Starting phenix.real_space_refine on Tue Jan 21 06:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sae_24950/01_2025/7sae_24950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sae_24950/01_2025/7sae_24950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sae_24950/01_2025/7sae_24950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sae_24950/01_2025/7sae_24950.map" model { file = "/net/cci-nas-00/data/ceres_data/7sae_24950/01_2025/7sae_24950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sae_24950/01_2025/7sae_24950.cif" } resolution = 3.0 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= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 2434 5.49 5 S 52 5.16 5 C 33503 2.51 5 N 12804 2.21 5 O 19778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 68571 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 52303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2434, 52303 Classifications: {'RNA': 2434} Modifications used: {'rna2p_pur': 254, 'rna2p_pyr': 126, 'rna3p_pur': 1176, 'rna3p_pyr': 878} Link IDs: {'rna2p': 380, 'rna3p': 2053} Chain breaks: 5 Chain: "C" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2052 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 1 Chain: "D" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1354 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain breaks: 1 Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 973 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 1 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "P" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 780 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 741 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "U" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "V" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Time building chain proxies: 27.28, per 1000 atoms: 0.40 Number of scatterers: 68571 At special positions: 0 Unit cell: (208.62, 196.65, 208.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 2434 15.00 O 19778 8.00 N 12804 7.00 C 33503 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: 11.91 Conformation dependent library (CDL) restraints added in 2.5 seconds 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 33 sheets defined 25.3% alpha, 19.5% beta 722 base pairs and 1351 stacking pairs defined. Time for finding SS restraints: 23.93 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.621A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.758A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.536A pdb=" N ASP C 267 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.917A pdb=" N VAL D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.869A pdb=" N TYR D 91 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.652A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 102 " --> pdb=" O VAL D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 102' Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'E' and resid 31 through 43 removed outlier: 4.017A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.590A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.783A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.624A pdb=" N VAL E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 39 removed outlier: 3.639A pdb=" N SER J 30 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.684A pdb=" N LYS J 62 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE J 63 " --> pdb=" O ALA J 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 63' Processing helix chain 'J' and resid 68 through 73 removed outlier: 3.611A pdb=" N LYS J 73 " --> pdb=" O LYS J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 95 Processing helix chain 'J' and resid 97 through 108 removed outlier: 3.626A pdb=" N MET J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU J 102 " --> pdb=" O PRO J 98 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.927A pdb=" N SER L 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY L 26 " --> pdb=" O ILE L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 22 through 26' Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.695A pdb=" N LEU L 61 " --> pdb=" O PHE L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.753A pdb=" N ASN L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'L' and resid 92 through 99 removed outlier: 3.553A pdb=" N LEU L 97 " --> pdb=" O PRO L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 137 removed outlier: 4.252A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 3.546A pdb=" N LYS N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 54 removed outlier: 3.621A pdb=" N GLU N 39 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET N 47 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR N 49 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 3.702A pdb=" N ARG N 59 " --> pdb=" O ASP N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.545A pdb=" N LEU N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 84' Processing helix chain 'P' and resid 6 through 10 Processing helix chain 'P' and resid 100 through 105 removed outlier: 3.589A pdb=" N LEU P 103 " --> pdb=" O LEU P 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG P 104 " --> pdb=" O TYR P 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 20 removed outlier: 3.929A pdb=" N LYS Q 12 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.835A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR Q 30 " --> pdb=" O SER Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 70 removed outlier: 5.053A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 removed outlier: 3.714A pdb=" N HIS Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.705A pdb=" N LEU Q 98 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 112 removed outlier: 3.671A pdb=" N ASN Q 107 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN Q 108 " --> pdb=" O THR Q 104 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 118 removed outlier: 3.744A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.260A pdb=" N LEU S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET S 21 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG S 25 " --> pdb=" O MET S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.700A pdb=" N VAL S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 62 removed outlier: 3.804A pdb=" N LYS S 49 " --> pdb=" O PRO S 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL S 50 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA S 56 " --> pdb=" O LYS S 52 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR S 62 " --> pdb=" O ALA S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'T' and resid 3 through 6 removed outlier: 3.510A pdb=" N ASP T 6 " --> pdb=" O ASP T 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 6' Processing helix chain 'T' and resid 16 through 21 Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.629A pdb=" N VAL T 39 " --> pdb=" O ASN T 35 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS T 40 " --> pdb=" O LYS T 36 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP T 41 " --> pdb=" O THR T 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.545A pdb=" N THR Z 22 " --> pdb=" O ASP Z 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Z 26 " --> pdb=" O THR Z 22 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY Z 27 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.777A pdb=" N ARG Z 44 " --> pdb=" O ASN Z 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 15 removed outlier: 3.584A pdb=" N LYS b 13 " --> pdb=" O SER b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 20 removed outlier: 4.276A pdb=" N HIS b 19 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE b 20 " --> pdb=" O ARG b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 20' Processing helix chain 'Y' and resid 10 through 15 removed outlier: 3.947A pdb=" N GLU Y 15 " --> pdb=" O THR Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 35 removed outlier: 3.592A pdb=" N ASN Y 27 " --> pdb=" O GLU Y 23 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 42 through 62 removed outlier: 3.561A pdb=" N LYS Y 48 " --> pdb=" O ARG Y 44 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA Y 49 " --> pdb=" O GLU Y 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG Y 60 " --> pdb=" O VAL Y 56 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU Y 61 " --> pdb=" O ILE Y 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 17 removed outlier: 4.238A pdb=" N VAL d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 removed outlier: 3.617A pdb=" N VAL d 30 " --> pdb=" O ASN d 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU d 31 " --> pdb=" O GLY d 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA d 32 " --> pdb=" O ARG d 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.505A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.736A pdb=" N VAL C 181 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 16 removed outlier: 5.880A pdb=" N LYS D 9 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU D 29 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N THR D 170 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY D 112 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 200 " --> pdb=" O GLY D 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 84 removed outlier: 6.597A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA D 48 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS D 38 " --> pdb=" O ALA D 48 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.698A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.935A pdb=" N LEU E 6 " --> pdb=" O GLY E 15 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 123 through 125 removed outlier: 6.130A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 123 through 125 removed outlier: 6.942A pdb=" N TRP J 16 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 74 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.729A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.191A pdb=" N VAL K 102 " --> pdb=" O ILE K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 75 through 78 removed outlier: 5.617A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU L 112 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL L 77 " --> pdb=" O LEU L 112 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS L 127 " --> pdb=" O VAL L 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 90 through 91 removed outlier: 6.298A pdb=" N VAL L 91 " --> pdb=" O LYS L 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU L 144 " --> pdb=" O VAL L 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.375A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 70 through 72 removed outlier: 6.888A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 71 through 78 removed outlier: 6.430A pdb=" N THR P 63 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE P 67 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLU P 47 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR P 28 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL P 89 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG P 30 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE P 87 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS P 32 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.583A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE R 100 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL R 58 " --> pdb=" O ILE R 100 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 71 through 73 Processing sheet with id=AC4, first strand: chain 'S' and resid 3 through 6 removed outlier: 6.431A pdb=" N SER S 108 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AC6, first strand: chain 'T' and resid 8 through 11 removed outlier: 3.583A pdb=" N ARG T 10 " --> pdb=" O GLU T 29 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG T 76 " --> pdb=" O ASN T 58 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN T 58 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS T 78 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE T 56 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE T 80 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL T 54 " --> pdb=" O ILE T 80 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS T 82 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 63 through 64 Processing sheet with id=AC8, first strand: chain 'U' and resid 63 through 64 removed outlier: 7.262A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 81 through 85 Processing sheet with id=AD1, first strand: chain 'V' and resid 30 through 31 removed outlier: 3.599A pdb=" N GLY V 30 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU V 67 " --> pdb=" O LEU V 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 54 through 55 Processing sheet with id=AD3, first strand: chain 'V' and resid 73 through 75 Processing sheet with id=AD4, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AD5, first strand: chain 'b' and resid 27 through 29 Processing sheet with id=AD6, first strand: chain 'b' and resid 48 through 49 removed outlier: 3.525A pdb=" N LYS b 52 " --> pdb=" O TYR b 49 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1837 hydrogen bonds 2976 hydrogen bond angles 0 basepair planarities 722 basepair parallelities 1351 stacking parallelities Total time for adding SS restraints: 92.28 Time building geometry restraints manager: 14.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6433 1.31 - 1.43: 34302 1.43 - 1.56: 29362 1.56 - 1.68: 4863 1.68 - 1.80: 97 Bond restraints: 75057 Sorted by residual: bond pdb=" CG ARG Q 92 " pdb=" CD ARG Q 92 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.07e+00 bond pdb=" C THR D 74 " pdb=" N ALA D 75 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.47e-02 4.63e+03 4.73e+00 bond pdb=" N9 A A1697 " pdb=" C8 A A1697 " ideal model delta sigma weight residual 1.373 1.330 0.043 2.00e-02 2.50e+03 4.73e+00 bond pdb=" N9 A A1832 " pdb=" C8 A A1832 " ideal model delta sigma weight residual 1.373 1.331 0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C5' U A 881 " pdb=" C4' U A 881 " ideal model delta sigma weight residual 1.508 1.539 -0.031 1.50e-02 4.44e+03 4.34e+00 ... (remaining 75052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 111151 2.94 - 5.87: 2017 5.87 - 8.81: 243 8.81 - 11.74: 25 11.74 - 14.68: 4 Bond angle restraints: 113440 Sorted by residual: angle pdb=" N ARG R 75 " pdb=" CA ARG R 75 " pdb=" C ARG R 75 " ideal model delta sigma weight residual 110.91 119.27 -8.36 1.17e+00 7.31e-01 5.10e+01 angle pdb=" O3' C A 880 " pdb=" P U A 881 " pdb=" O5' U A 881 " ideal model delta sigma weight residual 104.00 114.55 -10.55 1.50e+00 4.44e-01 4.94e+01 angle pdb=" C THR D 74 " pdb=" N ALA D 75 " pdb=" CA ALA D 75 " ideal model delta sigma weight residual 120.68 130.31 -9.63 1.52e+00 4.33e-01 4.01e+01 angle pdb=" N ILE C 133 " pdb=" CA ILE C 133 " pdb=" C ILE C 133 " ideal model delta sigma weight residual 113.47 107.57 5.90 1.01e+00 9.80e-01 3.41e+01 angle pdb=" C3' C A1652 " pdb=" O3' C A1652 " pdb=" P A A1653 " ideal model delta sigma weight residual 120.20 127.92 -7.72 1.50e+00 4.44e-01 2.65e+01 ... (remaining 113435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 41810 35.99 - 71.98: 5615 71.98 - 107.97: 589 107.97 - 143.96: 28 143.96 - 179.95: 34 Dihedral angle restraints: 48076 sinusoidal: 42167 harmonic: 5909 Sorted by residual: dihedral pdb=" C5' U A 837 " pdb=" C4' U A 837 " pdb=" C3' U A 837 " pdb=" O3' U A 837 " ideal model delta sinusoidal sigma weight residual 147.00 75.90 71.10 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' U A 837 " pdb=" C3' U A 837 " pdb=" C2' U A 837 " pdb=" C1' U A 837 " ideal model delta sinusoidal sigma weight residual -35.00 33.06 -68.06 1 8.00e+00 1.56e-02 9.40e+01 dihedral pdb=" O4' U A 633 " pdb=" C1' U A 633 " pdb=" N1 U A 633 " pdb=" C2 U A 633 " ideal model delta sinusoidal sigma weight residual -160.00 19.95 -179.95 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 48073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 13655 0.100 - 0.199: 882 0.199 - 0.299: 85 0.299 - 0.398: 30 0.398 - 0.498: 6 Chirality restraints: 14658 Sorted by residual: chirality pdb=" C3' G A 649 " pdb=" C4' G A 649 " pdb=" O3' G A 649 " pdb=" C2' G A 649 " both_signs ideal model delta sigma weight residual False -2.48 -1.98 -0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" C3' U A 837 " pdb=" C4' U A 837 " pdb=" O3' U A 837 " pdb=" C2' U A 837 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C3' U A2716 " pdb=" C4' U A2716 " pdb=" O3' U A2716 " pdb=" C2' U A2716 " both_signs ideal model delta sigma weight residual False -2.48 -1.99 -0.49 2.00e-01 2.50e+01 5.94e+00 ... (remaining 14655 not shown) Planarity restraints: 5266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 648 " 0.070 2.00e-02 2.50e+03 3.08e-02 2.84e+01 pdb=" N9 G A 648 " -0.075 2.00e-02 2.50e+03 pdb=" C8 G A 648 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G A 648 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 648 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 648 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G A 648 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G A 648 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A 648 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A 648 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G A 648 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G A 648 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 718 " 0.062 2.00e-02 2.50e+03 3.28e-02 2.42e+01 pdb=" N1 C A 718 " -0.072 2.00e-02 2.50e+03 pdb=" C2 C A 718 " -0.008 2.00e-02 2.50e+03 pdb=" O2 C A 718 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C A 718 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C A 718 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C A 718 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C A 718 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C A 718 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1245 " 0.062 2.00e-02 2.50e+03 2.68e-02 2.15e+01 pdb=" N9 G A1245 " -0.063 2.00e-02 2.50e+03 pdb=" C8 G A1245 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A1245 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A1245 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A1245 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G A1245 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G A1245 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G A1245 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G A1245 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A1245 " -0.017 2.00e-02 2.50e+03 pdb=" C4 G A1245 " -0.012 2.00e-02 2.50e+03 ... (remaining 5263 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 14421 2.78 - 3.31: 48959 3.31 - 3.84: 135131 3.84 - 4.37: 170975 4.37 - 4.90: 227943 Nonbonded interactions: 597429 Sorted by model distance: nonbonded pdb=" O2' U A 615 " pdb=" OP2 G A 617 " model vdw 2.251 3.040 nonbonded pdb=" O2' G A 906 " pdb=" O6 G A 963 " model vdw 2.256 3.040 nonbonded pdb=" O SER D 208 " pdb=" OG SER D 208 " model vdw 2.258 3.040 nonbonded pdb=" O2 C A1862 " pdb=" N2 G A2001 " model vdw 2.273 2.496 nonbonded pdb=" O2' G A 792 " pdb=" O2' G A 795 " model vdw 2.280 3.040 ... (remaining 597424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 2.180 Check model and map are aligned: 0.410 Set scattering table: 0.480 Process input model: 188.510 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.170 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:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 75057 Z= 0.485 Angle : 0.994 14.675 113440 Z= 0.503 Chirality : 0.055 0.498 14658 Planarity : 0.007 0.111 5266 Dihedral : 24.294 179.949 44280 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.81 % Favored : 92.09 % Rotamer: Outliers : 0.29 % Allowed : 8.12 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.10 % 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: -4.37 (0.14), residues: 2048 helix: -3.99 (0.14), residues: 451 sheet: -1.96 (0.23), residues: 431 loop : -2.89 (0.14), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 250 HIS 0.011 0.002 HIS Z 37 PHE 0.021 0.003 PHE D 119 TYR 0.016 0.002 TYR N 3 ARG 0.009 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 293 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 247 MET cc_start: 0.5526 (ppp) cc_final: 0.4859 (ttp) REVERT: N 23 ASP cc_start: 0.7892 (m-30) cc_final: 0.7688 (m-30) REVERT: N 76 ASN cc_start: 0.7971 (t0) cc_final: 0.7659 (t0) REVERT: R 52 THR cc_start: 0.8731 (m) cc_final: 0.8493 (p) REVERT: Y 4 ASN cc_start: 0.7801 (p0) cc_final: 0.7577 (p0) outliers start: 5 outliers final: 2 residues processed: 298 average time/residue: 1.6690 time to fit residues: 635.8741 Evaluate side-chains 244 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 186 optimal weight: 50.0000 chunk 114 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 348 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 chunk 259 optimal weight: 8.9990 chunk 403 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 HIS C 95 ASN ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 230 HIS ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 75 GLN E 121 ASN E 189 HIS J 131 HIS K 4 GLN L 38 GLN L 78 ASN P 32 HIS Q 37 GLN Q 81 HIS Q 107 ASN R 81 ASN R 86 GLN S 102 HIS U 64 HIS V 37 GLN V 58 ASN b 40 HIS b 55 ASN d 9 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.061460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.039952 restraints weight = 305059.597| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.28 r_work: 0.2670 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 75057 Z= 0.259 Angle : 0.636 9.161 113440 Z= 0.331 Chirality : 0.038 0.442 14658 Planarity : 0.005 0.110 5266 Dihedral : 24.642 179.650 40081 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.01 % Allowed : 13.87 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.16), residues: 2048 helix: -2.67 (0.19), residues: 467 sheet: -1.46 (0.24), residues: 435 loop : -2.43 (0.15), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 213 HIS 0.004 0.001 HIS R 74 PHE 0.011 0.001 PHE D 119 TYR 0.011 0.001 TYR C 83 ARG 0.010 0.001 ARG T 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 247 MET cc_start: 0.5021 (ppp) cc_final: 0.3934 (tpp) REVERT: D 103 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8520 (p) REVERT: K 18 GLU cc_start: 0.8852 (tt0) cc_final: 0.8564 (tp30) REVERT: K 54 LYS cc_start: 0.8479 (mttm) cc_final: 0.8077 (mmtp) REVERT: K 105 GLU cc_start: 0.8550 (mp0) cc_final: 0.8063 (mp0) REVERT: N 76 ASN cc_start: 0.9226 (t0) cc_final: 0.8839 (t0) REVERT: N 102 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8672 (mtp) REVERT: P 9 GLU cc_start: 0.8844 (pp20) cc_final: 0.8536 (pp20) REVERT: Q 102 ASP cc_start: 0.8789 (t0) cc_final: 0.8488 (t0) REVERT: R 28 GLU cc_start: 0.8491 (pm20) cc_final: 0.7561 (pm20) REVERT: R 31 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8611 (mp0) REVERT: R 52 THR cc_start: 0.8933 (m) cc_final: 0.8713 (p) REVERT: V 25 GLU cc_start: 0.7893 (tt0) cc_final: 0.7384 (pp20) REVERT: V 27 LYS cc_start: 0.7355 (mptt) cc_final: 0.6955 (mptt) REVERT: V 85 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7733 (mtmt) REVERT: Z 38 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8718 (mm-30) REVERT: Y 37 LEU cc_start: 0.8609 (tp) cc_final: 0.8389 (tp) outliers start: 35 outliers final: 17 residues processed: 281 average time/residue: 1.5545 time to fit residues: 568.2133 Evaluate side-chains 265 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 11 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 428 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 205 optimal weight: 30.0000 chunk 295 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 394 optimal weight: 0.3980 chunk 422 optimal weight: 20.0000 chunk 328 optimal weight: 2.9990 chunk 386 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 232 HIS ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS S 68 ASN Y 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.061490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040031 restraints weight = 304859.220| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.27 r_work: 0.2674 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 75057 Z= 0.240 Angle : 0.611 10.517 113440 Z= 0.317 Chirality : 0.037 0.352 14658 Planarity : 0.005 0.103 5266 Dihedral : 24.535 179.386 40079 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.88 % Allowed : 15.03 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.17), residues: 2048 helix: -1.89 (0.22), residues: 462 sheet: -1.09 (0.25), residues: 428 loop : -2.15 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 213 HIS 0.004 0.001 HIS Z 37 PHE 0.017 0.001 PHE V 38 TYR 0.011 0.001 TYR C 83 ARG 0.007 0.000 ARG Y 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 2.766 Fit side-chains revert: symmetry clash REVERT: C 247 MET cc_start: 0.5089 (ppp) cc_final: 0.3789 (tpp) REVERT: D 103 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8577 (p) REVERT: E 158 ASP cc_start: 0.8960 (p0) cc_final: 0.8623 (p0) REVERT: E 200 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: K 18 GLU cc_start: 0.8860 (tt0) cc_final: 0.8571 (tp30) REVERT: K 34 ASN cc_start: 0.8624 (t0) cc_final: 0.8282 (t0) REVERT: K 54 LYS cc_start: 0.8519 (mttm) cc_final: 0.8275 (mttm) REVERT: K 105 GLU cc_start: 0.8571 (mp0) cc_final: 0.7857 (mp0) REVERT: N 102 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8684 (mtp) REVERT: P 9 GLU cc_start: 0.8872 (pp20) cc_final: 0.8554 (pp20) REVERT: Q 102 ASP cc_start: 0.8817 (t0) cc_final: 0.8472 (t70) REVERT: R 28 GLU cc_start: 0.8502 (pm20) cc_final: 0.8165 (pm20) REVERT: V 25 GLU cc_start: 0.7926 (tt0) cc_final: 0.7403 (pp20) REVERT: V 27 LYS cc_start: 0.7412 (mptt) cc_final: 0.6884 (mptt) REVERT: V 52 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8278 (mmtp) REVERT: V 54 TYR cc_start: 0.7623 (m-10) cc_final: 0.7364 (m-10) REVERT: V 57 GLU cc_start: 0.7020 (pp20) cc_final: 0.6796 (pp20) REVERT: Z 39 ASP cc_start: 0.9286 (t0) cc_final: 0.9007 (t0) REVERT: Y 2 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7389 (tttm) REVERT: Y 5 GLU cc_start: 0.8910 (pp20) cc_final: 0.8626 (pp20) outliers start: 50 outliers final: 21 residues processed: 289 average time/residue: 1.5279 time to fit residues: 578.9417 Evaluate side-chains 269 residues out of total 1737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 102 MET Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 6 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain V residue 35 ASP Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain Z residue 55 SER Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 11 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 50.7922 > 50: distance: 70 - 76: 16.160 distance: 76 - 77: 18.334 distance: 77 - 78: 17.285 distance: 77 - 80: 12.580 distance: 78 - 79: 17.710 distance: 78 - 84: 17.432 distance: 80 - 81: 6.493 distance: 81 - 82: 9.913 distance: 81 - 83: 11.255 distance: 84 - 85: 7.377 distance: 85 - 86: 20.064 distance: 85 - 88: 7.846 distance: 86 - 87: 15.558 distance: 86 - 95: 22.301 distance: 88 - 89: 11.456 distance: 89 - 90: 8.779 distance: 89 - 91: 9.712 distance: 90 - 92: 10.701 distance: 91 - 93: 10.016 distance: 92 - 94: 7.650 distance: 93 - 94: 9.446 distance: 95 - 96: 10.603 distance: 96 - 97: 6.765 distance: 96 - 99: 12.505 distance: 97 - 98: 16.539 distance: 97 - 103: 14.157 distance: 99 - 100: 20.751 distance: 100 - 101: 38.850 distance: 101 - 102: 10.934 distance: 104 - 105: 3.767 distance: 104 - 107: 10.340 distance: 105 - 106: 27.365 distance: 105 - 112: 5.897 distance: 107 - 108: 20.639 distance: 108 - 109: 14.928 distance: 109 - 110: 21.557 distance: 110 - 111: 4.817 distance: 112 - 113: 11.000 distance: 113 - 114: 8.778 distance: 113 - 116: 9.153 distance: 114 - 115: 19.287 distance: 114 - 120: 15.152 distance: 116 - 117: 9.441 distance: 116 - 118: 12.414 distance: 117 - 119: 10.902 distance: 120 - 121: 3.361 distance: 121 - 122: 8.388 distance: 121 - 124: 6.642 distance: 122 - 123: 13.441 distance: 122 - 127: 4.891 distance: 124 - 125: 8.103 distance: 124 - 126: 10.329 distance: 127 - 128: 13.497 distance: 128 - 129: 18.562 distance: 128 - 131: 15.592 distance: 129 - 130: 35.202 distance: 129 - 133: 13.839 distance: 131 - 132: 26.568 distance: 133 - 134: 23.524 distance: 134 - 135: 6.339 distance: 134 - 137: 18.684 distance: 135 - 136: 25.996 distance: 135 - 141: 8.564 distance: 137 - 138: 5.731 distance: 138 - 139: 13.209 distance: 138 - 140: 8.749 distance: 141 - 142: 28.823 distance: 142 - 143: 11.178 distance: 142 - 145: 47.627 distance: 143 - 144: 8.600 distance: 143 - 146: 31.896 distance: 146 - 147: 14.172 distance: 146 - 152: 27.989 distance: 147 - 148: 22.011 distance: 147 - 150: 15.185 distance: 148 - 149: 27.895 distance: 148 - 153: 19.524 distance: 150 - 151: 41.184 distance: 151 - 152: 39.761