Starting phenix.real_space_refine on Sun May 25 12:07:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q97_52947/05_2025/9q97_52947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q97_52947/05_2025/9q97_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9q97_52947/05_2025/9q97_52947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q97_52947/05_2025/9q97_52947.map" model { file = "/net/cci-nas-00/data/ceres_data/9q97_52947/05_2025/9q97_52947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q97_52947/05_2025/9q97_52947.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 4, 'ASP:plan': 24, 'PHE:plan': 10, 'GLU:plan': 34, 'ARG:plan': 27} 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: {'GLN:plan1': 7, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 7, 'PHE:plan': 3, 'GLU:plan': 25, 'ARG:plan': 16} 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: {'GLN:plan1': 7, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 6, 'PHE:plan': 3, 'GLU:plan': 22, 'ARG:plan': 16} 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: {'GLN:plan1': 58, 'HIS:plan': 19, 'TYR:plan': 43, 'ASN:plan1': 51, 'TRP:plan': 4, 'ASP:plan': 92, 'PHE:plan': 44, 'GLU:plan': 121, 'ARG:plan': 90} 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: {'GLN:plan1': 49, 'HIS:plan': 20, 'TYR:plan': 34, 'ASN:plan1': 46, 'TRP:plan': 9, 'ASP:plan': 76, 'PHE:plan': 34, 'GLU:plan': 103, 'ARG:plan': 98} 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: {'GLN:plan1': 8, 'ASN:plan1': 4, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} 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: {'GLN:plan1': 8, 'ARG:plan': 22, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 23, 'ASP:plan': 14} 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: {'GLN:plan1': 8, 'ARG:plan': 22, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 12, 'GLU:plan': 23, 'ASP:plan': 14} 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: {'GLN:plan1': 8, 'ARG:plan': 22, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 12, 'GLU:plan': 23, 'ASP:plan': 14} 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: {'GLN:plan1': 8, 'ARG:plan': 22, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 12, 'GLU:plan': 24, 'HIS:plan': 5} 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: {'GLN:plan1': 8, 'ARG:plan': 22, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 12, 'GLU:plan': 24, 'HIS:plan': 5} 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: {'GLN:plan1': 5, 'ARG:plan': 21, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 11, 'GLU:plan': 23, 'HIS:plan': 3} 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: 16.33, per 1000 atoms: 0.61 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: 8.24 Conformation dependent library (CDL) restraints added in 4.8 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: 9.72 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: 15.51 Time building geometry restraints manager: 9.22 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=" N ARG M 8 " pdb=" CA ARG M 8 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.32e-02 5.74e+03 9.13e+00 bond pdb=" N ALA M 14 " pdb=" CA ALA M 14 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.62e+00 bond pdb=" N ILE M 170 " pdb=" CA ILE M 170 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.01e+00 ... (remaining 26959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 37637 3.95 - 7.89: 91 7.89 - 11.84: 3 11.84 - 15.79: 0 15.79 - 19.73: 1 Bond angle restraints: 37732 Sorted by residual: angle pdb=" C ILE C1079 " pdb=" N ASN C1080 " pdb=" CA ASN C1080 " ideal model delta sigma weight residual 120.94 140.67 -19.73 1.90e+00 2.77e-01 1.08e+02 angle pdb=" C SER B 50 " pdb=" N MET B 51 " pdb=" CA MET B 51 " ideal model delta sigma weight residual 122.56 131.15 -8.59 1.34e+00 5.57e-01 4.11e+01 angle pdb=" 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 angle pdb=" C GLU D 666 " pdb=" N GLN D 667 " pdb=" CA GLN D 667 " ideal model delta sigma weight residual 120.29 113.96 6.33 1.42e+00 4.96e-01 1.99e+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: 3667 0.044 - 0.088: 1019 0.088 - 0.131: 344 0.131 - 0.175: 22 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: 0.970 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 75.690 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.140 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 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= 0.641 Angle : 0.648 19.732 37732 Z= 0.407 Chirality : 0.044 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.16559 ( 1608) hydrogen bonds : angle 5.81738 ( 4519) covalent geometry : bond 0.00236 (26964) covalent geometry : angle 0.64804 (37732) Misc. bond : bond 0.30701 ( 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 : 2.897 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2250 time to fit residues: 57.2295 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 : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 432 optimal weight: 40.0000 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 0.6980 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 298 optimal weight: 20.0000 chunk 464 optimal weight: 30.0000 overall best weight: 11.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049614 restraints weight = 270621.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050042 restraints weight = 203499.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050580 restraints weight = 164553.918| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 26975 Z= 0.393 Angle : 0.750 12.130 37732 Z= 0.459 Chirality : 0.046 0.178 5056 Planarity : 0.004 0.024 5176 Dihedral : 15.004 160.191 5888 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.86 % Favored : 92.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 5079 helix: 0.90 (0.12), residues: 2029 sheet: -1.39 (0.24), residues: 420 loop : -2.09 (0.11), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.07708 ( 1608) hydrogen bonds : angle 5.45395 ( 4519) covalent geometry : bond 0.00612 (26964) covalent geometry : angle 0.74969 (37732) Misc. bond : bond 0.00608 ( 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 : 2.653 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2561 time to fit residues: 64.7552 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 : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 405 optimal weight: 6.9990 chunk 279 optimal weight: 20.0000 chunk 366 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 420 optimal weight: 40.0000 chunk 248 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 121 optimal weight: 40.0000 chunk 376 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048886 restraints weight = 273915.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049321 restraints weight = 199980.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049868 restraints weight = 161360.989| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26975 Z= 0.236 Angle : 0.606 11.933 37732 Z= 0.359 Chirality : 0.044 0.151 5056 Planarity : 0.003 0.023 5176 Dihedral : 15.066 171.677 5888 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.05 % Favored : 91.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 5079 helix: 1.27 (0.12), residues: 2050 sheet: -1.25 (0.24), residues: 442 loop : -2.09 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 1608) hydrogen bonds : angle 5.01718 ( 4519) covalent geometry : bond 0.00368 (26964) covalent geometry : angle 0.60646 (37732) Misc. bond : bond 0.00434 ( 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 : 3.220 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2338 time to fit residues: 59.0730 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 : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 444 optimal weight: 9.9990 chunk 149 optimal weight: 40.0000 chunk 407 optimal weight: 30.0000 chunk 360 optimal weight: 50.0000 chunk 378 optimal weight: 40.0000 chunk 405 optimal weight: 8.9990 chunk 146 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 306 optimal weight: 50.0000 chunk 422 optimal weight: 50.0000 chunk 459 optimal weight: 20.0000 overall best weight: 15.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046383 restraints weight = 286371.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.046755 restraints weight = 210869.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047231 restraints weight = 171771.674| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 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 = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 26975 Z= 0.422 Angle : 0.830 14.240 37732 Z= 0.505 Chirality : 0.048 0.234 5056 Planarity : 0.004 0.026 5176 Dihedral : 15.866 174.499 5888 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.56 % Favored : 88.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 5079 helix: 0.02 (0.11), residues: 2036 sheet: -1.86 (0.24), residues: 407 loop : -2.38 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.09549 ( 1608) hydrogen bonds : angle 6.39900 ( 4519) covalent geometry : bond 0.00699 (26964) covalent geometry : angle 0.83001 (37732) Misc. bond : bond 0.00387 ( 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 : 2.752 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2389 time to fit residues: 59.8348 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 : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 356 optimal weight: 50.0000 chunk 462 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 50.0000 chunk 378 optimal weight: 50.0000 chunk 489 optimal weight: 50.0000 chunk 332 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 306 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 373 optimal weight: 0.4980 overall best weight: 9.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046847 restraints weight = 277686.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047261 restraints weight = 201439.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.047727 restraints weight = 161356.286| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- 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: 4 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26975 Z= 0.248 Angle : 0.633 13.044 37732 Z= 0.375 Chirality : 0.044 0.162 5056 Planarity : 0.003 0.021 5176 Dihedral : 15.677 161.618 5888 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.22 % Favored : 89.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 5079 helix: 0.63 (0.12), residues: 2067 sheet: -1.95 (0.24), residues: 415 loop : -2.34 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.05757 ( 1608) hydrogen bonds : angle 5.51042 ( 4519) covalent geometry : bond 0.00401 (26964) covalent geometry : angle 0.63327 (37732) Misc. bond : bond 0.00200 ( 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 : 2.862 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2437 time to fit residues: 61.4576 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 : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 102 optimal weight: 50.0000 chunk 352 optimal weight: 2.9990 chunk 417 optimal weight: 7.9990 chunk 279 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 436 optimal weight: 50.0000 chunk 489 optimal weight: 50.0000 chunk 502 optimal weight: 40.0000 chunk 23 optimal weight: 30.0000 chunk 134 optimal weight: 40.0000 overall best weight: 14.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045743 restraints weight = 288409.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046079 restraints weight = 213247.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046570 restraints weight = 176117.871| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 26975 Z= 0.393 Angle : 0.785 14.603 37732 Z= 0.475 Chirality : 0.048 0.209 5056 Planarity : 0.004 0.022 5176 Dihedral : 16.057 152.050 5888 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.84 % Favored : 86.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 5079 helix: -0.02 (0.11), residues: 2034 sheet: -2.31 (0.23), residues: 415 loop : -2.55 (0.12), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.08796 ( 1608) hydrogen bonds : angle 6.35578 ( 4519) covalent geometry : bond 0.00650 (26964) covalent geometry : angle 0.78530 (37732) Misc. bond : bond 0.00247 ( 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 : 2.662 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2319 time to fit residues: 58.0509 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 : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 1 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 443 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 chunk 401 optimal weight: 30.0000 chunk 476 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 chunk 218 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045843 restraints weight = 288994.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.046233 restraints weight = 211296.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.046704 restraints weight = 170288.668| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- 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: 3 | |-----------------------------------------------------------------------------| |-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: 3 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.7357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26975 Z= 0.352 Angle : 0.742 14.652 37732 Z= 0.447 Chirality : 0.046 0.220 5056 Planarity : 0.004 0.020 5176 Dihedral : 16.116 166.134 5888 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.07 % Favored : 86.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.11), residues: 5079 helix: -0.02 (0.11), residues: 2027 sheet: -2.54 (0.24), residues: 399 loop : -2.69 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.07040 ( 1608) hydrogen bonds : angle 6.20676 ( 4519) covalent geometry : bond 0.00562 (26964) covalent geometry : angle 0.74189 (37732) Misc. bond : bond 0.00202 ( 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 : 2.774 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2532 time to fit residues: 63.2377 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 : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 211 optimal weight: 20.0000 chunk 404 optimal weight: 0.0980 chunk 346 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 375 optimal weight: 50.0000 chunk 343 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 323 optimal weight: 50.0000 chunk 249 optimal weight: 8.9990 chunk 365 optimal weight: 30.0000 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046313 restraints weight = 277186.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046735 restraints weight = 202199.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047233 restraints weight = 161711.402| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26975 Z= 0.190 Angle : 0.590 12.316 37732 Z= 0.343 Chirality : 0.044 0.174 5056 Planarity : 0.002 0.016 5176 Dihedral : 15.773 174.404 5888 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 5079 helix: 0.84 (0.12), residues: 2051 sheet: -2.53 (0.24), residues: 417 loop : -2.52 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.05139 ( 1608) hydrogen bonds : angle 5.31034 ( 4519) covalent geometry : bond 0.00317 (26964) covalent geometry : angle 0.58969 (37732) Misc. bond : bond 0.00167 ( 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 : 2.926 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2573 time to fit residues: 63.7505 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 : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 27 optimal weight: 40.0000 chunk 500 optimal weight: 50.0000 chunk 471 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 450 optimal weight: 0.9990 chunk 432 optimal weight: 40.0000 chunk 305 optimal weight: 30.0000 chunk 315 optimal weight: 50.0000 chunk 239 optimal weight: 40.0000 chunk 100 optimal weight: 50.0000 chunk 468 optimal weight: 0.5980 overall best weight: 11.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045532 restraints weight = 286832.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045919 restraints weight = 210413.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046396 restraints weight = 170341.447| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.7696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 26975 Z= 0.343 Angle : 0.722 14.332 37732 Z= 0.434 Chirality : 0.046 0.198 5056 Planarity : 0.003 0.019 5176 Dihedral : 16.028 174.441 5888 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.57 % Favored : 85.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 5079 helix: 0.39 (0.12), residues: 2037 sheet: -2.62 (0.24), residues: 383 loop : -2.69 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.07683 ( 1608) hydrogen bonds : angle 6.01742 ( 4519) covalent geometry : bond 0.00565 (26964) covalent geometry : angle 0.72198 (37732) Misc. bond : bond 0.00210 ( 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 : 2.746 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2343 time to fit residues: 58.6597 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 : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 344 optimal weight: 0.0970 chunk 196 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 401 optimal weight: 30.0000 chunk 313 optimal weight: 50.0000 chunk 267 optimal weight: 9.9990 chunk 147 optimal weight: 40.0000 chunk 357 optimal weight: 50.0000 chunk 443 optimal weight: 30.0000 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046299 restraints weight = 274635.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046715 restraints weight = 198035.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047229 restraints weight = 158405.298| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.7616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26975 Z= 0.193 Angle : 0.579 11.955 37732 Z= 0.339 Chirality : 0.044 0.199 5056 Planarity : 0.002 0.016 5176 Dihedral : 15.729 173.142 5888 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 5079 helix: 1.08 (0.12), residues: 2049 sheet: -2.45 (0.25), residues: 383 loop : -2.55 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 1608) hydrogen bonds : angle 5.17681 ( 4519) covalent geometry : bond 0.00317 (26964) covalent geometry : angle 0.57942 (37732) Misc. bond : bond 0.00140 ( 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 : 3.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2484 time to fit residues: 62.6700 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 : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 197 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 377 optimal weight: 50.0000 chunk 188 optimal weight: 40.0000 chunk 78 optimal weight: 50.0000 chunk 406 optimal weight: 20.0000 chunk 500 optimal weight: 50.0000 chunk 368 optimal weight: 50.0000 chunk 7 optimal weight: 20.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045292 restraints weight = 283259.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045673 restraints weight = 207506.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046141 restraints weight = 169046.579| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.8019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 26975 Z= 0.345 Angle : 0.715 13.985 37732 Z= 0.431 Chirality : 0.046 0.212 5056 Planarity : 0.003 0.019 5176 Dihedral : 15.996 173.515 5888 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 15.34 % Favored : 84.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 5079 helix: 0.51 (0.12), residues: 2039 sheet: -2.69 (0.24), residues: 380 loop : -2.72 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP M 126 PHE 0.000 0.000 PHE M 133 TYR 0.000 0.000 TYR M 112 Details of bonding type rmsd hydrogen bonds : bond 0.07562 ( 1608) hydrogen bonds : angle 5.96552 ( 4519) covalent geometry : bond 0.00565 (26964) covalent geometry : angle 0.71503 (37732) Misc. bond : bond 0.00192 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9103.76 seconds wall clock time: 157 minutes 32.03 seconds (9452.03 seconds total)