Starting phenix.real_space_refine on Mon Jul 6 07:16:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abf_15319/07_2026/8abf_15319.cif" } resolution = 2.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.402 46.555 29.358 1.00138.94 S ATOM 4207 SG CYS P 187 31.996 44.352 27.417 1.00153.13 S Time building chain proxies: 6.95, per 1000 atoms: 0.21 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 165.726, 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) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 21 sheets defined 61.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 52 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.761A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.527A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.910A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.791A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.821A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 347 through 365 removed outlier: 4.138A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 Processing helix chain 'P' and resid 58 through 89 removed outlier: 3.608A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 100 Processing helix chain 'P' and resid 131 through 139 Processing helix chain 'P' and resid 151 through 156 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix removed outlier: 3.513A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.253A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 111 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.579A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.518A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 155 removed outlier: 4.027A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.991A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.521A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.007A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.637A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.513A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.661A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.598A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.564A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.831A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 354 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.639A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.610A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 removed outlier: 4.007A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 139 " --> pdb=" O TRP D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.362A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.528A pdb=" N ILE I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'J' and resid 25 through 50 removed outlier: 3.563A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.747A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.675A pdb=" N ASN J 80 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.770A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.546A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.907A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.792A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.816A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 319 through 340 Processing helix chain 'N' and resid 347 through 365 removed outlier: 4.132A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 383 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.639A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.521A pdb=" N GLY R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 63 through 83 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.269A pdb=" N ALA Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 111 Processing helix chain 'Q' and resid 123 through 137 Processing helix chain 'Q' and resid 138 through 145 removed outlier: 3.579A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 80 removed outlier: 3.507A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 4.020A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 160 removed outlier: 3.574A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 157 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 removed outlier: 3.506A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 4.020A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 328 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.628A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.706A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 414 Processing helix chain 'L' and resid 419 through 429 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.669A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.602A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.554A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.839A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.766A pdb=" N VAL M 283 " --> pdb=" O GLN M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.892A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.585A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 removed outlier: 3.500A pdb=" N LEU M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 removed outlier: 4.012A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL O 139 " --> pdb=" O TRP O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 134 through 139' Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.360A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.541A pdb=" N ILE T 53 " --> pdb=" O GLN T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'U' and resid 25 through 50 removed outlier: 3.582A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.747A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.674A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.884A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 176 through 177 removed outlier: 3.515A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG P 202 " --> pdb=" O HIS P 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.541A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 3.975A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.179A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.621A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'J' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.541A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 307 through 308 removed outlier: 3.954A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.154A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.611A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1886 hydrogen bonds defined for protein. 5319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.76 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13535 1.40 - 1.61: 19622 1.61 - 1.82: 163 1.82 - 2.03: 27 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.460 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C18 XP4 J 101 " pdb=" O7 XP4 J 101 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 43757 3.97 - 7.94: 1413 7.94 - 11.91: 147 11.91 - 15.87: 27 15.87 - 19.84: 8 Bond angle restraints: 45352 Sorted by residual: angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 93.83 17.44 1.47e+00 4.63e-01 1.41e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.45 12.88 1.14e+00 7.69e-01 1.28e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 94.76 16.51 1.47e+00 4.63e-01 1.26e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.40 12.93 1.20e+00 6.94e-01 1.16e+02 angle pdb=" CG ARG O 289 " pdb=" CD ARG O 289 " pdb=" NE ARG O 289 " ideal model delta sigma weight residual 112.00 92.16 19.84 2.20e+00 2.07e-01 8.14e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 18544 31.82 - 63.65: 881 63.65 - 95.47: 88 95.47 - 127.29: 0 127.29 - 159.11: 2 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -103.26 -19.34 0 2.50e+00 1.60e-01 5.98e+01 dihedral pdb=" C GLU D 283 " pdb=" N GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta harmonic sigma weight residual -122.60 -103.42 -19.18 0 2.50e+00 1.60e-01 5.89e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -105.01 -17.59 0 2.50e+00 1.60e-01 4.95e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 4690 0.217 - 0.434: 262 0.434 - 0.651: 5 0.651 - 0.868: 3 0.868 - 1.085: 2 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB VAL C 146 " pdb=" CA VAL C 146 " pdb=" CG1 VAL C 146 " pdb=" CG2 VAL C 146 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.08 2.00e-01 2.50e+01 2.94e+01 chirality pdb=" CB4 CDL N 505 " pdb=" CB3 CDL N 505 " pdb=" CB6 CDL N 505 " pdb=" OB6 CDL N 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.64 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.71 -0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 76 " 0.347 9.50e-02 1.11e+02 1.59e-01 2.72e+01 pdb=" NE ARG R 76 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG R 76 " 0.057 2.00e-02 2.50e+03 pdb=" NH1 ARG R 76 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG R 76 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 76 " -0.341 9.50e-02 1.11e+02 1.56e-01 2.58e+01 pdb=" NE ARG G 76 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG G 76 " -0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG G 76 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG G 76 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.053 2.00e-02 2.50e+03 4.02e-02 2.43e+01 pdb=" CG HIS N 96 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.039 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 358 2.64 - 3.21: 29336 3.21 - 3.77: 53732 3.77 - 4.34: 78187 4.34 - 4.90: 121495 Nonbonded interactions: 283108 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.075 3.080 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.076 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.076 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.118 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.239 3.080 ... (remaining 283103 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'L' and resid 26 through 3002) } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.720 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9494 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 : 0.012 0.682 33385 Z= 0.823 Angle : 1.758 23.722 45365 Z= 1.081 Chirality : 0.114 1.085 4962 Planarity : 0.009 0.159 5700 Dihedral : 17.451 159.114 12014 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.22 % Allowed : 7.22 % Favored : 89.56 % Cbeta Deviations : 1.47 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.12), residues: 3955 helix: -0.78 (0.09), residues: 2145 sheet: 0.05 (0.25), residues: 351 loop : -0.62 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.003 ARG R 76 TYR 0.055 0.008 TYR O 120 PHE 0.063 0.008 PHE B 107 TRP 0.044 0.009 TRP L 474 HIS 0.022 0.005 HIS N 57 Details of bonding type rmsd/Z covalent geometry : bond 0.01042 / 0.64 (33367) covalent geometry : angle 1.75190 / 1.08 (45352) SS BOND : bond 0.02804 / 1.66 ( 5) SS BOND : angle 2.54062 / 1.34 ( 10) hydrogen bonds : bond 0.18287 / 12.34 ( 1886) hydrogen bonds : angle 6.86762 / 5.00 ( 5319) metal coordination : bond 0.07880 / 3.99 ( 4) metal coordination : angle 17.19427 / 9.14 ( 3) Misc. bond : bond 0.32626 / 16.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 474 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: P 106 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6582 (mmmt) REVERT: P 131 THR cc_start: 0.7604 (p) cc_final: 0.7262 (p) REVERT: P 134 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8431 (mm-30) REVERT: P 158 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6965 (mtpt) REVERT: P 178 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7041 (mm-30) REVERT: P 182 PHE cc_start: 0.7567 (m-80) cc_final: 0.7313 (m-80) REVERT: F 84 GLU cc_start: 0.8690 (tt0) cc_final: 0.8280 (tp30) REVERT: F 88 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7858 (mm-30) REVERT: F 131 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8951 (mm-40) REVERT: A 68 TYR cc_start: 0.8770 (m-80) cc_final: 0.8564 (m-80) REVERT: A 153 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7917 (ttt-90) REVERT: A 390 LYS cc_start: 0.9050 (tptt) cc_final: 0.8658 (mttp) REVERT: B 236 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7768 (tpp-160) REVERT: N 288 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8674 (tttt) REVERT: E 55 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7896 (p0) REVERT: L 48 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8721 (tp) REVERT: L 51 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8947 (p) REVERT: L 87 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8511 (mtt90) REVERT: L 97 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8894 (mm-30) REVERT: L 153 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7802 (ttt90) REVERT: M 16 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8495 (p) REVERT: M 236 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8243 (mmm160) REVERT: M 356 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8376 (t0) REVERT: S 78 GLU cc_start: 0.8853 (tt0) cc_final: 0.8585 (tm-30) REVERT: U 73 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8742 (mtt180) outliers start: 107 outliers final: 10 residues processed: 539 average time/residue: 0.8075 time to fit residues: 501.8086 Evaluate side-chains 353 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 332 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 90 ASN ** P 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN A 50 GLN A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN B 377 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS L 50 GLN L 332 ASN L 371 ASN M 87 HIS M 197 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.058029 restraints weight = 55445.587| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.66 r_work: 0.2612 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9363 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.429 33385 Z= 0.140 Angle : 0.633 16.133 45365 Z= 0.311 Chirality : 0.042 0.168 4962 Planarity : 0.004 0.039 5700 Dihedral : 11.991 132.017 4869 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.74 % Allowed : 10.38 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.13), residues: 3955 helix: 1.16 (0.11), residues: 2152 sheet: 0.37 (0.26), residues: 369 loop : 0.12 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 339 TYR 0.020 0.002 TYR D 237 PHE 0.023 0.002 PHE B 107 TRP 0.031 0.002 TRP C 156 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (33367) covalent geometry : angle 0.63179 / 0.31 (45352) SS BOND : bond 0.00228 / 0.13 ( 5) SS BOND : angle 0.62436 / 0.32 ( 10) hydrogen bonds : bond 0.05114 / 3.42 ( 1886) hydrogen bonds : angle 4.66971 / 3.39 ( 5319) metal coordination : bond 0.00518 / 0.26 ( 4) metal coordination : angle 4.71329 / 2.66 ( 3) Misc. bond : bond 0.24507 / 14.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 367 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 158 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6843 (mtpt) REVERT: P 216 PHE cc_start: 0.7109 (m-80) cc_final: 0.6432 (m-80) REVERT: G 115 GLU cc_start: 0.9008 (tt0) cc_final: 0.8798 (tt0) REVERT: F 84 GLU cc_start: 0.8759 (tt0) cc_final: 0.8485 (tp30) REVERT: F 96 HIS cc_start: 0.8870 (t-90) cc_final: 0.8570 (t-170) REVERT: F 103 GLU cc_start: 0.8747 (tp30) cc_final: 0.8458 (tm-30) REVERT: F 126 GLU cc_start: 0.9058 (mp0) cc_final: 0.8851 (mp0) REVERT: A 153 ARG cc_start: 0.8578 (ttp-110) cc_final: 0.8168 (ttt-90) REVERT: A 240 GLN cc_start: 0.8329 (mp10) cc_final: 0.8094 (pm20) REVERT: A 390 LYS cc_start: 0.9035 (tptt) cc_final: 0.8721 (mttp) REVERT: A 397 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 251 GLU cc_start: 0.8138 (pm20) cc_final: 0.7781 (pm20) REVERT: H 57 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8601 (tt) REVERT: R 33 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8946 (ttpt) REVERT: Q 84 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8422 (mt-10) REVERT: Q 95 LYS cc_start: 0.8779 (tptt) cc_final: 0.8520 (tttp) REVERT: Q 96 HIS cc_start: 0.8857 (t-90) cc_final: 0.8393 (t70) REVERT: Q 107 LYS cc_start: 0.9001 (tttp) cc_final: 0.8752 (mtpt) REVERT: Q 137 ASN cc_start: 0.8974 (m-40) cc_final: 0.8758 (m-40) REVERT: L 51 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8958 (p) REVERT: L 87 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7266 (mtp85) REVERT: L 97 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8785 (mm-30) REVERT: L 153 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8056 (ttt90) REVERT: M 16 SER cc_start: 0.8285 (m) cc_final: 0.7889 (p) REVERT: M 60 PHE cc_start: 0.9529 (OUTLIER) cc_final: 0.9058 (t80) REVERT: M 170 TYR cc_start: 0.8128 (p90) cc_final: 0.7741 (p90) REVERT: S 78 GLU cc_start: 0.8897 (tt0) cc_final: 0.8341 (tm-30) outliers start: 58 outliers final: 8 residues processed: 407 average time/residue: 0.7597 time to fit residues: 358.7024 Evaluate side-chains 338 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 322 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 384 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 HIS F 137 ASN B 316 GLN B 354 ASN B 377 ASN M 92 HIS M 316 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.055547 restraints weight = 55787.145| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.67 r_work: 0.2562 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9398 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.380 33385 Z= 0.199 Angle : 0.618 15.349 45365 Z= 0.303 Chirality : 0.044 0.153 4962 Planarity : 0.004 0.046 5700 Dihedral : 11.081 99.815 4830 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.74 % Allowed : 10.77 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.13), residues: 3955 helix: 1.67 (0.11), residues: 2139 sheet: 0.61 (0.26), residues: 363 loop : 0.45 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 55 TYR 0.020 0.002 TYR N 225 PHE 0.024 0.002 PHE L 334 TRP 0.016 0.002 TRP N 142 HIS 0.013 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (33367) covalent geometry : angle 0.61499 / 0.30 (45352) SS BOND : bond 0.00273 / 0.15 ( 5) SS BOND : angle 0.66481 / 0.33 ( 10) hydrogen bonds : bond 0.05336 / 3.59 ( 1886) hydrogen bonds : angle 4.46361 / 3.24 ( 5319) metal coordination : bond 0.01134 / 0.57 ( 4) metal coordination : angle 7.89624 / 4.53 ( 3) Misc. bond : bond 0.22783 / 12.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 116 VAL cc_start: 0.7354 (OUTLIER) cc_final: 0.7148 (m) REVERT: P 182 PHE cc_start: 0.7515 (m-80) cc_final: 0.7286 (m-80) REVERT: P 194 TYR cc_start: 0.8246 (m-80) cc_final: 0.7862 (m-80) REVERT: P 202 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7298 (ttp80) REVERT: G 112 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: F 84 GLU cc_start: 0.8788 (tt0) cc_final: 0.8519 (tp30) REVERT: F 88 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7873 (mm-30) REVERT: F 109 GLN cc_start: 0.9026 (mt0) cc_final: 0.8753 (mt0) REVERT: F 126 GLU cc_start: 0.9054 (mp0) cc_final: 0.8817 (mp0) REVERT: A 153 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8115 (ttt-90) REVERT: A 240 GLN cc_start: 0.8333 (mp10) cc_final: 0.7997 (pm20) REVERT: A 390 LYS cc_start: 0.9036 (tptt) cc_final: 0.8695 (mttp) REVERT: A 397 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 205 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 251 GLU cc_start: 0.8223 (pm20) cc_final: 0.7826 (pm20) REVERT: H 57 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8687 (tt) REVERT: J 10 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8532 (ttmp) REVERT: J 15 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8559 (ptmm) REVERT: E 55 ASP cc_start: 0.8245 (p0) cc_final: 0.7893 (p0) REVERT: Q 84 GLU cc_start: 0.8771 (tp30) cc_final: 0.8548 (tt0) REVERT: Q 95 LYS cc_start: 0.8787 (tptt) cc_final: 0.8541 (tttp) REVERT: Q 96 HIS cc_start: 0.8945 (t-90) cc_final: 0.8519 (t70) REVERT: Q 100 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8163 (mt-10) REVERT: Q 137 ASN cc_start: 0.8887 (m-40) cc_final: 0.8686 (m110) REVERT: L 51 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.8873 (p) REVERT: M 16 SER cc_start: 0.8317 (m) cc_final: 0.7988 (p) REVERT: M 139 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8941 (ttmm) REVERT: M 170 TYR cc_start: 0.8248 (p90) cc_final: 0.7782 (p90) REVERT: M 236 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7956 (mtp85) REVERT: O 248 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8371 (ttm) REVERT: S 78 GLU cc_start: 0.8902 (tt0) cc_final: 0.8372 (tm-30) outliers start: 58 outliers final: 19 residues processed: 376 average time/residue: 0.8295 time to fit residues: 360.6647 Evaluate side-chains 341 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 192 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 139 LYS Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 230 VAL Chi-restraints excluded: chain O residue 248 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5693 > 50: distance: 28 - 129: 26.535 distance: 31 - 126: 31.172 distance: 74 - 78: 10.250 distance: 78 - 79: 24.963 distance: 79 - 80: 20.238 distance: 79 - 82: 10.270 distance: 80 - 81: 27.921 distance: 80 - 87: 4.078 distance: 82 - 83: 4.228 distance: 83 - 84: 32.506 distance: 84 - 85: 6.109 distance: 84 - 86: 15.186 distance: 87 - 88: 5.804 distance: 88 - 89: 18.706 distance: 89 - 90: 8.026 distance: 89 - 91: 41.146 distance: 91 - 92: 16.445 distance: 92 - 93: 25.343 distance: 92 - 95: 22.491 distance: 93 - 94: 17.366 distance: 93 - 99: 21.482 distance: 95 - 96: 17.736 distance: 96 - 97: 15.059 distance: 96 - 98: 19.040 distance: 99 - 100: 15.763 distance: 99 - 105: 15.177 distance: 100 - 101: 24.503 distance: 100 - 103: 38.827 distance: 101 - 102: 18.411 distance: 101 - 106: 6.354 distance: 103 - 104: 25.012 distance: 104 - 105: 23.755 distance: 106 - 107: 12.920 distance: 107 - 108: 26.386 distance: 107 - 110: 28.284 distance: 108 - 109: 20.124 distance: 108 - 117: 19.522 distance: 110 - 111: 19.250 distance: 112 - 113: 16.408 distance: 113 - 114: 12.629 distance: 114 - 115: 22.875 distance: 114 - 116: 13.219 distance: 117 - 118: 14.257 distance: 118 - 119: 13.247 distance: 118 - 121: 10.001 distance: 119 - 120: 6.145 distance: 121 - 122: 14.021 distance: 122 - 123: 9.787 distance: 124 - 125: 4.419 distance: 126 - 127: 12.078 distance: 127 - 128: 15.922 distance: 127 - 130: 20.375 distance: 128 - 129: 17.416 distance: 128 - 137: 17.247 distance: 130 - 131: 8.689 distance: 131 - 132: 8.969 distance: 132 - 133: 11.377 distance: 133 - 134: 11.598 distance: 134 - 135: 11.174 distance: 134 - 136: 15.586 distance: 137 - 138: 13.449 distance: 137 - 143: 37.092 distance: 138 - 139: 3.266 distance: 139 - 140: 11.532 distance: 139 - 144: 56.457 distance: 141 - 142: 36.073 distance: 145 - 146: 38.132 distance: 146 - 147: 7.220 distance: 146 - 148: 26.642 distance: 148 - 149: 7.188 distance: 149 - 150: 18.928 distance: 149 - 152: 14.588 distance: 150 - 151: 27.197 distance: 150 - 157: 11.909 distance: 152 - 153: 7.258 distance: 154 - 155: 10.613 distance: 155 - 156: 7.276