Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 10 03:13:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/05_2023/8dk2_27481_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/05_2023/8dk2_27481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/05_2023/8dk2_27481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/05_2023/8dk2_27481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/05_2023/8dk2_27481_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk2_27481/05_2023/8dk2_27481_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians P 58 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 14634 2.51 5 N 4387 2.21 5 O 4595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 23727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3527 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2738 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5720 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 17, 'TRANS': 705} Chain breaks: 2 Chain: "D" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5680 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 17, 'TRANS': 700} Chain breaks: 2 Chain: "F" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 507 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "G" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "H" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "I" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.42, per 1000 atoms: 0.52 Number of scatterers: 23727 At special positions: 0 Unit cell: (168.67, 145.203, 288.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 58 15.00 Mg 2 11.99 O 4595 8.00 N 4387 7.00 C 14634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.73 Conformation dependent library (CDL) restraints added in 3.5 seconds 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 17 sheets defined 60.3% alpha, 8.0% beta 26 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 7.66 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 Processing helix chain 'A' and resid 20 through 26 Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.879A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 142 Processing helix chain 'A' and resid 149 through 169 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.829A pdb=" N SER A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.660A pdb=" N GLU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 257 through 271 removed outlier: 3.674A pdb=" N VAL A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 319 removed outlier: 3.861A pdb=" N VAL A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.765A pdb=" N LEU A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 410 through 424 Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'B' and resid 6 through 18 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 52 through 64 removed outlier: 4.170A pdb=" N ALA B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 3.630A pdb=" N ARG B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.656A pdb=" N LEU B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 142 Processing helix chain 'B' and resid 147 through 169 Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.645A pdb=" N SER B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 219 removed outlier: 3.872A pdb=" N GLU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.563A pdb=" N VAL B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 279 No H-bonds generated for 'chain 'B' and resid 276 through 279' Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 291 through 319 removed outlier: 3.534A pdb=" N VAL B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.796A pdb=" N LEU B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER B 341 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'C' and resid 49 through 59 removed outlier: 3.722A pdb=" N VAL C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 165 through 174 removed outlier: 4.014A pdb=" N MET C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 174 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 234 through 341 removed outlier: 4.488A pdb=" N SER C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Proline residue: C 264 - end of helix Proline residue: C 290 - end of helix Processing helix chain 'C' and resid 692 through 740 Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.604A pdb=" N ALA C 755 " --> pdb=" O GLU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 807 Processing helix chain 'C' and resid 819 through 849 Proline residue: C 823 - end of helix removed outlier: 4.301A pdb=" N LEU C 837 " --> pdb=" O THR C 833 " (cutoff:3.500A) Proline residue: C 838 - end of helix removed outlier: 4.248A pdb=" N GLU C 846 " --> pdb=" O LYS C 842 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN C 849 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 883 removed outlier: 3.836A pdb=" N ILE C 863 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR C 880 " --> pdb=" O ASP C 876 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN C 882 " --> pdb=" O ASN C 878 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG C 883 " --> pdb=" O SER C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 917 removed outlier: 4.058A pdb=" N ARG C 905 " --> pdb=" O GLU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 942 Processing helix chain 'C' and resid 948 through 954 Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.595A pdb=" N GLU C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1009 Processing helix chain 'C' and resid 1029 through 1042 Processing helix chain 'C' and resid 1056 through 1061 Processing helix chain 'C' and resid 1082 through 1087 removed outlier: 3.694A pdb=" N GLU C1087 " --> pdb=" O GLU C1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 59 removed outlier: 4.354A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.805A pdb=" N MET D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 Processing helix chain 'D' and resid 201 through 209 removed outlier: 3.570A pdb=" N ALA D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 223 Processing helix chain 'D' and resid 232 through 340 removed outlier: 3.888A pdb=" N PHE D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Proline residue: D 264 - end of helix removed outlier: 4.121A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Proline residue: D 290 - end of helix Processing helix chain 'D' and resid 692 through 740 Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'D' and resid 762 through 807 removed outlier: 3.973A pdb=" N LEU D 765 " --> pdb=" O THR D 762 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLY D 766 " --> pdb=" O ASP D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 834 Proline residue: D 823 - end of helix Processing helix chain 'D' and resid 836 through 849 removed outlier: 4.075A pdb=" N PHE D 844 " --> pdb=" O LYS D 840 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN D 849 " --> pdb=" O LEU D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 883 removed outlier: 3.711A pdb=" N SER D 879 " --> pdb=" O ASP D 875 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR D 880 " --> pdb=" O ASP D 876 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN D 882 " --> pdb=" O ASN D 878 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG D 883 " --> pdb=" O SER D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 917 Processing helix chain 'D' and resid 928 through 943 Processing helix chain 'D' and resid 948 through 954 Processing helix chain 'D' and resid 956 through 958 No H-bonds generated for 'chain 'D' and resid 956 through 958' Processing helix chain 'D' and resid 986 through 1004 Processing helix chain 'D' and resid 1029 through 1041 Processing helix chain 'D' and resid 1055 through 1061 removed outlier: 3.784A pdb=" N HIS D1060 " --> pdb=" O ARG D1056 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 62 Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'G' and resid 50 through 62 Processing helix chain 'G' and resid 71 through 89 removed outlier: 3.844A pdb=" N ASN G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 149 Processing helix chain 'G' and resid 162 through 173 Proline residue: G 167 - end of helix removed outlier: 3.850A pdb=" N TYR G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 196 removed outlier: 3.768A pdb=" N HIS G 196 " --> pdb=" O GLN G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 217 Processing helix chain 'G' and resid 220 through 234 Processing helix chain 'H' and resid 50 through 62 Processing helix chain 'H' and resid 71 through 78 Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 131 through 149 removed outlier: 4.204A pdb=" N LEU H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 173 removed outlier: 3.646A pdb=" N ILE H 166 " --> pdb=" O VAL H 162 " (cutoff:3.500A) Proline residue: H 167 - end of helix removed outlier: 4.278A pdb=" N TYR H 172 " --> pdb=" O GLN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 196 removed outlier: 3.590A pdb=" N HIS H 196 " --> pdb=" O GLN H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 214 No H-bonds generated for 'chain 'H' and resid 212 through 214' Processing helix chain 'H' and resid 220 through 235 Processing helix chain 'I' and resid 50 through 62 Processing helix chain 'I' and resid 71 through 91 removed outlier: 3.670A pdb=" N ASN I 80 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE I 81 " --> pdb=" O ALA I 77 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 83 " --> pdb=" O THR I 79 " (cutoff:3.500A) Proline residue: I 90 - end of helix Processing helix chain 'I' and resid 131 through 149 Processing helix chain 'I' and resid 162 through 173 Proline residue: I 167 - end of helix removed outlier: 3.831A pdb=" N TYR I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 196 removed outlier: 3.765A pdb=" N HIS I 196 " --> pdb=" O GLN I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 217 Processing helix chain 'I' and resid 220 through 234 Processing sheet with id= A, first strand: chain 'A' and resid 94 through 96 Processing sheet with id= B, first strand: chain 'A' and resid 466 through 470 removed outlier: 3.693A pdb=" N LEU A 482 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 468 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 94 through 96 Processing sheet with id= D, first strand: chain 'C' and resid 29 through 33 removed outlier: 7.232A pdb=" N THR C 113 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE C 18 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA C 111 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU C 20 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA C 109 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 112 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 116 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY C 124 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 1076 through 1081 removed outlier: 3.651A pdb=" N THR C 39 " --> pdb=" O ALA C1046 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C1018 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE C1049 " --> pdb=" O ILE C1018 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU C1020 " --> pdb=" O ILE C1049 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 890 through 898 removed outlier: 3.754A pdb=" N GLU C 976 " --> pdb=" O VAL C 966 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 968 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 974 " --> pdb=" O ASP C 968 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 29 through 33 removed outlier: 7.001A pdb=" N THR D 113 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE D 18 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA D 111 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 20 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA D 109 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.886A pdb=" N THR D 39 " --> pdb=" O ALA D1046 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D1048 " --> pdb=" O THR D 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 890 through 898 removed outlier: 3.980A pdb=" N GLU D 976 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 968 " --> pdb=" O LEU D 974 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 974 " --> pdb=" O ASP D 968 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 1064 through 1071 removed outlier: 3.902A pdb=" N ALA D1065 " --> pdb=" O LEU D1080 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= L, first strand: chain 'G' and resid 64 through 66 Processing sheet with id= M, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.746A pdb=" N ALA G 158 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 64 through 66 Processing sheet with id= O, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.164A pdb=" N ALA H 158 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 64 through 66 Processing sheet with id= Q, first strand: chain 'I' and resid 159 through 161 1304 hydrogen bonds defined for protein. 3549 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 8.50 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 8289 1.36 - 1.51: 5987 1.51 - 1.65: 9836 1.65 - 1.80: 49 1.80 - 1.95: 37 Bond restraints: 24198 Sorted by residual: bond pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.58e+00 bond pdb=" CA GLN D 263 " pdb=" C GLN D 263 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.26e-02 6.30e+03 1.32e+00 bond pdb=" CA GLN C 263 " pdb=" C GLN C 263 " ideal model delta sigma weight residual 1.521 1.535 -0.013 1.17e-02 7.31e+03 1.31e+00 bond pdb=" N LEU D 289 " pdb=" CA LEU D 289 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.30e+00 bond pdb=" C LEU D 289 " pdb=" O LEU D 289 " ideal model delta sigma weight residual 1.238 1.251 -0.014 1.28e-02 6.10e+03 1.13e+00 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.78: 853 106.78 - 113.61: 13548 113.61 - 120.43: 9100 120.43 - 127.25: 9100 127.25 - 134.08: 323 Bond angle restraints: 32924 Sorted by residual: angle pdb=" C ALA C 231 " pdb=" N PHE C 232 " pdb=" CA PHE C 232 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 angle pdb=" N LEU D 289 " pdb=" CA LEU D 289 " pdb=" C LEU D 289 " ideal model delta sigma weight residual 109.81 117.24 -7.43 2.21e+00 2.05e-01 1.13e+01 angle pdb=" N VAL C1073 " pdb=" CA VAL C1073 " pdb=" C VAL C1073 " ideal model delta sigma weight residual 113.20 110.46 2.74 9.60e-01 1.09e+00 8.12e+00 angle pdb=" C SER C 230 " pdb=" N ALA C 231 " pdb=" CA ALA C 231 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.69e+00 angle pdb=" CA LEU D 860 " pdb=" CB LEU D 860 " pdb=" CG LEU D 860 " ideal model delta sigma weight residual 116.30 124.15 -7.85 3.50e+00 8.16e-02 5.02e+00 ... (remaining 32919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 13944 26.56 - 53.12: 591 53.12 - 79.68: 53 79.68 - 106.23: 4 106.23 - 132.79: 1 Dihedral angle restraints: 14593 sinusoidal: 6377 harmonic: 8216 Sorted by residual: dihedral pdb=" O1A AGS C1201 " pdb=" O3A AGS C1201 " pdb=" PA AGS C1201 " pdb=" PB AGS C1201 " ideal model delta sinusoidal sigma weight residual -67.73 65.06 -132.79 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CA THR C1050 " pdb=" C THR C1050 " pdb=" N PRO C1051 " pdb=" CA PRO C1051 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA GLN A 18 " pdb=" C GLN A 18 " pdb=" N HIS A 19 " pdb=" CA HIS A 19 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 14590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2397 0.025 - 0.050: 776 0.050 - 0.075: 337 0.075 - 0.101: 132 0.101 - 0.126: 76 Chirality restraints: 3718 Sorted by residual: chirality pdb=" CA ILE D1049 " pdb=" N ILE D1049 " pdb=" C ILE D1049 " pdb=" CB ILE D1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE C1049 " pdb=" N ILE C1049 " pdb=" C ILE C1049 " pdb=" CB ILE C1049 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL A 485 " pdb=" N VAL A 485 " pdb=" C VAL A 485 " pdb=" CB VAL A 485 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 3715 not shown) Planarity restraints: 4130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 780 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C GLN D 780 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN D 780 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY D 781 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 783 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C LEU D 783 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU D 783 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS D 784 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 782 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C GLN D 782 " -0.030 2.00e-02 2.50e+03 pdb=" O GLN D 782 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 783 " 0.010 2.00e-02 2.50e+03 ... (remaining 4127 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 207 2.57 - 3.15: 19148 3.15 - 3.74: 37482 3.74 - 4.32: 47406 4.32 - 4.90: 77958 Nonbonded interactions: 182201 Sorted by model distance: nonbonded pdb=" NH2 ARG D 78 " pdb="MG MG D1202 " model vdw 1.988 2.250 nonbonded pdb=" N ALA C 69 " pdb="MG MG C1202 " model vdw 2.030 2.250 nonbonded pdb=" NE ARG D 78 " pdb="MG MG D1202 " model vdw 2.047 2.250 nonbonded pdb=" N SER C 70 " pdb="MG MG C1202 " model vdw 2.098 2.250 nonbonded pdb=" O ASN C 67 " pdb="MG MG C1202 " model vdw 2.102 2.170 ... (remaining 182196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 10 through 1083 or resid 1201 through 1202)) selection = chain 'D' } ncs_group { reference = (chain 'G' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) selection = chain 'H' selection = (chain 'I' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.690 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 66.260 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.002 0.039 24198 Z= 0.160 Angle : 0.466 7.846 32924 Z= 0.256 Chirality : 0.035 0.126 3718 Planarity : 0.004 0.044 4130 Dihedral : 13.545 132.792 9253 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.17), residues: 2798 helix: 2.62 (0.13), residues: 1708 sheet: -0.02 (0.33), residues: 279 loop : -0.97 (0.22), residues: 811 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 162 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 23 residues processed: 229 average time/residue: 0.3691 time to fit residues: 130.7602 Evaluate side-chains 102 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 2.692 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2036 time to fit residues: 12.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.2980 chunk 215 optimal weight: 0.0170 chunk 119 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 222 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 257 optimal weight: 20.0000 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 163 HIS B 6 GLN B 80 GLN B 133 GLN B 163 HIS B 240 ASN C 97 GLN C 99 HIS C 103 GLN C 258 GLN C 276 GLN C 336 HIS C 775 HIS ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 HIS C1060 HIS D 312 HIS D 712 GLN ** D 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 HIS ** D 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN G 57 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 116 GLN G 127 GLN G 149 GLN G 157 GLN G 196 HIS G 216 HIS H 57 GLN H 69 HIS H 233 GLN I 57 GLN I 80 ASN I 110 GLN I 127 GLN I 142 GLN I 149 GLN I 157 GLN I 168 GLN I 224 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 24198 Z= 0.157 Angle : 0.513 8.973 32924 Z= 0.269 Chirality : 0.037 0.235 3718 Planarity : 0.004 0.058 4130 Dihedral : 12.945 136.034 3682 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.17), residues: 2798 helix: 2.48 (0.13), residues: 1717 sheet: 0.13 (0.32), residues: 285 loop : -0.98 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 104 average time/residue: 0.4023 time to fit residues: 65.8116 Evaluate side-chains 71 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 2.738 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2034 time to fit residues: 4.1102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 258 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 144 ASN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 163 HIS ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 24198 Z= 0.246 Angle : 0.534 8.841 32924 Z= 0.281 Chirality : 0.037 0.195 3718 Planarity : 0.004 0.039 4130 Dihedral : 13.004 129.322 3682 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.78 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.17), residues: 2798 helix: 2.43 (0.13), residues: 1722 sheet: 0.02 (0.32), residues: 285 loop : -1.10 (0.22), residues: 791 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.3896 time to fit residues: 56.5868 Evaluate side-chains 64 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 0.3980 chunk 194 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 259 optimal weight: 30.0000 chunk 274 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 245 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN C 314 GLN C 775 HIS ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 722 GLN ** D 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 24198 Z= 0.278 Angle : 0.557 7.770 32924 Z= 0.295 Chirality : 0.038 0.145 3718 Planarity : 0.004 0.040 4130 Dihedral : 13.061 129.091 3682 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2798 helix: 2.24 (0.13), residues: 1720 sheet: -0.12 (0.32), residues: 285 loop : -1.06 (0.22), residues: 793 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.3979 time to fit residues: 51.2581 Evaluate side-chains 63 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.793 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 140 optimal weight: 0.2980 chunk 246 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN C 775 HIS ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 722 GLN ** D 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 24198 Z= 0.212 Angle : 0.508 8.705 32924 Z= 0.271 Chirality : 0.037 0.136 3718 Planarity : 0.004 0.038 4130 Dihedral : 13.019 129.981 3682 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2798 helix: 2.34 (0.13), residues: 1717 sheet: -0.12 (0.32), residues: 285 loop : -1.01 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3998 time to fit residues: 54.3092 Evaluate side-chains 63 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 274 optimal weight: 20.0000 chunk 228 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.0060 chunk 144 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 944 HIS D 722 GLN ** D 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 24198 Z= 0.154 Angle : 0.484 9.304 32924 Z= 0.257 Chirality : 0.036 0.133 3718 Planarity : 0.004 0.038 4130 Dihedral : 12.996 129.533 3682 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.17), residues: 2798 helix: 2.44 (0.13), residues: 1718 sheet: 0.00 (0.32), residues: 285 loop : -0.95 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.3954 time to fit residues: 52.8774 Evaluate side-chains 60 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 2.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 155 optimal weight: 0.0980 chunk 231 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 273 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 HIS ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 722 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 24198 Z= 0.145 Angle : 0.469 9.498 32924 Z= 0.249 Chirality : 0.036 0.129 3718 Planarity : 0.004 0.041 4130 Dihedral : 12.991 127.118 3682 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.17), residues: 2798 helix: 2.46 (0.13), residues: 1727 sheet: 0.07 (0.32), residues: 285 loop : -0.97 (0.22), residues: 786 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.4087 time to fit residues: 53.7930 Evaluate side-chains 61 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 215 optimal weight: 0.7980 chunk 249 optimal weight: 30.0000 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 HIS ** C 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 722 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 24198 Z= 0.167 Angle : 0.477 9.003 32924 Z= 0.254 Chirality : 0.036 0.128 3718 Planarity : 0.004 0.040 4130 Dihedral : 12.969 124.611 3682 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 96.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2798 helix: 2.48 (0.13), residues: 1729 sheet: 0.10 (0.33), residues: 285 loop : -0.98 (0.22), residues: 784 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5596 Ramachandran restraints generated. 2798 Oldfield, 0 Emsley, 2798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3945 time to fit residues: 49.0111 Evaluate side-chains 62 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 56.4408 > 50: distance: 63 - 69: 27.717 distance: 69 - 70: 20.244 distance: 70 - 71: 22.296 distance: 70 - 73: 20.792 distance: 71 - 72: 45.888 distance: 71 - 83: 39.656 distance: 73 - 74: 17.144 distance: 74 - 75: 17.776 distance: 74 - 76: 7.082 distance: 75 - 77: 5.127 distance: 76 - 78: 8.182 distance: 76 - 79: 6.102 distance: 77 - 78: 7.305 distance: 78 - 80: 3.628 distance: 79 - 81: 10.948 distance: 80 - 82: 20.702 distance: 81 - 82: 10.060 distance: 83 - 84: 26.176 distance: 83 - 89: 28.510 distance: 84 - 85: 17.205 distance: 84 - 87: 21.473 distance: 85 - 86: 27.784 distance: 85 - 90: 15.636 distance: 87 - 88: 45.308 distance: 88 - 89: 35.607 distance: 90 - 91: 19.818 distance: 91 - 92: 56.441 distance: 91 - 94: 27.089 distance: 92 - 93: 42.330 distance: 92 - 102: 38.920 distance: 94 - 95: 23.372 distance: 95 - 96: 31.956 distance: 95 - 97: 22.135 distance: 96 - 98: 19.409 distance: 97 - 99: 14.330 distance: 98 - 100: 23.242 distance: 99 - 100: 6.077 distance: 100 - 101: 12.023 distance: 102 - 103: 20.201 distance: 102 - 108: 37.621 distance: 103 - 104: 19.820 distance: 103 - 106: 22.736 distance: 104 - 105: 13.769 distance: 104 - 109: 9.358 distance: 106 - 107: 33.633 distance: 107 - 108: 25.697 distance: 109 - 110: 8.013 distance: 110 - 111: 26.864 distance: 110 - 113: 25.135 distance: 111 - 112: 20.003 distance: 111 - 115: 30.116 distance: 113 - 114: 40.517 distance: 115 - 116: 10.749 distance: 116 - 117: 18.797 distance: 116 - 119: 13.920 distance: 117 - 118: 23.754 distance: 117 - 124: 21.044 distance: 119 - 120: 13.198 distance: 121 - 122: 13.467 distance: 122 - 123: 8.056 distance: 124 - 125: 14.712 distance: 125 - 126: 23.004 distance: 125 - 128: 17.673 distance: 126 - 127: 21.316 distance: 126 - 133: 38.436 distance: 127 - 157: 10.621 distance: 128 - 129: 26.862 distance: 129 - 130: 14.374 distance: 130 - 131: 10.090 distance: 131 - 132: 4.530 distance: 133 - 134: 33.541 distance: 134 - 135: 34.716 distance: 134 - 137: 35.804 distance: 135 - 136: 33.254 distance: 135 - 138: 34.448 distance: 136 - 162: 10.849 distance: 138 - 139: 22.527 distance: 139 - 140: 21.708 distance: 139 - 142: 11.072 distance: 140 - 141: 26.781 distance: 140 - 149: 31.658 distance: 141 - 172: 23.242 distance: 142 - 143: 13.483 distance: 143 - 144: 17.885 distance: 143 - 145: 7.840 distance: 144 - 146: 15.921 distance: 145 - 147: 15.874 distance: 146 - 148: 20.275 distance: 147 - 148: 26.568 distance: 149 - 150: 5.612 distance: 150 - 151: 14.721 distance: 150 - 153: 19.491 distance: 151 - 152: 3.278 distance: 151 - 157: 9.633 distance: 152 - 179: 8.933 distance: 153 - 154: 20.894 distance: 154 - 155: 14.802 distance: 154 - 156: 9.528