Starting phenix.real_space_refine on Sun Jul 5 08:46:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q97_52947/07_2026/9q97_52947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q97_52947/07_2026/9q97_52947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q97_52947/07_2026/9q97_52947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q97_52947/07_2026/9q97_52947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q97_52947/07_2026/9q97_52947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q97_52947/07_2026/9q97_52947.map" } resolution = 4.6 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= 0.001 sd= 0.006 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: 7 Type Number sf(0) Gaussians Al 5 5.89 5 P 78 5.49 5 Mg 5 5.21 5 C 15724 2.51 5 N 5408 2.21 5 O 5584 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 26819 Number of models: 1 Model: "" Number of chains: 19 Chain: "M" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2060 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 367} Link IDs: {'PTRANS': 17, 'TRANS': 397} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1286 Unresolved non-hydrogen angles: 1642 Unresolved non-hydrogen dihedrals: 1032 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 34, 'ARG:plan': 27, 'GLU:plan': 34, 'ASN:plan1': 12, 'TYR:plan': 9, 'ASP:plan': 24, 'TRP:plan': 4, 'PHE:plan': 10, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 699 Chain: "A" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1130 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PTRANS': 9, 'TRANS': 219} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 667 Unresolved non-hydrogen angles: 856 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLU:plan': 25, 'PHE:plan': 3, 'ARG:plan': 16, 'ASP:plan': 14, 'GLN:plan1': 7, 'HIS:plan': 7, 'ASN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 349 Chain: "B" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1101 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 500 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLU:plan': 22, 'PHE:plan': 3, 'ARG:plan': 16, 'ASP:plan': 14, 'GLN:plan1': 7, 'HIS:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 332 Chain: "C" Number of atoms: 6599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 6599 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 1156} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved chain link angles: 56 Unresolved non-hydrogen bonds: 4146 Unresolved non-hydrogen angles: 5269 Unresolved non-hydrogen dihedrals: 3362 Unresolved non-hydrogen chiralities: 380 Planarities with less than four sites: {'TYR:plan': 43, 'GLU:plan': 121, 'ARG:plan': 90, 'ASP:plan': 92, 'PHE:plan': 44, 'GLN:plan1': 58, 'ASN:plan1': 51, 'HIS:plan': 19, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 2291 Chain: "D" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 6566 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 1120} Link IDs: {'PTRANS': 53, 'TRANS': 1280} Chain breaks: 5 Unresolved chain link angles: 53 Unresolved non-hydrogen bonds: 3990 Unresolved non-hydrogen angles: 5068 Unresolved non-hydrogen dihedrals: 3238 Unresolved non-hydrogen chiralities: 398 Planarities with less than four sites: {'ASP:plan': 76, 'PHE:plan': 34, 'GLN:plan1': 49, 'GLU:plan': 103, 'ARG:plan': 98, 'TRP:plan': 9, 'ASN:plan1': 46, 'TYR:plan': 34, 'HIS:plan': 20} Unresolved non-hydrogen planarities: 2087 Chain: "E" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 366 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 8, 'ASP:plan': 5, 'GLU:plan': 9, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "1" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1224 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 800 Unresolved non-hydrogen angles: 1023 Unresolved non-hydrogen dihedrals: 655 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 11, 'GLU:plan': 23, 'PHE:plan': 11, 'GLN:plan1': 8, 'HIS:plan': 5, 'ARG:plan': 22, 'TYR:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 460 Chain: "2" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1257 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 15, 'TRANS': 239} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 816 Unresolved non-hydrogen angles: 1043 Unresolved non-hydrogen dihedrals: 670 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 11, 'GLU:plan': 23, 'PHE:plan': 12, 'GLN:plan1': 8, 'HIS:plan': 5, 'ARG:plan': 22, 'TYR:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 466 Chain: "3" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1257 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 15, 'TRANS': 239} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 816 Unresolved non-hydrogen angles: 1043 Unresolved non-hydrogen dihedrals: 670 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 11, 'GLU:plan': 23, 'PHE:plan': 12, 'GLN:plan1': 8, 'HIS:plan': 5, 'ARG:plan': 22, 'TYR:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 466 Chain: "4" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1277 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 15, 'TRANS': 243} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 831 Unresolved non-hydrogen angles: 1062 Unresolved non-hydrogen dihedrals: 684 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLU:plan': 24, 'TYR:plan': 7, 'ASP:plan': 14, 'ASN:plan1': 11, 'PHE:plan': 12, 'GLN:plan1': 8, 'HIS:plan': 5, 'ARG:plan': 22, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 477 Chain: "5" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1267 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'PTRANS': 14, 'TRANS': 242} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1055 Unresolved non-hydrogen dihedrals: 678 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLU:plan': 24, 'TYR:plan': 7, 'ASP:plan': 14, 'ASN:plan1': 11, 'PHE:plan': 12, 'GLN:plan1': 8, 'HIS:plan': 5, 'ARG:plan': 22, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 477 Chain: "6" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1161 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 13, 'TRANS': 221} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 769 Unresolved non-hydrogen angles: 984 Unresolved non-hydrogen dihedrals: 630 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLU:plan': 23, 'TYR:plan': 7, 'ASP:plan': 14, 'ASN:plan1': 11, 'PHE:plan': 11, 'GLN:plan1': 5, 'HIS:plan': 3, 'ARG:plan': 21, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 440 Chain: "N" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 694 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 700 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY M 166 " occ=0.70 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.70 residue: pdb=" N GLY M 171 " occ=0.36 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.36 Time building chain proxies: 6.87, per 1000 atoms: 0.26 Number of scatterers: 26819 At special positions: 0 Unit cell: (209, 207.9, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) P 78 15.00 Al 5 13.00 Mg 5 11.99 F 15 9.00 O 5584 8.00 N 5408 7.00 C 15724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9528 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 52 sheets defined 42.0% alpha, 9.2% beta 29 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'M' and resid 17 through 26 Processing helix chain 'M' and resid 30 through 44 Processing helix chain 'M' and resid 121 through 131 Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 186 removed outlier: 3.635A pdb=" N ASP M 186 " --> pdb=" O ILE M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 206 Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.591A pdb=" N ASP M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 229 Processing helix chain 'M' and resid 231 through 240 Processing helix chain 'M' and resid 245 through 255 removed outlier: 3.972A pdb=" N ALA M 249 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 264 Processing helix chain 'M' and resid 300 through 309 Processing helix chain 'M' and resid 312 through 357 removed outlier: 5.976A pdb=" N ALA M 353 " --> pdb=" O GLU M 349 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE M 354 " --> pdb=" O GLN M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 362 Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.667A pdb=" N ALA M 373 " --> pdb=" O ASP M 369 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 400 through 402 No H-bonds generated for 'chain 'M' and resid 400 through 402' Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 449 removed outlier: 3.547A pdb=" N GLN M 449 " --> pdb=" O MET M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 465 Processing helix chain 'M' and resid 469 through 474 Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.577A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.608A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.765A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.636A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 212 through 233 removed outlier: 4.576A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 4.157A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.577A pdb=" N ALA C 51 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 162 through 166 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.872A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.733A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 removed outlier: 3.895A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.773A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.719A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.720A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.758A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.800A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.651A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 4.217A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 737 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.102A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.612A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 4.070A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 4.068A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.033A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1167 through 1176 removed outlier: 3.580A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.653A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.542A pdb=" N GLY C1282 " --> pdb=" O LEU C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.042A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.797A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 removed outlier: 3.619A pdb=" N GLN D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.612A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.825A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.526A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 265 through 284 removed outlier: 3.881A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 513 removed outlier: 3.675A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 538 removed outlier: 4.280A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.584A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.775A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.643A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.869A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.907A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 Processing helix chain 'D' and resid 768 through 775 Processing helix chain 'D' and resid 775 through 804 removed outlier: 4.417A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 875 Processing helix chain 'D' and resid 897 through 899 No H-bonds generated for 'chain 'D' and resid 897 through 899' Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.522A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1226 through 1245 removed outlier: 4.237A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1279 through 1291 Processing helix chain 'D' and resid 1308 through 1313 removed outlier: 3.548A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 4.157A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.118A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D1376 " --> pdb=" O ARG D1372 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 17 through 33 Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.658A pdb=" N GLY E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 Processing helix chain '1' and resid 12 through 26 Processing helix chain '1' and resid 42 through 53 Processing helix chain '1' and resid 54 through 57 removed outlier: 4.513A pdb=" N GLN 1 57 " --> pdb=" O SER 1 54 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 54 through 57' Processing helix chain '1' and resid 69 through 71 No H-bonds generated for 'chain '1' and resid 69 through 71' Processing helix chain '1' and resid 72 through 77 Processing helix chain '1' and resid 94 through 99 Processing helix chain '1' and resid 113 through 125 removed outlier: 4.037A pdb=" N GLU 1 125 " --> pdb=" O LEU 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 152 through 158 Processing helix chain '1' and resid 162 through 169 Processing helix chain '1' and resid 185 through 201 Processing helix chain '1' and resid 210 through 219 Processing helix chain '1' and resid 225 through 241 Processing helix chain '2' and resid 12 through 25 Processing helix chain '2' and resid 41 through 53 removed outlier: 3.587A pdb=" N ILE 2 45 " --> pdb=" O GLY 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 64 through 68 Processing helix chain '2' and resid 94 through 99 Processing helix chain '2' and resid 113 through 127 removed outlier: 3.767A pdb=" N ARG 2 122 " --> pdb=" O GLU 2 118 " (cutoff:3.500A) Processing helix chain '2' and resid 151 through 158 removed outlier: 3.570A pdb=" N MET 2 155 " --> pdb=" O ASP 2 151 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN 2 157 " --> pdb=" O PRO 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 162 through 169 Processing helix chain '2' and resid 178 through 183 Processing helix chain '2' and resid 185 through 201 Processing helix chain '2' and resid 210 through 220 Processing helix chain '2' and resid 225 through 239 Processing helix chain '3' and resid 12 through 26 Processing helix chain '3' and resid 42 through 53 removed outlier: 3.590A pdb=" N ALA 3 46 " --> pdb=" O LYS 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 57 Processing helix chain '3' and resid 66 through 68 No H-bonds generated for 'chain '3' and resid 66 through 68' Processing helix chain '3' and resid 72 through 79 Processing helix chain '3' and resid 94 through 100 Processing helix chain '3' and resid 113 through 126 Processing helix chain '3' and resid 151 through 159 Processing helix chain '3' and resid 162 through 169 removed outlier: 3.974A pdb=" N LEU 3 169 " --> pdb=" O LEU 3 165 " (cutoff:3.500A) Processing helix chain '3' and resid 178 through 183 Processing helix chain '3' and resid 185 through 201 Processing helix chain '3' and resid 210 through 219 Processing helix chain '3' and resid 225 through 241 removed outlier: 3.863A pdb=" N VAL 3 233 " --> pdb=" O LEU 3 229 " (cutoff:3.500A) Processing helix chain '4' and resid 14 through 26 Processing helix chain '4' and resid 41 through 53 Processing helix chain '4' and resid 70 through 79 removed outlier: 3.614A pdb=" N ASP 4 74 " --> pdb=" O GLU 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 94 through 99 Processing helix chain '4' and resid 113 through 124 removed outlier: 3.659A pdb=" N GLN 4 117 " --> pdb=" O PRO 4 113 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG 4 122 " --> pdb=" O GLU 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 151 through 159 Processing helix chain '4' and resid 162 through 169 Processing helix chain '4' and resid 178 through 183 removed outlier: 3.671A pdb=" N GLU 4 183 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 201 Processing helix chain '4' and resid 210 through 220 Processing helix chain '4' and resid 227 through 239 Processing helix chain '4' and resid 244 through 248 removed outlier: 3.552A pdb=" N ASP 4 248 " --> pdb=" O TYR 4 245 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 26 Processing helix chain '5' and resid 41 through 53 Processing helix chain '5' and resid 70 through 79 Processing helix chain '5' and resid 92 through 100 removed outlier: 4.108A pdb=" N PHE 5 96 " --> pdb=" O HIS 5 92 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA 5 99 " --> pdb=" O ARG 5 95 " (cutoff:3.500A) Processing helix chain '5' and resid 109 through 112 Processing helix chain '5' and resid 113 through 127 removed outlier: 3.515A pdb=" N TYR 5 126 " --> pdb=" O ARG 5 122 " (cutoff:3.500A) Processing helix chain '5' and resid 151 through 159 Processing helix chain '5' and resid 162 through 170 Processing helix chain '5' and resid 183 through 201 Processing helix chain '5' and resid 210 through 220 Processing helix chain '5' and resid 226 through 239 Processing helix chain '6' and resid 3 through 7 removed outlier: 3.610A pdb=" N ASN 6 7 " --> pdb=" O TYR 6 4 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 26 Processing helix chain '6' and resid 42 through 52 removed outlier: 3.636A pdb=" N ALA 6 46 " --> pdb=" O LYS 6 42 " (cutoff:3.500A) Processing helix chain '6' and resid 69 through 77 Processing helix chain '6' and resid 109 through 112 Processing helix chain '6' and resid 113 through 124 removed outlier: 3.525A pdb=" N ILE 6 124 " --> pdb=" O LEU 6 120 " (cutoff:3.500A) Processing helix chain '6' and resid 151 through 158 Processing helix chain '6' and resid 162 through 170 Processing helix chain '6' and resid 183 through 201 removed outlier: 4.194A pdb=" N MET 6 187 " --> pdb=" O GLU 6 183 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU 6 188 " --> pdb=" O SER 6 184 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 226 through 241 Processing sheet with id=AA1, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'M' and resid 276 through 281 Processing sheet with id=AA3, first strand: chain 'M' and resid 389 through 391 Processing sheet with id=AA4, first strand: chain 'M' and resid 406 through 408 Processing sheet with id=AA5, first strand: chain 'A' and resid 14 through 17 removed outlier: 4.913A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 105 removed outlier: 8.360A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA9, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.967A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.261A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.609A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.609A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 96 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.996A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 156 removed outlier: 3.540A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.590A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.590A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC3, first strand: chain 'C' and resid 717 through 718 removed outlier: 3.585A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 723 through 727 removed outlier: 7.299A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.575A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.583A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 839 removed outlier: 6.746A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.522A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 4.135A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C1340 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 105 Processing sheet with id=AD6, first strand: chain 'D' and resid 316 through 317 removed outlier: 3.535A pdb=" N THR D 317 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 355 through 357 removed outlier: 3.620A pdb=" N LEU D 449 " --> pdb=" O THR D 356 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.346A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 434 through 437 Processing sheet with id=AE1, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE2, first strand: chain 'D' and resid 552 through 559 removed outlier: 3.846A pdb=" N ASP D 558 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 809 through 811 removed outlier: 7.012A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.969A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 826 through 827 removed outlier: 3.883A pdb=" N GLU D 827 " --> pdb=" O ASP D 830 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE7, first strand: chain 'D' and resid 1265 through 1266 Processing sheet with id=AE8, first strand: chain '1' and resid 32 through 33 removed outlier: 5.999A pdb=" N VAL 1 32 " --> pdb=" O CYS 1 146 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE 1 61 " --> pdb=" O PHE 1 105 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP 1 107 " --> pdb=" O ILE 1 61 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU 1 63 " --> pdb=" O ASP 1 107 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '1' and resid 129 through 131 Processing sheet with id=AF1, first strand: chain '2' and resid 60 through 61 removed outlier: 5.796A pdb=" N ILE 2 61 " --> pdb=" O PHE 2 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP 2 107 " --> pdb=" O ILE 2 61 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR 2 148 " --> pdb=" O ILE 2 34 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '3' and resid 33 through 35 removed outlier: 6.996A pdb=" N ILE 3 34 " --> pdb=" O THR 3 148 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU 3 63 " --> pdb=" O ASP 3 107 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '4' and resid 33 through 35 Processing sheet with id=AF4, first strand: chain '4' and resid 60 through 62 removed outlier: 7.139A pdb=" N ILE 4 61 " --> pdb=" O PHE 4 105 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU 4 104 " --> pdb=" O VAL 4 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain '4' and resid 128 through 129 Processing sheet with id=AF6, first strand: chain '5' and resid 105 through 107 removed outlier: 3.595A pdb=" N LEU 5 106 " --> pdb=" O VAL 5 145 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU 5 33 " --> pdb=" O VAL 5 174 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '6' and resid 104 through 107 removed outlier: 3.732A pdb=" N THR 6 148 " --> pdb=" O ILE 6 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU 6 33 " --> pdb=" O VAL 6 174 " (cutoff:3.500A) 1539 hydrogen bonds defined for protein. 4371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 5195 1.30 - 1.39: 5612 1.39 - 1.47: 5482 1.47 - 1.55: 10510 1.55 - 1.64: 165 Bond restraints: 26964 Sorted by residual: bond pdb=" C TRP 1 222 " pdb=" O TRP 1 222 " ideal model delta sigma weight residual 1.235 1.255 -0.020 4.70e-03 4.53e+04 1.82e+01 bond pdb=" N LEU M 9 " pdb=" CA LEU M 9 " ideal model delta sigma weight residual 1.454 1.502 -0.048 1.18e-02 7.18e+03 1.69e+01 bond pdb=" C3' DG N -29 " pdb=" C2' DG N -29 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C3' DA N -12 " pdb=" C2' DA N -12 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DC N -13 " pdb=" C2' DC N -13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 26959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 37637 3.95 - 7.89: 91 7.89 - 11.84: 3 11.84 - 15.79: 0 15.79 - 19.73: 1 Bond angle restraints: 37732 Sorted by residual: angle pdb=" C ILE C1079 " pdb=" N ASN C1080 " pdb=" CA ASN C1080 " ideal model delta sigma weight residual 120.94 140.67 -19.73 1.90e+00 2.77e-01 1.08e+02 angle pdb=" C SER B 50 " pdb=" N MET B 51 " pdb=" CA MET B 51 " ideal model delta sigma weight residual 122.56 131.15 -8.59 1.34e+00 5.57e-01 4.11e+01 angle pdb=" O4' DG T 4 " pdb=" C4' DG T 4 " pdb=" C3' DG T 4 " ideal model delta sigma weight residual 106.00 102.51 3.49 6.00e-01 2.78e+00 3.39e+01 angle pdb=" CA ARG M 8 " pdb=" C ARG M 8 " pdb=" O ARG M 8 " ideal model delta sigma weight residual 121.36 116.36 5.00 1.06e+00 8.90e-01 2.22e+01 angle pdb=" C ALA D 657 " pdb=" N GLU D 658 " pdb=" CA GLU D 658 " ideal model delta sigma weight residual 120.28 113.59 6.69 1.44e+00 4.82e-01 2.16e+01 ... (remaining 37727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 15023 31.79 - 63.57: 367 63.57 - 95.36: 19 95.36 - 127.15: 3 127.15 - 158.93: 4 Dihedral angle restraints: 15416 sinusoidal: 786 harmonic: 14630 Sorted by residual: dihedral pdb=" CA GLY D 351 " pdb=" C GLY D 351 " pdb=" N ARG D 352 " pdb=" CA ARG D 352 " ideal model delta harmonic sigma weight residual 180.00 146.91 33.09 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" O2A ADP 1 601 " pdb=" O3A ADP 1 601 " pdb=" PA ADP 1 601 " pdb=" PB ADP 1 601 " ideal model delta sinusoidal sigma weight residual -60.00 68.58 -128.57 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" CA ARG D 339 " pdb=" C ARG D 339 " pdb=" N GLN D 340 " pdb=" CA GLN D 340 " ideal model delta harmonic sigma weight residual 180.00 -149.66 -30.34 0 5.00e+00 4.00e-02 3.68e+01 ... (remaining 15413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3634 0.044 - 0.088: 1032 0.088 - 0.131: 362 0.131 - 0.175: 24 0.175 - 0.219: 4 Chirality restraints: 5056 Sorted by residual: chirality pdb=" CA GLU D 666 " pdb=" N GLU D 666 " pdb=" C GLU D 666 " pdb=" CB GLU D 666 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA GLU D 658 " pdb=" N GLU D 658 " pdb=" C GLU D 658 " pdb=" CB GLU D 658 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO C 43 " pdb=" N PRO C 43 " pdb=" C PRO C 43 " pdb=" CB PRO C 43 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 5053 not shown) Planarity restraints: 5176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC T 33 " 0.004 2.00e-02 2.50e+03 1.74e-02 6.80e+00 pdb=" N1 DC T 33 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DC T 33 " 0.042 2.00e-02 2.50e+03 pdb=" O2 DC T 33 " -0.026 2.00e-02 2.50e+03 pdb=" N3 DC T 33 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC T 33 " 0.010 2.00e-02 2.50e+03 pdb=" N4 DC T 33 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC T 33 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC T 33 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 7 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C LEU M 7 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU M 7 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG M 8 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 656 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C GLU D 656 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU D 656 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA D 657 " 0.013 2.00e-02 2.50e+03 ... (remaining 5173 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 17 2.35 - 2.99: 14133 2.99 - 3.62: 40441 3.62 - 4.26: 46326 4.26 - 4.90: 74224 Nonbonded interactions: 175141 Sorted by model distance: nonbonded pdb=" O3B ADP 3 601 " pdb="MG MG 3 603 " model vdw 1.711 2.170 nonbonded pdb=" O3B ADP 4 601 " pdb="MG MG 4 602 " model vdw 1.956 2.170 nonbonded pdb=" F3 AF3 1 602 " pdb="MG MG 1 603 " model vdw 1.986 2.120 nonbonded pdb=" O2B ADP 2 601 " pdb="MG MG 2 603 " model vdw 2.022 2.170 nonbonded pdb=" O1B ADP 1 601 " pdb="MG MG 1 603 " model vdw 2.023 2.170 ... (remaining 175136 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 '1' and (resid 6 through 79 or resid 93 through 132 or resid 141 through \ 258)) selection = (chain '2' and (resid 6 through 79 or resid 93 through 132 or resid 141 through \ 258)) selection = (chain '3' and (resid 6 through 79 or resid 93 through 132 or resid 141 through \ 258)) selection = (chain '4' and (resid 6 through 79 or resid 93 through 132 or resid 141 through \ 258)) selection = (chain '5' and (resid 6 through 79 or resid 93 through 132 or resid 141 through \ 258)) selection = (chain '6' and resid 6 through 258) } ncs_group { reference = (chain 'A' and (resid 5 through 159 or resid 172 through 233)) selection = (chain 'B' and resid 5 through 233) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 32.420 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 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 : 0.007 0.635 26975 Z= 0.663 Angle : 0.666 19.732 37732 Z= 0.452 Chirality : 0.045 0.219 5056 Planarity : 0.002 0.025 5176 Dihedral : 14.612 158.934 5888 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.62 (0.12), residues: 5079 helix: 1.66 (0.13), residues: 1878 sheet: -1.12 (0.23), residues: 470 loop : -1.88 (0.11), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR M 112 PHE 0.000 0.000 PHE M 133 TRP 0.000 0.000 TRP M 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.23 (26964) covalent geometry : angle 0.66601 / 0.45 (37732) hydrogen bonds : bond 0.16559 / 12.71 ( 1608) hydrogen bonds : angle 5.81738 / 4.44 ( 4519) Misc. bond : bond 0.30701 / 22.88 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1129 time to fit residues: 27.5501 Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 265 optimal weight: 20.0000 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 50.0000 chunk 366 optimal weight: 40.0000 chunk 223 optimal weight: 0.0670 chunk 142 optimal weight: 8.9990 overall best weight: 8.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.066334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051519 restraints weight = 266346.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051922 restraints weight = 196758.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.052570 restraints weight = 161903.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.052776 restraints weight = 134732.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053123 restraints weight = 120426.880| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26975 Z= 0.250 Angle : 0.640 8.769 37732 Z= 0.381 Chirality : 0.046 0.263 5056 Planarity : 0.003 0.018 5176 Dihedral : 14.746 157.392 5888 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.79 (0.12), residues: 5079 helix: 1.28 (0.12), residues: 2004 sheet: -1.18 (0.24), residues: 458 loop : -1.94 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR M 112 PHE 0.000 0.000 PHE M 133 TRP 0.000 0.000 TRP M 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.25 (26964) covalent geometry : angle 0.63961 / 0.38 (37732) hydrogen bonds : bond 0.06544 / 4.99 ( 1608) hydrogen bonds : angle 4.90843 / 3.74 ( 4519) Misc. bond : bond 0.01531 / 1.13 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1052 time to fit residues: 26.0287 Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 280 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 199 optimal weight: 30.0000 chunk 389 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 442 optimal weight: 40.0000 chunk 281 optimal weight: 7.9990 chunk 236 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 chunk 395 optimal weight: 50.0000 chunk 385 optimal weight: 50.0000 overall best weight: 12.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048075 restraints weight = 278381.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048494 restraints weight = 205270.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049009 restraints weight = 166626.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049182 restraints weight = 141305.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049199 restraints weight = 127290.918| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26975 Z= 0.308 Angle : 0.776 12.830 37732 Z= 0.465 Chirality : 0.047 0.269 5056 Planarity : 0.004 0.026 5176 Dihedral : 15.494 171.182 5888 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.29 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.11), residues: 5079 helix: 0.33 (0.11), residues: 2017 sheet: -1.53 (0.24), residues: 424 loop : -2.29 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR M 112 PHE 0.000 0.000 PHE M 133 TRP 0.000 0.000 TRP M 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.31 (26964) covalent geometry : angle 0.77614 / 0.46 (37732) hydrogen bonds : bond 0.08461 / 6.44 ( 1608) hydrogen bonds : angle 5.92427 / 4.52 ( 4519) Misc. bond : bond 0.01085 / 0.81 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1032 time to fit residues: 25.4794 Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 237 optimal weight: 30.0000 chunk 104 optimal weight: 50.0000 chunk 288 optimal weight: 0.8980 chunk 126 optimal weight: 50.0000 chunk 379 optimal weight: 10.0000 chunk 447 optimal weight: 40.0000 chunk 135 optimal weight: 40.0000 chunk 277 optimal weight: 30.0000 chunk 186 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 overall best weight: 18.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.059845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045945 restraints weight = 285885.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.046296 restraints weight = 209289.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046790 restraints weight = 171669.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047100 restraints weight = 142768.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047346 restraints weight = 125769.338| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 26975 Z= 0.448 Angle : 0.966 15.055 37732 Z= 0.582 Chirality : 0.052 0.350 5056 Planarity : 0.006 0.031 5176 Dihedral : 16.362 163.781 5888 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.82 % Favored : 86.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.99 (0.11), residues: 5079 helix: -0.98 (0.10), residues: 1994 sheet: -2.21 (0.24), residues: 398 loop : -2.82 (0.11), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR M 112 PHE 0.000 0.000 PHE M 133 TRP 0.000 0.000 TRP M 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.45 (26964) covalent geometry : angle 0.96644 / 0.58 (37732) hydrogen bonds : bond 0.11366 / 8.63 ( 1608) hydrogen bonds : angle 7.10678 / 5.42 ( 4519) Misc. bond : bond 0.00682 / 0.48 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.851 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1086 time to fit residues: 26.5567 Evaluate side-chains 125 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 70.6894 > 50: distance: 45 - 47: 35.845 distance: 47 - 48: 40.212 distance: 48 - 49: 41.186 distance: 48 - 51: 39.324 distance: 49 - 52: 55.993 distance: 52 - 53: 55.896 distance: 53 - 54: 55.194 distance: 53 - 56: 38.693 distance: 54 - 55: 46.919 distance: 54 - 57: 39.553 distance: 57 - 58: 39.899 distance: 58 - 59: 69.393 distance: 58 - 61: 41.196 distance: 59 - 62: 50.013 distance: 62 - 63: 51.728 distance: 63 - 64: 56.204 distance: 63 - 66: 16.274 distance: 64 - 65: 30.909 distance: 64 - 67: 56.773 distance: 67 - 68: 39.768 distance: 68 - 69: 41.112 distance: 68 - 71: 40.307 distance: 69 - 70: 55.992 distance: 69 - 72: 44.425 distance: 72 - 73: 45.418 distance: 73 - 76: 67.824 distance: 74 - 75: 57.613 distance: 74 - 77: 55.424 distance: 77 - 78: 41.846 distance: 78 - 79: 39.429 distance: 78 - 81: 41.410 distance: 79 - 80: 70.425 distance: 79 - 82: 39.694 distance: 82 - 83: 45.395 distance: 83 - 84: 60.532 distance: 83 - 86: 45.708 distance: 84 - 85: 39.802 distance: 84 - 87: 55.559 distance: 88 - 89: 55.655 distance: 88 - 91: 57.983 distance: 89 - 90: 39.815 distance: 89 - 92: 56.162 distance: 92 - 93: 41.269 distance: 93 - 94: 69.535 distance: 93 - 96: 69.310 distance: 94 - 95: 39.963 distance: 94 - 97: 33.531