Starting phenix.real_space_refine on Sun May 25 05:22:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uf0_42181/05_2025/8uf0_42181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uf0_42181/05_2025/8uf0_42181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uf0_42181/05_2025/8uf0_42181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uf0_42181/05_2025/8uf0_42181.map" model { file = "/net/cci-nas-00/data/ceres_data/8uf0_42181/05_2025/8uf0_42181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uf0_42181/05_2025/8uf0_42181.cif" } resolution = 2.02 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= 0.008 sd= 0.100 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 48 5.16 5 C 16776 2.51 5 N 4332 2.21 5 O 5844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27000 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "V" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "X" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Restraints were copied for chains: D, F, H, J, L, N, P, R, T, V, X, C, E, G, I, K, M, O, Q, S, U, W Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" O HOH A 238 " occ=0.33 residue: pdb=" O HOH C 238 " occ=0.33 residue: pdb=" O HOH E 238 " occ=0.33 residue: pdb=" O HOH G 238 " occ=0.33 residue: pdb=" O HOH I 238 " occ=0.33 residue: pdb=" O HOH K 238 " occ=0.33 residue: pdb=" O HOH M 238 " occ=0.33 residue: pdb=" O HOH O 238 " occ=0.33 residue: pdb=" O HOH Q 238 " occ=0.33 residue: pdb=" O HOH S 238 " occ=0.33 residue: pdb=" O HOH U 238 " occ=0.33 residue: pdb=" O HOH W 238 " occ=0.33 Time building chain proxies: 7.06, per 1000 atoms: 0.26 Number of scatterers: 27000 At special positions: 0 Unit cell: (145.34, 141.04, 133.3, 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 48 16.00 O 5844 8.00 N 4332 7.00 C 16776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.87 Conformation dependent library (CDL) restraints added in 3.4 seconds 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 36 sheets defined 43.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 106 through 117 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 90 Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 143 Processing helix chain 'F' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 40 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 106 through 117 Processing helix chain 'H' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 Processing helix chain 'H' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE H 200 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 40 Processing helix chain 'I' and resid 75 through 77 No H-bonds generated for 'chain 'I' and resid 75 through 77' Processing helix chain 'I' and resid 78 through 90 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 167 through 183 removed outlier: 3.674A pdb=" N ARG J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 203 removed outlier: 4.067A pdb=" N ILE J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 106 through 117 Processing helix chain 'L' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 143 Processing helix chain 'L' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE L 200 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 40 Processing helix chain 'M' and resid 75 through 77 No H-bonds generated for 'chain 'M' and resid 75 through 77' Processing helix chain 'M' and resid 78 through 90 Processing helix chain 'M' and resid 106 through 117 Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 143 Processing helix chain 'N' and resid 167 through 183 removed outlier: 3.676A pdb=" N ARG N 176 " --> pdb=" O GLU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE N 200 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 40 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 78 through 90 Processing helix chain 'O' and resid 106 through 117 Processing helix chain 'P' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA P 44 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU P 105 " --> pdb=" O LEU P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 143 Processing helix chain 'P' and resid 167 through 183 removed outlier: 3.676A pdb=" N ARG P 176 " --> pdb=" O GLU P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE P 200 " --> pdb=" O VAL P 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 40 Processing helix chain 'Q' and resid 75 through 77 No H-bonds generated for 'chain 'Q' and resid 75 through 77' Processing helix chain 'Q' and resid 78 through 90 Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'R' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 143 Processing helix chain 'R' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG R 176 " --> pdb=" O GLU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE R 200 " --> pdb=" O VAL R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 40 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 78 through 90 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'T' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA T 44 " --> pdb=" O ALA T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY T 82 " --> pdb=" O LEU T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU T 105 " --> pdb=" O LEU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 143 Processing helix chain 'T' and resid 167 through 183 removed outlier: 3.674A pdb=" N ARG T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE T 200 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 40 Processing helix chain 'U' and resid 75 through 77 No H-bonds generated for 'chain 'U' and resid 75 through 77' Processing helix chain 'U' and resid 78 through 90 Processing helix chain 'U' and resid 106 through 117 Processing helix chain 'V' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA V 44 " --> pdb=" O ALA V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY V 82 " --> pdb=" O LEU V 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 143 Processing helix chain 'V' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG V 176 " --> pdb=" O GLU V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE V 200 " --> pdb=" O VAL V 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 40 Processing helix chain 'W' and resid 75 through 77 No H-bonds generated for 'chain 'W' and resid 75 through 77' Processing helix chain 'W' and resid 78 through 90 Processing helix chain 'W' and resid 106 through 117 Processing helix chain 'X' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY X 82 " --> pdb=" O LEU X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU X 105 " --> pdb=" O LEU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 143 Processing helix chain 'X' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG X 176 " --> pdb=" O GLU X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE X 200 " --> pdb=" O VAL X 196 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA A 46 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR A 73 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE A 48 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 71 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A 69 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU B 48 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 50 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 22 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 93 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 24 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR B 91 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU B 26 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU B 147 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 165 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 149 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 121 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE B 191 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 123 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 189 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU B 125 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'C' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA C 46 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR C 73 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 48 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR C 71 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 69 " --> pdb=" O PRO C 50 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU D 48 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU D 64 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 50 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU D 22 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D 93 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 24 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR D 91 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU D 26 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'D' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU D 147 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 165 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 149 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 121 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE D 191 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 123 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D 189 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU D 125 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'E' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA E 46 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR E 73 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE E 48 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR E 71 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 69 " --> pdb=" O PRO E 50 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'F' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU F 48 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 64 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS F 50 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU F 22 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 93 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 24 " --> pdb=" O TYR F 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR F 91 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU F 26 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'F' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU F 147 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 165 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 149 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE F 121 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE F 191 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 123 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU F 189 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU F 125 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'G' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA G 46 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR G 73 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE G 48 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 71 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG G 69 " --> pdb=" O PRO G 50 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU H 48 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU H 64 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 50 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU H 22 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU H 93 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE H 24 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR H 91 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU H 26 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU H 147 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE H 165 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER H 149 " --> pdb=" O THR H 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE H 121 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE H 191 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 123 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU H 189 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU H 125 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA I 46 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR I 73 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE I 48 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR I 71 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG I 69 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU J 48 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU J 64 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS J 50 " --> pdb=" O MET J 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU J 22 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU J 93 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE J 24 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR J 91 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU J 26 " --> pdb=" O ILE J 89 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'J' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU J 147 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE J 165 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER J 149 " --> pdb=" O THR J 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE J 121 " --> pdb=" O ILE J 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE J 191 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL J 123 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU J 189 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU J 125 " --> pdb=" O LEU J 187 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'K' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA K 46 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR K 73 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE K 48 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR K 71 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG K 69 " --> pdb=" O PRO K 50 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'L' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU L 48 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU L 64 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS L 50 " --> pdb=" O MET L 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU L 22 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU L 93 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE L 24 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR L 91 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU L 26 " --> pdb=" O ILE L 89 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'L' and resid 146 through 151 removed outlier: 5.655A pdb=" N LEU L 147 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE L 165 " --> pdb=" O LEU L 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER L 149 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE L 121 " --> pdb=" O ILE L 191 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE L 191 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL L 123 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU L 189 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU L 125 " --> pdb=" O LEU L 187 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'M' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA M 46 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR M 73 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE M 48 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR M 71 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG M 69 " --> pdb=" O PRO M 50 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'N' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU N 48 " --> pdb=" O LEU N 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU N 64 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS N 50 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU N 22 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU N 93 " --> pdb=" O LEU N 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE N 24 " --> pdb=" O TYR N 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR N 91 " --> pdb=" O ILE N 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU N 26 " --> pdb=" O ILE N 89 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'N' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU N 147 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE N 165 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER N 149 " --> pdb=" O THR N 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE N 121 " --> pdb=" O ILE N 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE N 191 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL N 123 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU N 189 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU N 125 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'O' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA O 46 " --> pdb=" O TYR O 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR O 73 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE O 48 " --> pdb=" O THR O 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR O 71 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG O 69 " --> pdb=" O PRO O 50 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'P' and resid 47 through 54 removed outlier: 5.671A pdb=" N LEU P 48 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU P 64 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS P 50 " --> pdb=" O MET P 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU P 93 " --> pdb=" O LEU P 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE P 24 " --> pdb=" O TYR P 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR P 91 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU P 26 " --> pdb=" O ILE P 89 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'P' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU P 147 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE P 165 " --> pdb=" O LEU P 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER P 149 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE P 121 " --> pdb=" O ILE P 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE P 191 " --> pdb=" O ILE P 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL P 123 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU P 189 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU P 125 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA Q 46 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR Q 73 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE Q 48 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR Q 71 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG Q 69 " --> pdb=" O PRO Q 50 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'R' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU R 48 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU R 64 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS R 50 " --> pdb=" O MET R 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU R 22 " --> pdb=" O LEU R 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU R 93 " --> pdb=" O LEU R 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE R 24 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR R 91 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU R 26 " --> pdb=" O ILE R 89 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'R' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU R 147 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE R 165 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER R 149 " --> pdb=" O THR R 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE R 121 " --> pdb=" O ILE R 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE R 191 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL R 123 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU R 189 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU R 125 " --> pdb=" O LEU R 187 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'S' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA S 46 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR S 73 " --> pdb=" O ALA S 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE S 48 " --> pdb=" O THR S 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR S 71 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG S 69 " --> pdb=" O PRO S 50 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'T' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU T 48 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU T 64 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS T 50 " --> pdb=" O MET T 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU T 22 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU T 93 " --> pdb=" O LEU T 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE T 24 " --> pdb=" O TYR T 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR T 91 " --> pdb=" O ILE T 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU T 26 " --> pdb=" O ILE T 89 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'T' and resid 146 through 151 removed outlier: 5.653A pdb=" N LEU T 147 " --> pdb=" O ILE T 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE T 165 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER T 149 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE T 121 " --> pdb=" O ILE T 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE T 191 " --> pdb=" O ILE T 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL T 123 " --> pdb=" O LEU T 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU T 189 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU T 125 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'U' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA U 46 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR U 73 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE U 48 " --> pdb=" O THR U 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR U 71 " --> pdb=" O ILE U 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG U 69 " --> pdb=" O PRO U 50 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'V' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU V 48 " --> pdb=" O LEU V 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU V 64 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS V 50 " --> pdb=" O MET V 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU V 22 " --> pdb=" O LEU V 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU V 93 " --> pdb=" O LEU V 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE V 24 " --> pdb=" O TYR V 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR V 91 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU V 26 " --> pdb=" O ILE V 89 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'V' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU V 147 " --> pdb=" O ILE V 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE V 165 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER V 149 " --> pdb=" O THR V 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE V 121 " --> pdb=" O ILE V 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE V 191 " --> pdb=" O ILE V 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL V 123 " --> pdb=" O LEU V 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU V 189 " --> pdb=" O VAL V 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU V 125 " --> pdb=" O LEU V 187 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'W' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA W 46 " --> pdb=" O TYR W 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR W 73 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE W 48 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR W 71 " --> pdb=" O ILE W 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG W 69 " --> pdb=" O PRO W 50 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'X' and resid 47 through 54 removed outlier: 5.671A pdb=" N LEU X 48 " --> pdb=" O LEU X 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU X 64 " --> pdb=" O LEU X 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS X 50 " --> pdb=" O MET X 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU X 22 " --> pdb=" O LEU X 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU X 93 " --> pdb=" O LEU X 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE X 24 " --> pdb=" O TYR X 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR X 91 " --> pdb=" O ILE X 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU X 26 " --> pdb=" O ILE X 89 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'X' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU X 147 " --> pdb=" O ILE X 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE X 165 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER X 149 " --> pdb=" O THR X 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE X 121 " --> pdb=" O ILE X 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE X 191 " --> pdb=" O ILE X 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL X 123 " --> pdb=" O LEU X 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU X 189 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU X 125 " --> pdb=" O LEU X 187 " (cutoff:3.500A) 1488 hydrogen bonds defined for protein. 4212 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: 9.97 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8679 1.34 - 1.46: 3461 1.46 - 1.58: 14380 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 26604 Sorted by residual: bond pdb=" CB GLU L 66 " pdb=" CG GLU L 66 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CB GLU K 75 " pdb=" CG GLU K 75 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CB GLU G 75 " pdb=" CG GLU G 75 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLU E 75 " pdb=" CG GLU E 75 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 26599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 34998 1.76 - 3.52: 1088 3.52 - 5.29: 106 5.29 - 7.05: 0 7.05 - 8.81: 24 Bond angle restraints: 36216 Sorted by residual: angle pdb=" CA LEU T 83 " pdb=" CB LEU T 83 " pdb=" CG LEU T 83 " ideal model delta sigma weight residual 116.30 124.87 -8.57 3.50e+00 8.16e-02 5.99e+00 angle pdb=" CA LEU J 83 " pdb=" CB LEU J 83 " pdb=" CG LEU J 83 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CA LEU L 83 " pdb=" CB LEU L 83 " pdb=" CG LEU L 83 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CA LEU R 83 " pdb=" CB LEU R 83 " pdb=" CG LEU R 83 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.97e+00 angle pdb=" CA LEU B 83 " pdb=" CB LEU B 83 " pdb=" CG LEU B 83 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 ... (remaining 36211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 14313 16.89 - 33.77: 1671 33.77 - 50.66: 444 50.66 - 67.54: 216 67.54 - 84.43: 60 Dihedral angle restraints: 16704 sinusoidal: 6636 harmonic: 10068 Sorted by residual: dihedral pdb=" CA ASP R 137 " pdb=" CB ASP R 137 " pdb=" CG ASP R 137 " pdb=" OD1 ASP R 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.89 59.89 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP X 137 " pdb=" CB ASP X 137 " pdb=" CG ASP X 137 " pdb=" OD1 ASP X 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.87 59.87 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP T 137 " pdb=" CB ASP T 137 " pdb=" CG ASP T 137 " pdb=" OD1 ASP T 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 16701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1828 0.029 - 0.057: 1432 0.057 - 0.086: 652 0.086 - 0.115: 256 0.115 - 0.143: 272 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA PRO E 93 " pdb=" N PRO E 93 " pdb=" C PRO E 93 " pdb=" CB PRO E 93 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA PRO M 93 " pdb=" N PRO M 93 " pdb=" C PRO M 93 " pdb=" CB PRO M 93 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA PRO O 93 " pdb=" N PRO O 93 " pdb=" C PRO O 93 " pdb=" CB PRO O 93 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 4437 not shown) Planarity restraints: 4656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 90 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO G 91 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 91 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS K 90 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO K 91 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO K 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 91 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS W 90 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO W 91 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO W 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO W 91 " 0.023 5.00e-02 4.00e+02 ... (remaining 4653 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 12 0.99 - 1.97: 0 1.97 - 2.95: 10725 2.95 - 3.92: 68434 3.92 - 4.90: 124559 Warning: very small nonbonded interaction distances. Nonbonded interactions: 203730 Sorted by model distance: nonbonded pdb=" O HOH G 238 " pdb=" O HOH K 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH A 238 " pdb=" O HOH I 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH O 238 " pdb=" O HOH S 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH M 238 " pdb=" O HOH W 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH G 238 " pdb=" O HOH U 238 " model vdw 0.013 3.040 ... (remaining 203725 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: 0.24 Found NCS groups: 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' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } 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=0.33 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: 1.010 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: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 48.110 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 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 0.045 26604 Z= 0.282 Angle : 0.756 8.812 36216 Z= 0.408 Chirality : 0.054 0.143 4440 Planarity : 0.006 0.041 4656 Dihedral : 17.495 84.429 10152 Min Nonbonded Distance : 0.013 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.54 % Allowed : 19.37 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3408 helix: 0.96 (0.14), residues: 1392 sheet: 1.42 (0.19), residues: 756 loop : -1.89 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 112 HIS 0.005 0.002 HIS W 90 PHE 0.018 0.003 PHE I 115 TYR 0.014 0.002 TYR L 91 ARG 0.004 0.001 ARG V 141 Details of bonding type rmsd hydrogen bonds : bond 0.27623 ( 1488) hydrogen bonds : angle 7.04476 ( 4212) covalent geometry : bond 0.00659 (26604) covalent geometry : angle 0.75612 (36216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 295 time to evaluate : 2.958 Fit side-chains REVERT: D 159 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7340 (mtt180) REVERT: N 83 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4901 (tp) REVERT: V 83 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4920 (tp) outliers start: 15 outliers final: 11 residues processed: 310 average time/residue: 1.8641 time to fit residues: 650.6834 Evaluate side-chains 279 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 266 time to evaluate : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain X residue 54 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.0317 > 50: distance: 92 - 95: 14.405 distance: 95 - 96: 13.523 distance: 96 - 97: 36.735 distance: 96 - 99: 28.185 distance: 97 - 98: 56.213 distance: 97 - 103: 43.094 distance: 99 - 100: 15.816 distance: 99 - 101: 22.912 distance: 100 - 102: 13.219 distance: 103 - 104: 35.813 distance: 104 - 105: 29.971 distance: 104 - 107: 45.064 distance: 105 - 106: 17.215 distance: 105 - 111: 17.539 distance: 107 - 108: 47.193 distance: 107 - 109: 46.161 distance: 108 - 110: 46.738 distance: 111 - 112: 31.225 distance: 112 - 113: 54.598 distance: 112 - 115: 25.713 distance: 113 - 114: 46.200 distance: 113 - 118: 42.952 distance: 115 - 116: 7.953 distance: 115 - 117: 16.431 distance: 118 - 119: 37.765 distance: 118 - 124: 44.212 distance: 119 - 120: 27.082 distance: 119 - 122: 41.405 distance: 120 - 121: 16.889 distance: 120 - 125: 29.824 distance: 122 - 123: 29.486 distance: 123 - 124: 22.232 distance: 125 - 126: 18.084 distance: 126 - 127: 31.709 distance: 126 - 129: 13.801 distance: 127 - 128: 21.863 distance: 127 - 130: 16.078 distance: 130 - 131: 7.670 distance: 130 - 231: 15.580 distance: 131 - 132: 18.502 distance: 131 - 134: 12.483 distance: 132 - 133: 27.209 distance: 132 - 138: 48.256 distance: 133 - 228: 35.106 distance: 134 - 135: 15.133 distance: 135 - 136: 12.574 distance: 135 - 137: 18.657 distance: 138 - 139: 43.898 distance: 139 - 140: 18.470 distance: 139 - 142: 20.075 distance: 140 - 141: 14.312 distance: 140 - 145: 45.185 distance: 142 - 143: 29.909 distance: 142 - 144: 33.358 distance: 145 - 146: 16.248 distance: 145 - 215: 30.275 distance: 146 - 147: 13.683 distance: 146 - 149: 11.466 distance: 147 - 148: 13.154 distance: 147 - 154: 36.309 distance: 148 - 212: 28.170 distance: 149 - 150: 31.699 distance: 150 - 151: 60.410 distance: 151 - 152: 41.525 distance: 152 - 153: 10.959 distance: 154 - 155: 15.196 distance: 155 - 156: 10.250 distance: 155 - 158: 27.356 distance: 156 - 157: 7.862 distance: 156 - 162: 9.160 distance: 158 - 159: 55.481 distance: 158 - 160: 39.013 distance: 159 - 161: 31.834 distance: 162 - 163: 8.079 distance: 162 - 200: 10.578 distance: 163 - 164: 11.710 distance: 163 - 166: 9.530 distance: 164 - 165: 34.690 distance: 164 - 174: 8.764 distance: 165 - 197: 27.908 distance: 166 - 167: 19.968 distance: 167 - 168: 12.121 distance: 167 - 169: 18.403 distance: 168 - 170: 4.624 distance: 169 - 171: 31.041 distance: 170 - 172: 23.713 distance: 171 - 172: 25.823 distance: 172 - 173: 4.764