraints: 21980 Sorted by residual: angle pdb=" N PRO H 179 " pdb=" CA PRO H 179 " pdb=" C PRO H 179 " ideal model delta sigma weight residual 114.98 108.22 6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PRO A 179 " pdb=" CA PRO A 179 " pdb=" C PRO A 179 " ideal model delta sigma weight residual 114.98 108.22 6.76 1.46e+00 4.69e-01 2.14e+01 angle pdb=" N PRO G 179 " pdb=" CA PRO G 179 " pdb=" C PRO G 179 " ideal model delta sigma weight residual 114.98 108.22 6.76 1.46e+00 4.69e-01 2.14e+01 angle pdb=" N PRO B 179 " pdb=" CA PRO B 179 " pdb=" C PRO B 179 " ideal model delta sigma weight residual 114.98 108.24 6.74 1.46e+00 4.69e-01 2.13e+01 angle pdb=" N PRO C 179 " pdb=" CA PRO C 179 " pdb=" C PRO C 179 " ideal model delta sigma weight residual 114.98 108.24 6.74 1.46e+00 4.69e-01 2.13e+01 ... (remaining 21975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 8516 14.09 - 28.19: 764 28.19 - 42.28: 193 42.28 - 56.38: 77 56.38 - 70.47: 40 Dihedral angle restraints: 9590 sinusoidal: 3800 harmonic: 5790 Sorted by residual: dihedral pdb=" CA PRO B 178 " pdb=" C PRO B 178 " pdb=" N PRO B 179 " pdb=" CA PRO B 179 " ideal model delta harmonic sigma weight residual 180.00 135.38 44.62 0 5.00e+00 4.00e-02 7.96e+01 dihedral pdb=" CA PRO I 178 " pdb=" C PRO I 178 " pdb=" N PRO I 179 " pdb=" CA PRO I 179 " ideal model delta harmonic sigma weight residual 180.00 135.41 44.59 0 5.00e+00 4.00e-02 7.95e+01 dihedral pdb=" CA PRO D 178 " pdb=" C PRO D 178 " pdb=" N PRO D 179 " pdb=" CA PRO D 179 " ideal model delta harmonic sigma weight residual 180.00 135.42 44.58 0 5.00e+00 4.00e-02 7.95e+01 ... (remaining 9587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1546 0.037 - 0.073: 711 0.073 - 0.110: 279 0.110 - 0.146: 54 0.146 - 0.183: 20 Chirality restraints: 2610 Sorted by residual: chirality pdb=" CG LEU H 39 " pdb=" CB LEU H 39 " pdb=" CD1 LEU H 39 " pdb=" CD2 LEU H 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CG LEU G 39 " pdb=" CB LEU G 39 " pdb=" CD1 LEU G 39 " pdb=" CD2 LEU G 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CG LEU A 39 " pdb=" CB LEU A 39 " pdb=" CD1 LEU A 39 " pdb=" CD2 LEU A 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 2607 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 178 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO H 179 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO H 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 179 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 178 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO C 179 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO J 178 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO J 179 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO J 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO J 179 " -0.040 5.00e-02 4.00e+02 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2636 2.76 - 3.30: 15693 3.30 - 3.83: 25483 3.83 - 4.37: 27763 4.37 - 4.90: 47136 Nonbonded interactions: 118711 Sorted by model distance: nonbonded pdb=" NH2 ARG B 221 " pdb=" O ASP I 138 " model vdw 2.231 2.520 nonbonded pdb=" O THR J 13 " pdb=" ND2 ASN J 17 " model vdw 2.263 2.520 nonbonded pdb=" O THR E 13 " pdb=" ND2 ASN E 17 " model vdw 2.263 2.520 nonbonded pdb=" O THR H 13 " pdb=" ND2 ASN H 17 " model vdw 2.263 2.520 nonbonded pdb=" O THR G 13 " pdb=" ND2 ASN G 17 " model vdw 2.263 2.520 ... (remaining 118706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.220 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.120 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.110 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 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 : 0.004 0.038 16160 Z= 0.226 Angle : 0.937 6.765 21980 Z= 0.512 Chirality : 0.048 0.183 2610 Planarity : 0.009 0.073 2700 Dihedral : 12.918 70.469 5760 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.65 (0.19), residues: 1970 helix: 0.05 (0.15), residues: 1320 sheet: 2.14 (0.59), residues: 100 loop : -1.95 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 25 HIS 0.002 0.000 HIS C 146 PHE 0.022 0.002 PHE E 52 TYR 0.025 0.003 TYR I 143 ARG 0.005 0.001 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 815 time to evaluate : 1.693 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: 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: 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 outliers start: 0 outliers final: 0 residues processed: 815 average time/residue: 0.2938 time to fit residues: 339.3609 Evaluate side-chains 510 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9990 chunk 151 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 55 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 HIS ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16160 Z= 0.277 Angle : 0.902 13.098 21980 Z= 0.444 Chirality : 0.048 0.249 2610 Planarity : 0.008 0.099 2700 Dihedral : 6.201 56.719 2190 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 6.59 % Allowed : 20.35 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.45 (0.19), residues: 1970 helix: 0.25 (0.15), residues: 1290 sheet: 1.91 (0.55), residues: 100 loop : -1.83 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 202 HIS 0.009 0.001 HIS B 161 PHE 0.029 0.003 PHE F 173 TYR 0.024 0.002 TYR F 66 ARG 0.013 0.001 ARG J 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 579 time to evaluate : 1.736 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: 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: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 67 residues processed: 626 average time/residue: 0.2598 time to fit residues: 240.5681 Evaluate side-chains 515 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 448 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.1412 time to fit residues: 19.9056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 196 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 180 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 HIS ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 98 HIS ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16160 Z= 0.228 Angle : 0.871 14.048 21980 Z= 0.415 Chirality : 0.046 0.251 2610 Planarity : 0.007 0.107 2700 Dihedral : 6.022 52.859 2190 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.93 % Allowed : 26.13 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -0.20 (0.19), residues: 1970 helix: 0.42 (0.15), residues: 1300 sheet: 1.74 (0.55), residues: 100 loop : -1.63 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 78 HIS 0.012 0.001 HIS G 161 PHE 0.028 0.002 PHE D 26 TYR 0.028 0.002 TYR F 66 ARG 0.010 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 495 time to evaluate : 1.763 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: 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 outliers start: 68 outliers final: 49 residues processed: 536 average time/residue: 0.2518 time to fit residues: 201.7602 Evaluate side-chains 490 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 441 time to evaluate : 1.719 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 2 residues processed: 49 average time/residue: 0.1499 time to fit residues: 15.5773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 55.6112 > 50: distance: 8 - 115: 11.978 distance: 35 - 39: 19.268 distance: 39 - 40: 9.540 distance: 40 - 41: 30.862 distance: 41 - 42: 33.254 distance: 41 - 43: 22.970 distance: 43 - 44: 14.953 distance: 44 - 45: 10.869 distance: 44 - 47: 21.765 distance: 45 - 46: 13.780 distance: 45 - 54: 5.614 distance: 47 - 48: 18.623 distance: 48 - 49: 7.471 distance: 49 - 51: 4.794 distance: 50 - 52: 6.077 distance: 51 - 53: 5.834 distance: 52 - 53: 6.233 distance: 54 - 55: 19.120 distance: 55 - 56: 21.617 distance: 55 - 58: 16.810 distance: 56 - 57: 22.503 distance: 56 - 62: 23.714 distance: 58 - 59: 10.532 distance: 59 - 60: 8.531 distance: 59 - 61: 11.144 distance: 62 - 63: 17.243 distance: 63 - 64: 17.389 distance: 63 - 66: 33.606 distance: 64 - 65: 32.947 distance: 64 - 67: 29.158 distance: 67 - 68: 6.229 distance: 67 - 73: 17.579 distance: 68 - 69: 27.056 distance: 68 - 71: 40.350 distance: 69 - 70: 12.219 distance: 69 - 74: 13.307 distance: 71 - 72: 14.600 distance: 72 - 73: 38.094 distance: 74 - 75: 27.980 distance: 75 - 76: 18.587 distance: 75 - 78: 11.849 distance: 76 - 77: 5.826 distance: 76 - 83: 18.623 distance: 78 - 79: 17.151 distance: 79 - 80: 9.436 distance: 80 - 81: 15.540 distance: 81 - 82: 9.218 distance: 83 - 84: 25.186 distance: 84 - 85: 22.304 distance: 84 - 87: 23.890 distance: 85 - 86: 32.109 distance: 85 - 92: 19.855 distance: 87 - 88: 10.684 distance: 88 - 89: 7.049 distance: 89 - 90: 11.027 distance: 90 - 91: 6.002 distance: 92 - 93: 3.473 distance: 92 - 147: 13.589 distance: 93 - 94: 16.488 distance: 93 - 96: 10.034 distance: 94 - 95: 23.166 distance: 94 - 103: 16.845 distance: 95 - 144: 25.954 distance: 96 - 97: 16.839 distance: 97 - 98: 3.538 distance: 97 - 99: 5.517 distance: 98 - 100: 5.757 distance: 99 - 101: 18.063 distance: 100 - 102: 11.719 distance: 101 - 102: 6.703 distance: 103 - 104: 12.159 distance: 103 - 109: 12.914 distance: 104 - 105: 35.648 distance: 104 - 107: 25.235 distance: 105 - 106: 12.934 distance: 105 - 110: 13.647 distance: 107 - 108: 6.432 distance: 108 - 109: 23.526 distance: 110 - 111: 9.386 distance: 110 - 136: 20.118 distance: 111 - 112: 26.291 distance: 111 - 114: 28.900 distance: 112 - 113: 21.568 distance: 112 - 116: 10.261 distance: 113 - 133: 22.465 distance: 114 - 115: 17.719