Starting phenix.real_space_refine on Mon Jul 6 07:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abm_15326/07_2026/8abm_15326.cif" } resolution = 2.8 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= 0.002 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 130 residue(s): 0.02s 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: 32 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: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 287 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 138 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 337 Unusual residues: {'CDL': 3, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 188 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: "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 30.322 49.694 34.768 1.00105.62 S ATOM 4207 SG CYS P 187 32.789 46.843 33.790 1.00114.09 S Time building chain proxies: 6.17, per 1000 atoms: 0.19 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 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=2.05 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=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.5 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 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " 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: 198 helices and 21 sheets defined 61.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 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: 3.771A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'C' and resid 137 through 150 Processing helix chain 'C' and resid 151 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: 6.802A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.763A 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: 3.746A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.790A 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: 4.098A 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: 3.657A 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 99 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 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: 4.224A 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: 3.597A 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: 3.513A 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: 3.997A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 5.045A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.519A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.963A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.673A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.574A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.396A 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: 3.621A 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: 3.610A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.606A 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 removed outlier: 3.522A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.807A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.859A pdb=" N VAL B 283 " --> pdb=" O GLN B 280 " (cutoff:3.500A) 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: 3.705A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.592A 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: 3.939A pdb=" N LEU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.884A 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 220 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 56 removed outlier: 4.309A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 81 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: 3.527A 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: 3.535A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.831A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.643A 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: 3.778A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 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: 6.807A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.753A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.792A 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: 4.100A 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: 3.643A 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 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 84 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: 4.185A 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: 3.595A 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 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: 3.996A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.050A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 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: 3.519A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.965A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 329 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.675A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.650A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.413A 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: 3.624A 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: 3.603A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.599A 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 removed outlier: 3.529A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.817A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.852A 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: 3.829A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.602A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 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: 3.940A pdb=" N LEU O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) removed outlier: 3.901A 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 56 removed outlier: 4.305A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 56 through 81 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: 3.517A 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: 3.563A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.833A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.642A 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 removed outlier: 3.509A pdb=" N VAL P 103 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.894A 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: 3.606A 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: 6.525A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.323A 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: 3.950A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.833A 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: 6.568A pdb=" N LYS B 24 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY B 195 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA B 26 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.630A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.620A 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: 6.525A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.476A 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: 3.916A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.809A 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: 6.564A pdb=" N LYS M 24 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY M 195 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA M 26 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.637A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.611A 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 1881 hydrogen bonds defined for protein. 5304 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: 5.74 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13593 1.41 - 1.61: 19565 1.61 - 1.82: 173 1.82 - 2.03: 18 2.03 - 2.24: 18 Bond restraints: 33367 Sorted by residual: bond pdb=" C32 CDL A3001 " pdb=" C33 CDL A3001 " ideal model delta sigma weight residual 1.517 1.653 -0.136 1.70e-02 3.46e+03 6.38e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.607 -0.149 1.90e-02 2.77e+03 6.15e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.603 -0.145 1.90e-02 2.77e+03 5.86e+01 bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.465 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 42695 3.31 - 6.61: 2313 6.61 - 9.92: 276 9.92 - 13.23: 56 13.23 - 16.54: 12 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.81 10.52 1.14e+00 7.69e-01 8.52e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 98.08 13.19 1.47e+00 4.63e-01 8.05e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.64 10.69 1.20e+00 6.94e-01 7.94e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 95.46 16.54 2.20e+00 2.07e-01 5.65e+01 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 84.20 -8.54 1.14e+00 7.69e-01 5.61e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.30: 18524 32.30 - 64.59: 901 64.59 - 96.89: 88 96.89 - 129.18: 1 129.18 - 161.48: 1 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 -106.21 -16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -1.09 61.09 2 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -0.83 60.83 2 1.00e+01 1.00e-02 3.66e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 4551 0.198 - 0.396: 389 0.396 - 0.594: 16 0.594 - 0.792: 2 0.792 - 0.990: 4 Chirality restraints: 4962 Sorted by residual: 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 -1.58 -0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CB4 CDL C 507 " pdb=" CB3 CDL C 507 " pdb=" CB6 CDL C 507 " pdb=" OB6 CDL C 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.59 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CB4 CDL N 508 " pdb=" CB3 CDL N 508 " pdb=" CB6 CDL N 508 " pdb=" OB6 CDL N 508 " both_signs ideal model delta sigma weight residual False -2.57 -1.71 -0.86 2.00e-01 2.50e+01 1.87e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.012 2.00e-02 2.50e+03 3.33e-02 2.49e+01 pdb=" C2A HEC D 401 " -0.040 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.024 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.039 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.053 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.010 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.056 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.005 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM C 502 " 0.039 2.00e-02 2.50e+03 3.00e-02 2.02e+01 pdb=" C1B HEM C 502 " 0.025 2.00e-02 2.50e+03 pdb=" C2B HEM C 502 " 0.024 2.00e-02 2.50e+03 pdb=" C3B HEM C 502 " 0.012 2.00e-02 2.50e+03 pdb=" C4B HEM C 502 " 0.016 2.00e-02 2.50e+03 pdb=" CAB HEM C 502 " -0.014 2.00e-02 2.50e+03 pdb=" CHB HEM C 502 " -0.054 2.00e-02 2.50e+03 pdb=" CHC HEM C 502 " -0.042 2.00e-02 2.50e+03 pdb=" CMB HEM C 502 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 401 " 0.023 2.00e-02 2.50e+03 2.76e-02 1.71e+01 pdb=" C2C HEC D 401 " 0.018 2.00e-02 2.50e+03 pdb=" C3C HEC D 401 " -0.012 2.00e-02 2.50e+03 pdb=" C4C HEC D 401 " 0.009 2.00e-02 2.50e+03 pdb=" CAC HEC D 401 " -0.039 2.00e-02 2.50e+03 pdb=" CHC HEC D 401 " -0.055 2.00e-02 2.50e+03 pdb=" CHD HEC D 401 " 0.009 2.00e-02 2.50e+03 pdb=" CMC HEC D 401 " 0.030 2.00e-02 2.50e+03 pdb=" NC HEC D 401 " 0.017 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 229 2.62 - 3.19: 28447 3.19 - 3.76: 53227 3.76 - 4.33: 78638 4.33 - 4.90: 121609 Nonbonded interactions: 282150 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.055 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.057 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.069 3.120 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.164 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.226 3.080 ... (remaining 282145 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' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and resid 1 through 503) selection = (chain 'N' and resid 1 through 503) } 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' and resid 9 through 93) 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: 3.570 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.980 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9486 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 : 0.011 0.206 33382 Z= 0.651 Angle : 1.759 16.537 45365 Z= 1.095 Chirality : 0.116 0.990 4962 Planarity : 0.007 0.042 5700 Dihedral : 17.783 161.478 12014 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.40 % Rotamer: Outliers : 3.85 % Allowed : 7.67 % Favored : 88.48 % 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: -1.57 (0.12), residues: 3955 helix: -1.19 (0.09), residues: 2104 sheet: -0.19 (0.25), residues: 363 loop : -0.75 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 283 TYR 0.044 0.007 TYR B 166 PHE 0.048 0.006 PHE B 107 TRP 0.046 0.007 TRP A 474 HIS 0.028 0.004 HIS N 96 Details of bonding type rmsd/Z covalent geometry : bond 0.01081 / 0.65 (33367) covalent geometry : angle 1.75623 / 1.09 (45352) SS BOND : bond 0.02774 / 1.64 ( 5) SS BOND : angle 2.87388 / 1.49 ( 10) hydrogen bonds : bond 0.18921 / 12.64 ( 1881) hydrogen bonds : angle 6.99454 / 5.07 ( 5304) metal coordination : bond 0.08981 / 4.39 ( 4) metal coordination : angle 12.40312 / 6.70 ( 3) Misc. bond : bond 0.13582 / 6.98 ( 6) *********************** 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 475 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 347 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: P 115 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7729 (p0) REVERT: P 176 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8836 (pp) REVERT: P 182 PHE cc_start: 0.8122 (m-80) cc_final: 0.7679 (m-80) REVERT: P 221 THR cc_start: 0.8633 (p) cc_final: 0.8269 (p) REVERT: F 99 ASP cc_start: 0.9325 (m-30) cc_final: 0.9041 (m-30) REVERT: F 122 ASP cc_start: 0.8641 (p0) cc_final: 0.8430 (p0) REVERT: F 137 ASN cc_start: 0.9266 (m-40) cc_final: 0.9020 (m-40) REVERT: A 87 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7828 (mtp85) REVERT: B 170 TYR cc_start: 0.8658 (p90) cc_final: 0.8193 (p90) REVERT: D 248 MET cc_start: 0.9335 (ttp) cc_final: 0.8562 (ttp) REVERT: H 78 GLU cc_start: 0.9392 (tt0) cc_final: 0.9110 (tm-30) REVERT: J 55 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8650 (ttm110) REVERT: J 74 GLU cc_start: 0.9006 (mp0) cc_final: 0.8502 (pp20) REVERT: N 288 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7948 (ttpm) REVERT: Q 84 GLU cc_start: 0.9147 (tt0) cc_final: 0.8687 (tp30) REVERT: Q 88 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8667 (mm-30) REVERT: Q 96 HIS cc_start: 0.8887 (m-70) cc_final: 0.8313 (m-70) REVERT: Q 100 GLU cc_start: 0.9485 (OUTLIER) cc_final: 0.8927 (mp0) REVERT: Q 114 TYR cc_start: 0.8716 (t80) cc_final: 0.8452 (t80) REVERT: L 97 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.9085 (mm-30) REVERT: M 19 GLU cc_start: 0.9404 (OUTLIER) cc_final: 0.9116 (mm-30) REVERT: M 331 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8964 (pm20) REVERT: M 343 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9017 (mttt) REVERT: S 78 GLU cc_start: 0.9402 (tt0) cc_final: 0.9095 (mt-10) REVERT: T 31 MET cc_start: 0.9387 (mmp) cc_final: 0.9106 (mmm) REVERT: U 13 SER cc_start: 0.9241 (t) cc_final: 0.8996 (p) REVERT: U 55 ARG cc_start: 0.9017 (ttm-80) cc_final: 0.8815 (ttm-80) outliers start: 128 outliers final: 21 residues processed: 444 average time/residue: 0.7098 time to fit residues: 366.3567 Evaluate side-chains 292 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 262 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 331 GLU Chi-restraints excluded: chain M residue 343 LYS 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: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 G 54 ASN F 109 GLN F 132 HIS A 135 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 215 GLN B 377 ASN D 193 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN Q 109 GLN Q 132 HIS L 135 GLN L 332 ASN L 371 ASN M 87 HIS M 92 HIS M 215 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.045721 restraints weight = 82469.256| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 2.22 r_work: 0.2509 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2375 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9314 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.466 33382 Z= 0.157 Angle : 0.638 16.923 45365 Z= 0.314 Chirality : 0.042 0.192 4962 Planarity : 0.004 0.044 5700 Dihedral : 12.110 133.102 4877 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.65 % Allowed : 11.34 % Favored : 87.01 % 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: 0.81 (0.13), residues: 3955 helix: 1.01 (0.11), residues: 2157 sheet: 0.45 (0.26), residues: 368 loop : 0.01 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 144 TYR 0.020 0.002 TYR O 237 PHE 0.019 0.002 PHE L 334 TRP 0.026 0.001 TRP C 156 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (33367) covalent geometry : angle 0.63424 / 0.31 (45352) SS BOND : bond 0.00188 / 0.11 ( 5) SS BOND : angle 0.72506 / 0.39 ( 10) hydrogen bonds : bond 0.05183 / 3.45 ( 1881) hydrogen bonds : angle 4.72592 / 3.41 ( 5304) metal coordination : bond 0.02156 / 1.08 ( 4) metal coordination : angle 8.60819 / 4.56 ( 3) Misc. bond : bond 0.32958 / 16.31 ( 6) *********************** 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 336 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 281 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8151 (t0) cc_final: 0.7902 (t0) REVERT: G 120 ASP cc_start: 0.8905 (m-30) cc_final: 0.8703 (m-30) REVERT: F 95 LYS cc_start: 0.9132 (tppt) cc_final: 0.8669 (tppp) REVERT: F 99 ASP cc_start: 0.9132 (m-30) cc_final: 0.8882 (m-30) REVERT: F 107 LYS cc_start: 0.9383 (ttmm) cc_final: 0.9182 (mtpp) REVERT: F 114 TYR cc_start: 0.8564 (t80) cc_final: 0.8274 (t80) REVERT: F 115 ASP cc_start: 0.8857 (p0) cc_final: 0.8607 (p0) REVERT: F 122 ASP cc_start: 0.8507 (p0) cc_final: 0.8064 (p0) REVERT: F 126 GLU cc_start: 0.9189 (mp0) cc_final: 0.8944 (mp0) REVERT: F 137 ASN cc_start: 0.8837 (m-40) cc_final: 0.8568 (m-40) REVERT: A 87 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7666 (mtp85) REVERT: B 170 TYR cc_start: 0.8592 (p90) cc_final: 0.7855 (p90) REVERT: H 51 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.6486 (ptm160) REVERT: H 57 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8627 (tp) REVERT: H 78 GLU cc_start: 0.9121 (tt0) cc_final: 0.8706 (tm-30) REVERT: I 34 GLU cc_start: 0.8660 (tt0) cc_final: 0.8323 (pt0) REVERT: J 15 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8497 (mtmm) REVERT: N 288 LYS cc_start: 0.8024 (tttp) cc_final: 0.7815 (ttpm) REVERT: R 19 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8617 (tm) REVERT: R 97 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8696 (mt-10) REVERT: R 115 GLU cc_start: 0.8879 (tt0) cc_final: 0.8673 (tt0) REVERT: R 116 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8516 (ttmt) REVERT: Q 84 GLU cc_start: 0.8888 (tt0) cc_final: 0.8534 (tp30) REVERT: Q 95 LYS cc_start: 0.9278 (tppt) cc_final: 0.8968 (tptm) REVERT: Q 99 ASP cc_start: 0.9142 (m-30) cc_final: 0.8903 (p0) REVERT: Q 100 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8598 (mt-10) REVERT: Q 114 TYR cc_start: 0.8607 (t80) cc_final: 0.8355 (t80) REVERT: Q 122 ASP cc_start: 0.8698 (p0) cc_final: 0.8006 (p0) REVERT: Q 126 GLU cc_start: 0.9306 (mp0) cc_final: 0.9082 (mp0) REVERT: M 19 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8904 (mm-30) REVERT: M 292 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8591 (p) REVERT: O 248 MET cc_start: 0.9241 (ttp) cc_final: 0.8738 (ttm) REVERT: S 51 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.6702 (ptm160) REVERT: S 57 LEU cc_start: 0.9083 (mm) cc_final: 0.8802 (tp) REVERT: S 78 GLU cc_start: 0.9227 (tt0) cc_final: 0.8847 (mt-10) REVERT: U 13 SER cc_start: 0.9046 (t) cc_final: 0.8612 (p) REVERT: U 55 ARG cc_start: 0.8893 (ttm-80) cc_final: 0.8521 (ttm-80) outliers start: 55 outliers final: 9 residues processed: 320 average time/residue: 0.7462 time to fit residues: 278.0954 Evaluate side-chains 273 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 0.9980 chunk 317 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 384 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 85 GLN P 115 ASN P 157 GLN F 109 GLN A 317 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 377 ASN D 193 GLN Q 109 GLN L 317 GLN M 316 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.045775 restraints weight = 83201.494| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.21 r_work: 0.2521 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2389 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9326 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.377 33382 Z= 0.150 Angle : 0.566 15.353 45365 Z= 0.276 Chirality : 0.041 0.169 4962 Planarity : 0.004 0.052 5700 Dihedral : 10.927 102.556 4833 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.47 % Allowed : 12.09 % Favored : 86.44 % 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: 1.60 (0.14), residues: 3955 helix: 1.66 (0.11), residues: 2154 sheet: 0.73 (0.27), residues: 367 loop : 0.38 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 62 TYR 0.017 0.001 TYR N 225 PHE 0.018 0.001 PHE L 334 TRP 0.018 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (33367) covalent geometry : angle 0.56070 / 0.28 (45352) SS BOND : bond 0.00252 / 0.15 ( 5) SS BOND : angle 0.98181 / 0.48 ( 10) hydrogen bonds : bond 0.04496 / 2.98 ( 1881) hydrogen bonds : angle 4.40476 / 3.17 ( 5304) metal coordination : bond 0.01819 / 0.91 ( 4) metal coordination : angle 9.27311 / 5.03 ( 3) Misc. bond : bond 0.27549 / 13.38 ( 6) *********************** 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 320 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8210 (t0) cc_final: 0.7957 (t0) REVERT: G 123 GLU cc_start: 0.9012 (tt0) cc_final: 0.8774 (tt0) REVERT: F 99 ASP cc_start: 0.9159 (m-30) cc_final: 0.8830 (m-30) REVERT: F 107 LYS cc_start: 0.9341 (ttmm) cc_final: 0.8262 (mtpp) REVERT: F 122 ASP cc_start: 0.8600 (p0) cc_final: 0.8132 (p0) REVERT: F 137 ASN cc_start: 0.8830 (m-40) cc_final: 0.8466 (m-40) REVERT: A 461 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8110 (p0) REVERT: B 170 TYR cc_start: 0.8576 (p90) cc_final: 0.7830 (p90) REVERT: H 22 LYS cc_start: 0.9495 (ttpp) cc_final: 0.9292 (tttt) REVERT: H 51 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.6637 (ptm160) REVERT: H 57 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8684 (tp) REVERT: H 78 GLU cc_start: 0.9097 (tt0) cc_final: 0.8750 (tm-30) REVERT: I 34 GLU cc_start: 0.8666 (tt0) cc_final: 0.8288 (pt0) REVERT: J 74 GLU cc_start: 0.7493 (pp20) cc_final: 0.7249 (pp20) REVERT: N 287 ASP cc_start: 0.8171 (t70) cc_final: 0.7843 (t0) REVERT: R 97 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8724 (mt-10) REVERT: Q 84 GLU cc_start: 0.8899 (tt0) cc_final: 0.8545 (tp30) REVERT: Q 99 ASP cc_start: 0.9188 (m-30) cc_final: 0.8946 (p0) REVERT: Q 114 TYR cc_start: 0.8615 (t80) cc_final: 0.8405 (t80) REVERT: Q 122 ASP cc_start: 0.8736 (p0) cc_final: 0.8418 (p0) REVERT: S 51 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7281 (ptm160) REVERT: S 57 LEU cc_start: 0.9078 (mm) cc_final: 0.8827 (tp) REVERT: S 78 GLU cc_start: 0.9222 (tt0) cc_final: 0.8878 (mt-10) REVERT: U 13 SER cc_start: 0.9056 (t) cc_final: 0.8595 (p) outliers start: 49 outliers final: 12 residues processed: 302 average time/residue: 0.7070 time to fit residues: 249.5103 Evaluate side-chains 269 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 71 THR 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: 51.489 > 50: distance: 77 - 83: 10.060 distance: 83 - 84: 9.234 distance: 84 - 85: 12.512 distance: 84 - 87: 9.098 distance: 85 - 86: 24.706 distance: 85 - 89: 26.653 distance: 87 - 88: 31.637 distance: 89 - 90: 5.832 distance: 90 - 91: 13.979 distance: 90 - 93: 16.105 distance: 91 - 92: 20.941 distance: 91 - 97: 38.602 distance: 92 - 126: 27.983 distance: 93 - 94: 25.685 distance: 94 - 95: 25.570 distance: 95 - 96: 15.676 distance: 97 - 98: 24.335 distance: 98 - 99: 12.241 distance: 98 - 101: 14.014 distance: 99 - 100: 18.533 distance: 99 - 107: 5.653 distance: 101 - 102: 9.739 distance: 102 - 103: 9.251 distance: 102 - 104: 18.630 distance: 103 - 105: 5.334 distance: 104 - 106: 5.490 distance: 105 - 106: 12.788 distance: 107 - 108: 18.352 distance: 107 - 113: 28.577 distance: 108 - 109: 25.103 distance: 108 - 111: 12.794 distance: 109 - 110: 36.878 distance: 109 - 114: 10.702 distance: 110 - 144: 19.096 distance: 111 - 112: 19.239 distance: 112 - 113: 20.731 distance: 114 - 115: 4.579 distance: 115 - 116: 13.459 distance: 115 - 118: 18.017 distance: 116 - 117: 8.849 distance: 116 - 126: 9.377 distance: 117 - 155: 3.800 distance: 118 - 119: 9.805 distance: 119 - 120: 6.686 distance: 120 - 122: 15.292 distance: 121 - 123: 6.416 distance: 122 - 124: 8.612 distance: 123 - 124: 3.838 distance: 124 - 125: 8.347 distance: 126 - 127: 6.100 distance: 127 - 128: 5.085 distance: 127 - 130: 17.900 distance: 128 - 129: 11.961 distance: 128 - 138: 10.464 distance: 129 - 164: 19.020 distance: 130 - 131: 23.741 distance: 131 - 132: 16.433 distance: 132 - 134: 5.876 distance: 133 - 135: 5.533 distance: 134 - 136: 9.132 distance: 135 - 136: 6.376 distance: 136 - 137: 5.036 distance: 138 - 139: 10.380 distance: 139 - 140: 10.463 distance: 140 - 141: 5.248 distance: 140 - 144: 5.264 distance: 141 - 172: 14.475 distance: 142 - 143: 14.015 distance: 144 - 145: 12.666 distance: 145 - 146: 4.843 distance: 145 - 148: 8.639 distance: 146 - 147: 6.027 distance: 148 - 149: 3.954 distance: 149 - 150: 4.702 distance: 149 - 151: 5.877 distance: 150 - 152: 6.725 distance: 151 - 153: 11.316 distance: 152 - 154: 10.293 distance: 153 - 154: 11.172 distance: 155 - 156: 4.166 distance: 156 - 157: 4.545 distance: 156 - 159: 4.562 distance: 157 - 164: 7.290 distance: 159 - 160: 7.762 distance: 160 - 161: 6.158 distance: 161 - 162: 7.877 distance: 162 - 163: 9.876 distance: 164 - 165: 8.331 distance: 165 - 168: 8.582 distance: 166 - 167: 6.976 distance: 166 - 172: 4.420 distance: 167 - 195: 9.775 distance: 168 - 169: 9.207 distance: 169 - 170: 8.449 distance: 169 - 171: 11.044