Starting phenix.real_space_refine on Sat Aug 8 07:48:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q97_52947/08_2026/9q97_52947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q97_52947/08_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_52947/08_2026/9q97_52947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q97_52947/08_2026/9q97_52947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q97_52947/08_2026/9q97_52947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q97_52947/08_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-2.2rc3-6140/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: 6.40, per 1000 atoms: 0.24 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: 2.19 Conformation dependent library (CDL) restraints added in 1.7 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: 3.46 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: 7.86 Time building geometry restraints manager: 2.82 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: 37636 3.95 - 7.89: 92 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.750 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- 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 : 0.667 19.732 37732 Z= 0.454 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 0.66707 / 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 : 0.814 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1006 time to fit residues: 24.7954 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 : 0.828 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.066066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051284 restraints weight = 267093.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051752 restraints weight = 197644.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052357 restraints weight = 158849.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.052586 restraints weight = 133266.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.052968 restraints weight = 118893.939| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 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 = 0.3182 r_free = 0.3182 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 (8 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26975 Z= 0.234 Angle : 0.641 12.501 37732 Z= 0.375 Chirality : 0.045 0.251 5056 Planarity : 0.003 0.020 5176 Dihedral : 14.781 156.933 5888 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.38 % Favored : 92.56 % 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: -0.90 (0.12), residues: 5079 helix: 1.15 (0.12), residues: 2012 sheet: -1.25 (0.24), residues: 458 loop : -1.97 (0.12), residues: 2609 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 0.00324 / 0.23 (26964) covalent geometry : angle 0.64067 / 0.37 (37732) hydrogen bonds : bond 0.06903 / 5.27 ( 1608) hydrogen bonds : angle 4.93985 / 3.76 ( 4519) Misc. bond : bond 0.02139 / 1.64 ( 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 : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1076 time to fit residues: 26.7167 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 : 0.939 ------------------------------------------------------------------------------- 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: 30.0000 chunk 327 optimal weight: 7.9990 chunk 199 optimal weight: 30.0000 chunk 389 optimal weight: 50.0000 chunk 91 optimal weight: 0.9980 chunk 442 optimal weight: 40.0000 chunk 281 optimal weight: 5.9990 chunk 236 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 395 optimal weight: 50.0000 chunk 385 optimal weight: 50.0000 overall best weight: 12.9992 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.062031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047893 restraints weight = 282225.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048416 restraints weight = 209248.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048648 restraints weight = 167907.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048974 restraints weight = 147114.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.049232 restraints weight = 131595.245| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26975 Z= 0.352 Angle : 0.829 13.851 37732 Z= 0.499 Chirality : 0.049 0.264 5056 Planarity : 0.005 0.028 5176 Dihedral : 15.631 171.173 5888 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.00 % Favored : 89.84 % 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 : 0.06 % 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: -1.97 (0.11), residues: 5079 helix: 0.01 (0.11), residues: 2017 sheet: -1.63 (0.24), residues: 411 loop : -2.40 (0.11), residues: 2651 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 0.00489 / 0.35 (26964) covalent geometry : angle 0.82863 / 0.50 (37732) hydrogen bonds : bond 0.09117 / 6.95 ( 1608) hydrogen bonds : angle 6.24456 / 4.76 ( 4519) Misc. bond : bond 0.01933 / 1.41 ( 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 : 0.847 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1088 time to fit residues: 26.7843 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 : 1.005 ------------------------------------------------------------------------------- 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: 8.9990 chunk 447 optimal weight: 30.0000 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: 17.9794 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.060025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046239 restraints weight = 285911.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046625 restraints weight = 210533.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046977 restraints weight = 170830.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047370 restraints weight = 146876.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047478 restraints weight = 129009.817| |-----------------------------------------------------------------------------| 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: 0.6965 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 26975 Z= 0.445 Angle : 0.939 14.668 37732 Z= 0.566 Chirality : 0.052 0.346 5056 Planarity : 0.006 0.030 5176 Dihedral : 16.244 163.148 5888 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.48 % Favored : 87.26 % 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: -2.89 (0.11), residues: 5079 helix: -0.89 (0.11), residues: 2033 sheet: -2.17 (0.24), residues: 387 loop : -2.80 (0.11), residues: 2659 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 0.00619 / 0.44 (26964) covalent geometry : angle 0.93941 / 0.57 (37732) hydrogen bonds : bond 0.10423 / 7.92 ( 1608) hydrogen bonds : angle 6.90642 / 5.26 ( 4519) Misc. bond : bond 0.01077 / 0.79 ( 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 : 0.981 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1113 time to fit residues: 26.8347 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 : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 45 optimal weight: 20.0000 chunk 393 optimal weight: 30.0000 chunk 240 optimal weight: 0.9980 chunk 497 optimal weight: 40.0000 chunk 172 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 114 optimal weight: 0.0010 chunk 266 optimal weight: 10.0000 chunk 301 optimal weight: 50.0000 chunk 332 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.061802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047475 restraints weight = 272190.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047867 restraints weight = 196037.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048421 restraints weight = 158789.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048759 restraints weight = 131184.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048877 restraints weight = 115476.539| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26975 Z= 0.165 Angle : 0.605 13.041 37732 Z= 0.350 Chirality : 0.045 0.250 5056 Planarity : 0.002 0.021 5176 Dihedral : 15.677 154.163 5888 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.64 % Favored : 91.34 % 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: -1.61 (0.12), residues: 5079 helix: 0.63 (0.12), residues: 2057 sheet: -2.08 (0.24), residues: 407 loop : -2.41 (0.12), residues: 2615 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 0.00224 / 0.17 (26964) covalent geometry : angle 0.60486 / 0.35 (37732) hydrogen bonds : bond 0.04857 / 3.70 ( 1608) hydrogen bonds : angle 5.32527 / 4.03 ( 4519) Misc. bond : bond 0.00296 / 0.21 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 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 : 0.940 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1021 time to fit residues: 25.2989 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 : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 144 optimal weight: 40.0000 chunk 326 optimal weight: 20.0000 chunk 492 optimal weight: 30.0000 chunk 241 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 342 optimal weight: 50.0000 chunk 120 optimal weight: 40.0000 chunk 473 optimal weight: 20.0000 chunk 359 optimal weight: 50.0000 chunk 182 optimal weight: 40.0000 overall best weight: 18.1396 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.059422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045616 restraints weight = 285016.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045976 restraints weight = 206542.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046476 restraints weight = 168370.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046657 restraints weight = 141976.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046895 restraints weight = 127688.113| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 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 = 0.3003 r_free = 0.3003 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: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 26975 Z= 0.456 Angle : 0.897 15.428 37732 Z= 0.543 Chirality : 0.051 0.288 5056 Planarity : 0.005 0.025 5176 Dihedral : 16.100 151.291 5888 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.41 % Favored : 85.49 % 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 : 0.08 % 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: -2.63 (0.11), residues: 5079 helix: -0.44 (0.11), residues: 2024 sheet: -2.55 (0.23), residues: 427 loop : -2.75 (0.11), residues: 2628 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 0.00634 / 0.46 (26964) covalent geometry : angle 0.89664 / 0.54 (37732) hydrogen bonds : bond 0.10062 / 7.64 ( 1608) hydrogen bonds : angle 6.79185 / 5.18 ( 4519) Misc. bond : bond 0.00345 / 0.23 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 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 : 0.910 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1031 time to fit residues: 25.4430 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 378 optimal weight: 50.0000 chunk 466 optimal weight: 50.0000 chunk 152 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 393 optimal weight: 40.0000 chunk 450 optimal weight: 40.0000 chunk 295 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 331 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 overall best weight: 7.1588 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.060856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046802 restraints weight = 275724.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047136 restraints weight = 201500.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047652 restraints weight = 165217.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047965 restraints weight = 138812.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048090 restraints weight = 122152.779| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26975 Z= 0.213 Angle : 0.639 13.173 37732 Z= 0.373 Chirality : 0.046 0.273 5056 Planarity : 0.003 0.020 5176 Dihedral : 15.785 152.552 5888 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.55 % Favored : 89.43 % 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 : 0.06 % 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: -1.85 (0.12), residues: 5079 helix: 0.48 (0.12), residues: 2057 sheet: -2.54 (0.23), residues: 435 loop : -2.52 (0.12), residues: 2587 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 0.00292 / 0.21 (26964) covalent geometry : angle 0.63910 / 0.37 (37732) hydrogen bonds : bond 0.05447 / 4.15 ( 1608) hydrogen bonds : angle 5.56686 / 4.22 ( 4519) Misc. bond : bond 0.00197 / 0.13 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.745 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1034 time to fit residues: 25.5448 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 : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 116 optimal weight: 50.0000 chunk 71 optimal weight: 40.0000 chunk 298 optimal weight: 20.0000 chunk 108 optimal weight: 50.0000 chunk 142 optimal weight: 0.6980 chunk 74 optimal weight: 50.0000 chunk 228 optimal weight: 20.0000 chunk 334 optimal weight: 50.0000 chunk 376 optimal weight: 40.0000 chunk 468 optimal weight: 20.0000 chunk 234 optimal weight: 50.0000 overall best weight: 20.1396 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.058776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045206 restraints weight = 292475.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045572 restraints weight = 215551.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046025 restraints weight = 175077.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046198 restraints weight = 148973.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046421 restraints weight = 133891.650| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 26975 Z= 0.498 Angle : 0.968 17.042 37732 Z= 0.588 Chirality : 0.052 0.295 5056 Planarity : 0.005 0.027 5176 Dihedral : 16.383 153.899 5888 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.50 % Favored : 83.24 % 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: -3.07 (0.11), residues: 5079 helix: -0.83 (0.11), residues: 2000 sheet: -2.90 (0.23), residues: 416 loop : -2.95 (0.11), residues: 2663 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 0.00691 / 0.50 (26964) covalent geometry : angle 0.96829 / 0.59 (37732) hydrogen bonds : bond 0.11383 / 8.65 ( 1608) hydrogen bonds : angle 7.17770 / 5.48 ( 4519) Misc. bond : bond 0.00421 / 0.29 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.962 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1013 time to fit residues: 24.6782 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 278 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 461 optimal weight: 30.0000 chunk 497 optimal weight: 30.0000 chunk 308 optimal weight: 30.0000 chunk 502 optimal weight: 30.0000 chunk 273 optimal weight: 50.0000 chunk 140 optimal weight: 0.0010 chunk 64 optimal weight: 30.0000 chunk 259 optimal weight: 30.0000 chunk 396 optimal weight: 20.0000 overall best weight: 13.0000 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.059493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045707 restraints weight = 280599.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.046074 restraints weight = 205613.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046543 restraints weight = 167425.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046704 restraints weight = 142076.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.046934 restraints weight = 128089.817| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 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 = 0.3009 r_free = 0.3009 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: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26975 Z= 0.338 Angle : 0.770 15.118 37732 Z= 0.459 Chirality : 0.048 0.353 5056 Planarity : 0.004 0.021 5176 Dihedral : 16.191 160.201 5888 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.41 % Favored : 85.57 % 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 : 0.08 % 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: -2.74 (0.11), residues: 5079 helix: -0.44 (0.11), residues: 2028 sheet: -2.88 (0.23), residues: 406 loop : -2.87 (0.11), residues: 2645 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 0.00468 / 0.34 (26964) covalent geometry : angle 0.77041 / 0.46 (37732) hydrogen bonds : bond 0.07436 / 5.65 ( 1608) hydrogen bonds : angle 6.42387 / 4.89 ( 4519) Misc. bond : bond 0.00189 / 0.11 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 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 : 0.941 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1047 time to fit residues: 25.8862 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 : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 330 optimal weight: 50.0000 chunk 446 optimal weight: 50.0000 chunk 155 optimal weight: 9.9990 chunk 114 optimal weight: 0.0770 chunk 24 optimal weight: 40.0000 chunk 339 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 511 optimal weight: 20.0000 chunk 165 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.060733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.047999 restraints weight = 271709.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047581 restraints weight = 184850.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047630 restraints weight = 186123.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047644 restraints weight = 159860.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047682 restraints weight = 153275.951| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26975 Z= 0.164 Angle : 0.600 11.610 37732 Z= 0.343 Chirality : 0.045 0.372 5056 Planarity : 0.002 0.017 5176 Dihedral : 15.840 172.262 5888 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % 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 : 0.02 % 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: -1.75 (0.12), residues: 5079 helix: 0.76 (0.12), residues: 2059 sheet: -2.77 (0.23), residues: 422 loop : -2.60 (0.12), residues: 2598 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 0.00224 / 0.16 (26964) covalent geometry : angle 0.59969 / 0.34 (37732) hydrogen bonds : bond 0.04794 / 3.65 ( 1608) hydrogen bonds : angle 5.28890 / 4.00 ( 4519) Misc. bond : bond 0.00151 / 0.10 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 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 : 0.954 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0958 time to fit residues: 23.8740 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 388 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 10 optimal weight: 40.0000 chunk 117 optimal weight: 20.0000 chunk 132 optimal weight: 50.0000 chunk 206 optimal weight: 0.0980 chunk 405 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 312 optimal weight: 40.0000 chunk 181 optimal weight: 30.0000 chunk 400 optimal weight: 30.0000 overall best weight: 18.0196 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.058810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045337 restraints weight = 284159.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045695 restraints weight = 213228.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.045898 restraints weight = 169305.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.046243 restraints weight = 148541.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046455 restraints weight = 129209.912| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.7575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26975 Z= 0.440 Angle : 0.871 15.749 37732 Z= 0.528 Chirality : 0.050 0.323 5056 Planarity : 0.005 0.024 5176 Dihedral : 16.279 172.031 5888 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 16.72 % Favored : 83.24 % 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 : 0.10 % 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: -2.70 (0.11), residues: 5079 helix: -0.31 (0.11), residues: 2015 sheet: -2.94 (0.24), residues: 386 loop : -2.90 (0.11), residues: 2678 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 0.00613 / 0.44 (26964) covalent geometry : angle 0.87063 / 0.53 (37732) hydrogen bonds : bond 0.09566 / 7.28 ( 1608) hydrogen bonds : angle 6.65961 / 5.07 ( 4519) Misc. bond : bond 0.00259 / 0.16 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4896.29 seconds wall clock time: 83 minutes 50.62 seconds (5030.62 seconds total)