Starting phenix.real_space_refine on Thu Sep 26 05:40:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/09_2024/6pvk_20491.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/09_2024/6pvk_20491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/09_2024/6pvk_20491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/09_2024/6pvk_20491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/09_2024/6pvk_20491.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvk_20491/09_2024/6pvk_20491.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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 2169 5.49 5 S 43 5.16 5 C 29531 2.51 5 N 11276 2.21 5 O 17535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 60554 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 46617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2169, 46617 Classifications: {'RNA': 2169} Modifications used: {'rna2p_pur': 214, 'rna2p_pyr': 104, 'rna3p_pur': 1062, 'rna3p_pyr': 789} Link IDs: {'rna2p': 318, 'rna3p': 1850} Chain breaks: 13 Chain: "C" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1680 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain: "D" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1264 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 1 Chain: "E" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1391 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1119 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "K" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 886 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "L" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 716 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 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: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "R" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 761 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 96} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 780 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain breaks: 1 Chain: "T" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 712 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 684 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 2 Chain: "b" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 414 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "Y" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 517 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "d" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 327 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 25.90, per 1000 atoms: 0.43 Number of scatterers: 60554 At special positions: 0 Unit cell: (207.089, 151.293, 223.184, 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 43 16.00 P 2169 15.00 O 17535 8.00 N 11276 7.00 C 29531 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: 10.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 29 sheets defined 25.0% alpha, 15.4% beta 537 base pairs and 1039 stacking pairs defined. Time for finding SS restraints: 23.48 Creating SS restraints... Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 201 removed outlier: 4.073A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.219A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.753A pdb=" N SER D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 69 removed outlier: 3.810A pdb=" N VAL D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.583A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 removed outlier: 3.624A pdb=" N ARG E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 43 " --> pdb=" O MET E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.758A pdb=" N LYS E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 146 removed outlier: 3.944A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.807A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 37 removed outlier: 4.318A pdb=" N GLU J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA J 35 " --> pdb=" O SER J 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 92 through 97 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.394A pdb=" N MET J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU J 102 " --> pdb=" O PRO J 98 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'K' and resid 111 through 118 removed outlier: 4.032A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER K 116 " --> pdb=" O MET K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 129 through 139 Processing helix chain 'N' and resid 9 through 23 removed outlier: 4.600A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 41 removed outlier: 3.784A pdb=" N GLU N 39 " --> pdb=" O THR N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 54 removed outlier: 3.811A pdb=" N THR N 49 " --> pdb=" O GLU N 45 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 4.386A pdb=" N TYR N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 11 removed outlier: 4.105A pdb=" N ILE P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 104 removed outlier: 3.607A pdb=" N ARG P 104 " --> pdb=" O TYR P 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 19 removed outlier: 4.335A pdb=" N LYS Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 36 Processing helix chain 'Q' and resid 36 through 41 Processing helix chain 'Q' and resid 44 through 49 Processing helix chain 'Q' and resid 51 through 56 Processing helix chain 'Q' and resid 57 through 70 removed outlier: 3.743A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 73 No H-bonds generated for 'chain 'Q' and resid 71 through 73' Processing helix chain 'Q' and resid 75 through 83 removed outlier: 3.651A pdb=" N GLY Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 112 removed outlier: 3.907A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 34 removed outlier: 3.720A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 removed outlier: 3.706A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 removed outlier: 3.966A 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 14 through 21 removed outlier: 3.515A pdb=" N MET T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 48 removed outlier: 3.979A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 15 removed outlier: 3.628A pdb=" N ARG b 14 " --> pdb=" O LYS b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 18 No H-bonds generated for 'chain 'b' and resid 16 through 18' Processing helix chain 'Y' and resid 2 through 6 removed outlier: 3.708A pdb=" N ILE Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 2 through 6' Processing helix chain 'Y' and resid 9 through 33 removed outlier: 3.835A pdb=" N GLU Y 13 " --> pdb=" O LEU Y 9 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL Y 18 " --> pdb=" O ILE Y 14 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Y 19 " --> pdb=" O GLU Y 15 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 61 removed outlier: 4.184A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 17 removed outlier: 4.006A pdb=" N LYS d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 27 through 38 removed outlier: 3.827A pdb=" N LEU d 31 " --> pdb=" O GLY d 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.505A pdb=" N LYS C 4 " --> pdb=" O THR C 18 " (cutoff:3.500A) 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: 6.463A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.729A 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: 3.506A pdb=" N ALA C 190 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 171 through 175 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.828A pdb=" N ASP D 180 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS D 189 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE D 176 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.786A pdb=" N ILE D 49 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 55 removed outlier: 6.036A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.934A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 123 through 126 removed outlier: 7.041A pdb=" N VAL E 155 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 123 through 125 Processing sheet with id=AB4, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'K' and resid 7 through 9 removed outlier: 7.095A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 110 through 111 Processing sheet with id=AB7, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.651A 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: 6.770A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 43 through 49 removed outlier: 7.368A pdb=" N THR P 28 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL P 89 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG P 30 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ILE P 87 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS P 32 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 61 through 68 removed outlier: 3.767A pdb=" N VAL P 64 " --> pdb=" O ARG P 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 12 through 14 Processing sheet with id=AC3, first strand: chain 'R' and resid 20 through 22 removed outlier: 3.555A pdb=" N LYS R 64 " --> pdb=" O LYS R 94 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE R 100 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL R 58 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 58 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 71 through 75 Processing sheet with id=AC5, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.372A pdb=" N SER S 101 " --> pdb=" O THR S 9 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR S 104 " --> pdb=" O ALA S 74 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AC7, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.696A pdb=" N GLU T 29 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N THR T 27 " --> pdb=" O PRO T 11 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 63 through 66 removed outlier: 3.666A pdb=" N TYR T 69 " --> pdb=" O VAL T 66 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.518A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 27 through 28 removed outlier: 3.618A pdb=" N LYS b 37 " --> pdb=" O THR b 28 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1265 hydrogen bonds 2026 hydrogen bond angles 0 basepair planarities 537 basepair parallelities 1039 stacking parallelities Total time for adding SS restraints: 60.17 Time building geometry restraints manager: 13.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6534 1.32 - 1.44: 29834 1.44 - 1.57: 25538 1.57 - 1.69: 4324 1.69 - 1.81: 79 Bond restraints: 66309 Sorted by residual: bond pdb=" CA HIS S 102 " pdb=" CB HIS S 102 " ideal model delta sigma weight residual 1.531 1.452 0.078 1.52e-02 4.33e+03 2.65e+01 bond pdb=" CB TRP Q 61 " pdb=" CG TRP Q 61 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.10e+00 bond pdb=" C5 G A2717 " pdb=" C6 G A2717 " ideal model delta sigma weight residual 1.419 1.373 0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" C5 G A1712 " pdb=" C6 G A1712 " ideal model delta sigma weight residual 1.419 1.373 0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" CB ARG d 34 " pdb=" CG ARG d 34 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.96e+00 ... (remaining 66304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.37: 100031 5.37 - 10.73: 268 10.73 - 16.10: 4 16.10 - 21.46: 7 21.46 - 26.83: 2 Bond angle restraints: 100312 Sorted by residual: angle pdb=" N HIS S 102 " pdb=" CA HIS S 102 " pdb=" C HIS S 102 " ideal model delta sigma weight residual 109.07 82.24 26.83 1.61e+00 3.86e-01 2.78e+02 angle pdb=" N ALA b 45 " pdb=" CA ALA b 45 " pdb=" C ALA b 45 " ideal model delta sigma weight residual 112.45 129.75 -17.30 1.39e+00 5.18e-01 1.55e+02 angle pdb=" C ARG D 84 " pdb=" CA ARG D 84 " pdb=" CB ARG D 84 " ideal model delta sigma weight residual 110.24 88.11 22.13 1.88e+00 2.83e-01 1.39e+02 angle pdb=" N ALA S 74 " pdb=" CA ALA S 74 " pdb=" C ALA S 74 " ideal model delta sigma weight residual 107.23 88.32 18.91 1.67e+00 3.59e-01 1.28e+02 angle pdb=" N ARG P 54 " pdb=" CA ARG P 54 " pdb=" C ARG P 54 " ideal model delta sigma weight residual 110.23 94.04 16.19 1.45e+00 4.76e-01 1.25e+02 ... (remaining 100307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 36240 35.98 - 71.97: 5514 71.97 - 107.95: 658 107.95 - 143.93: 25 143.93 - 179.91: 33 Dihedral angle restraints: 42470 sinusoidal: 37385 harmonic: 5085 Sorted by residual: dihedral pdb=" C ARG D 84 " pdb=" N ARG D 84 " pdb=" CA ARG D 84 " pdb=" CB ARG D 84 " ideal model delta harmonic sigma weight residual -122.60 -94.10 -28.50 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" O4' U A 892 " pdb=" C1' U A 892 " pdb=" N1 U A 892 " pdb=" C2 U A 892 " ideal model delta sinusoidal sigma weight residual 200.00 36.53 163.47 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' U A 478 " pdb=" C1' U A 478 " pdb=" N1 U A 478 " pdb=" C2 U A 478 " ideal model delta sinusoidal sigma weight residual 200.00 38.05 161.95 1 1.50e+01 4.44e-03 8.32e+01 ... (remaining 42467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 12374 0.111 - 0.221: 584 0.221 - 0.332: 32 0.332 - 0.443: 17 0.443 - 0.553: 1 Chirality restraints: 13008 Sorted by residual: chirality pdb=" CA ARG D 84 " pdb=" N ARG D 84 " pdb=" C ARG D 84 " pdb=" CB ARG D 84 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C1' G A1246 " pdb=" O4' G A1246 " pdb=" C2' G A1246 " pdb=" N9 G A1246 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' G A 377 " pdb=" C4' G A 377 " pdb=" O3' G A 377 " pdb=" C2' G A 377 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 13005 not shown) Planarity restraints: 4580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 179 " -0.040 2.00e-02 2.50e+03 1.94e-02 1.04e+01 pdb=" N9 A A 179 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A A 179 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A A 179 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A A 179 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A A 179 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A A 179 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 179 " -0.007 2.00e-02 2.50e+03 pdb=" C2 A A 179 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A A 179 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A 179 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1359 " -0.041 2.00e-02 2.50e+03 1.85e-02 1.03e+01 pdb=" N9 G A1359 " 0.044 2.00e-02 2.50e+03 pdb=" C8 G A1359 " 0.013 2.00e-02 2.50e+03 pdb=" N7 G A1359 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G A1359 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A1359 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G A1359 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A1359 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A1359 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A1359 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A1359 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A1359 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1712 " 0.042 2.00e-02 2.50e+03 1.82e-02 9.99e+00 pdb=" N9 G A1712 " -0.043 2.00e-02 2.50e+03 pdb=" C8 G A1712 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A1712 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A1712 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G A1712 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A1712 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A1712 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A1712 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G A1712 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A1712 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G A1712 " -0.004 2.00e-02 2.50e+03 ... (remaining 4577 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 25 2.08 - 2.78: 14689 2.78 - 3.49: 80159 3.49 - 4.19: 185383 4.19 - 4.90: 253285 Nonbonded interactions: 533541 Sorted by model distance: nonbonded pdb=" C2 U A 522 " pdb=" N6 A A 526 " model vdw 1.370 3.340 nonbonded pdb=" N2 G A1526 " pdb=" N2 G A1558 " model vdw 1.418 3.200 nonbonded pdb=" N3 U A 522 " pdb=" N6 A A 526 " model vdw 1.466 3.200 nonbonded pdb=" O2 U A 522 " pdb=" N6 A A 526 " model vdw 1.475 3.120 nonbonded pdb=" N2 G A 631 " pdb=" NZ LYS L 33 " model vdw 1.565 3.200 ... (remaining 533536 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: 2.960 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: 0.060 Extract box with map and model: 1.940 Check model and map are aligned: 0.350 Set scattering table: 0.460 Process input model: 151.910 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.160 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 : 0.010 0.108 66309 Z= 0.595 Angle : 1.026 26.826 100312 Z= 0.528 Chirality : 0.054 0.553 13008 Planarity : 0.005 0.079 4580 Dihedral : 25.564 179.914 39190 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 1.04 % Allowed : 10.31 % Favored : 88.66 % Rotamer: Outliers : 6.50 % Allowed : 14.54 % Favored : 78.95 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.15), residues: 1737 helix: -4.42 (0.12), residues: 431 sheet: -2.81 (0.25), residues: 317 loop : -2.95 (0.16), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 16 HIS 0.014 0.002 HIS C 53 PHE 0.030 0.003 PHE D 16 TYR 0.022 0.002 TYR J 97 ARG 0.020 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 455 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 ASN cc_start: 0.7852 (t0) cc_final: 0.7598 (t0) REVERT: C 102 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6380 (mtp-110) REVERT: C 116 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.6844 (mm) REVERT: C 177 ASN cc_start: 0.5305 (t0) cc_final: 0.4970 (t0) REVERT: C 197 ASN cc_start: 0.6962 (t0) cc_final: 0.6260 (t0) REVERT: C 198 GLU cc_start: 0.6766 (mp0) cc_final: 0.6562 (mp0) REVERT: D 164 MET cc_start: 0.8026 (ttp) cc_final: 0.7479 (ttm) REVERT: D 175 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6069 (tm-30) REVERT: E 39 MET cc_start: 0.7980 (tmm) cc_final: 0.7736 (tmm) REVERT: E 41 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.5700 (mmm160) REVERT: E 78 ILE cc_start: 0.7547 (tt) cc_final: 0.7346 (tp) REVERT: E 153 LEU cc_start: 0.6577 (mt) cc_final: 0.6133 (mt) REVERT: E 161 GLU cc_start: 0.7341 (tp30) cc_final: 0.7053 (tp30) REVERT: E 165 LEU cc_start: 0.7416 (mt) cc_final: 0.7185 (tp) REVERT: J 127 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5787 (mtp-110) REVERT: J 134 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8248 (mp0) REVERT: K 13 ASN cc_start: 0.5908 (p0) cc_final: 0.4956 (p0) REVERT: K 18 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6600 (tm-30) REVERT: K 23 LYS cc_start: 0.7212 (tptt) cc_final: 0.6852 (ttpp) REVERT: N 14 LYS cc_start: 0.7651 (tttp) cc_final: 0.6995 (ttpt) REVERT: N 27 ASN cc_start: 0.8312 (m-40) cc_final: 0.7524 (m-40) REVERT: N 28 GLU cc_start: 0.7960 (mp0) cc_final: 0.7063 (mp0) REVERT: N 39 GLU cc_start: 0.8143 (tp30) cc_final: 0.7940 (tp30) REVERT: N 46 LYS cc_start: 0.6976 (tttt) cc_final: 0.6185 (tttt) REVERT: N 84 PHE cc_start: 0.7702 (m-80) cc_final: 0.7130 (m-80) REVERT: N 92 GLU cc_start: 0.7511 (pm20) cc_final: 0.7308 (pm20) REVERT: P 66 LYS cc_start: 0.7694 (tttt) cc_final: 0.7126 (ptmm) REVERT: P 68 SER cc_start: 0.7938 (t) cc_final: 0.7417 (m) REVERT: P 71 VAL cc_start: 0.7741 (t) cc_final: 0.7128 (p) REVERT: P 86 LYS cc_start: 0.7354 (mttt) cc_final: 0.6637 (tptt) REVERT: Q 12 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8123 (mttm) REVERT: Q 16 LYS cc_start: 0.7873 (mttt) cc_final: 0.7560 (mttt) REVERT: Q 59 LYS cc_start: 0.7631 (mttt) cc_final: 0.7348 (ttmt) REVERT: Q 102 ASP cc_start: 0.5192 (OUTLIER) cc_final: 0.4926 (p0) REVERT: R 15 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7472 (mt-10) REVERT: R 18 GLN cc_start: 0.7531 (tt0) cc_final: 0.7006 (tt0) REVERT: R 24 LYS cc_start: 0.8007 (tttm) cc_final: 0.7543 (tttm) REVERT: R 86 GLN cc_start: 0.8015 (tt0) cc_final: 0.7585 (tt0) REVERT: R 98 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7348 (pp20) REVERT: S 4 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7634 (tttp) REVERT: S 11 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7845 (ttt-90) REVERT: S 15 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7974 (mtm110) REVERT: S 27 LYS cc_start: 0.6466 (mmtt) cc_final: 0.6102 (mttm) REVERT: S 64 MET cc_start: 0.6704 (mtm) cc_final: 0.5751 (mmp) REVERT: T 9 LYS cc_start: 0.8179 (mttt) cc_final: 0.7862 (mtpt) REVERT: T 10 ARG cc_start: 0.7851 (ptp-170) cc_final: 0.6780 (ptm160) REVERT: T 35 ASN cc_start: 0.8431 (m-40) cc_final: 0.8143 (m110) REVERT: T 40 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7532 (ttmm) REVERT: T 50 LYS cc_start: 0.8466 (mmtp) cc_final: 0.7632 (tttp) REVERT: T 69 TYR cc_start: 0.6784 (m-80) cc_final: 0.6537 (m-80) REVERT: U 10 MET cc_start: 0.5305 (mmm) cc_final: 0.5078 (ptt) REVERT: U 32 ARG cc_start: 0.7018 (mmt-90) cc_final: 0.6576 (mmt180) REVERT: U 60 GLU cc_start: 0.7420 (mp0) cc_final: 0.7164 (mp0) REVERT: U 84 LYS cc_start: 0.7357 (tptp) cc_final: 0.6861 (pttt) REVERT: U 96 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.4536 (mmtp) REVERT: b 46 CYS cc_start: 0.6381 (OUTLIER) cc_final: 0.5845 (p) REVERT: b 48 SER cc_start: 0.7857 (p) cc_final: 0.7580 (t) REVERT: Y 15 GLU cc_start: 0.8115 (tp30) cc_final: 0.7510 (tp30) REVERT: Y 16 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6987 (tm-30) REVERT: Y 19 LYS cc_start: 0.8096 (mttt) cc_final: 0.7605 (mtmt) REVERT: Y 52 ARG cc_start: 0.8297 (ptp-170) cc_final: 0.7991 (ptp90) REVERT: d 28 ARG cc_start: 0.7009 (ttm110) cc_final: 0.6753 (ptp-110) outliers start: 97 outliers final: 20 residues processed: 509 average time/residue: 0.6812 time to fit residues: 552.5096 Evaluate side-chains 344 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 318 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain E residue 24 PHE Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 35 THR Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain Q residue 108 GLN Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain U residue 96 LYS Chi-restraints excluded: chain b residue 37 LYS Chi-restraints excluded: chain b residue 46 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5797 > 50: distance: 32 - 50: 24.923 distance: 35 - 47: 25.048 distance: 43 - 47: 27.328 distance: 47 - 48: 21.044 distance: 48 - 49: 20.948 distance: 48 - 51: 29.350 distance: 49 - 50: 37.597 distance: 49 - 54: 23.035 distance: 51 - 52: 9.485 distance: 51 - 53: 19.693 distance: 54 - 55: 28.588 distance: 55 - 56: 21.135 distance: 55 - 58: 15.522 distance: 56 - 57: 14.910 distance: 56 - 62: 10.468 distance: 58 - 59: 9.230 distance: 58 - 60: 21.666 distance: 59 - 61: 19.256 distance: 62 - 63: 15.594 distance: 63 - 64: 19.131 distance: 63 - 66: 21.776 distance: 64 - 65: 32.780 distance: 64 - 70: 12.145 distance: 66 - 67: 34.229 distance: 66 - 68: 24.231 distance: 67 - 69: 28.147 distance: 70 - 71: 3.794 distance: 71 - 72: 29.666 distance: 71 - 74: 24.422 distance: 72 - 73: 27.378 distance: 72 - 81: 20.803 distance: 74 - 75: 3.416 distance: 75 - 76: 29.993 distance: 76 - 77: 15.597 distance: 77 - 78: 8.615 distance: 78 - 79: 17.040 distance: 78 - 80: 20.894 distance: 81 - 82: 47.005 distance: 82 - 83: 18.612 distance: 82 - 85: 17.613 distance: 83 - 84: 33.078 distance: 83 - 89: 22.132 distance: 85 - 86: 3.138 distance: 86 - 87: 20.647 distance: 86 - 88: 12.698 distance: 89 - 90: 44.367 distance: 90 - 91: 40.450 distance: 90 - 93: 19.882 distance: 91 - 92: 36.164 distance: 91 - 97: 22.199 distance: 93 - 94: 28.148 distance: 94 - 96: 47.667 distance: 97 - 98: 32.078 distance: 98 - 99: 12.119 distance: 98 - 101: 9.565 distance: 99 - 100: 37.668 distance: 99 - 106: 45.946 distance: 101 - 102: 45.797 distance: 102 - 103: 31.740 distance: 103 - 104: 48.595 distance: 104 - 105: 25.598 distance: 106 - 107: 11.986 distance: 107 - 108: 21.561 distance: 107 - 110: 20.346 distance: 108 - 109: 15.785 distance: 108 - 112: 14.679 distance: 110 - 111: 16.193 distance: 112 - 113: 17.559 distance: 112 - 118: 18.343 distance: 113 - 114: 28.408 distance: 113 - 116: 19.971 distance: 114 - 115: 48.299 distance: 114 - 119: 24.404 distance: 116 - 117: 17.729 distance: 117 - 118: 23.736 distance: 119 - 120: 10.128 distance: 120 - 121: 36.843 distance: 120 - 123: 33.556 distance: 121 - 122: 19.338 distance: 121 - 130: 23.799 distance: 123 - 124: 21.101 distance: 124 - 125: 30.665 distance: 125 - 126: 6.572 distance: 126 - 127: 26.872 distance: 127 - 128: 29.406 distance: 127 - 129: 10.819