Starting phenix.real_space_refine on Fri Mar 6 22:24:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgr_25116/03_2026/7sgr_25116.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgr_25116/03_2026/7sgr_25116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sgr_25116/03_2026/7sgr_25116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgr_25116/03_2026/7sgr_25116.map" model { file = "/net/cci-nas-00/data/ceres_data/7sgr_25116/03_2026/7sgr_25116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgr_25116/03_2026/7sgr_25116.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.104 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 C 22817 2.51 5 N 5907 2.21 5 O 6179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34989 Number of models: 1 Model: "" Number of chains: 21 Chain: "J" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4505 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 552} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5549 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 5543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5543 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4509 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "E" Number of atoms: 5535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5535 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 679} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4509 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 17, 'TRANS': 552} Chain: "H" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "L" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "D" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 581 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "C" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1035 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 8, 'PHE:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1026 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 8, 'PHE:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "K" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "J" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {'6OU': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'6OU:plan-2': 6, '6OU:plan-3': 6, '6OU:plan-1': 4} Unresolved non-hydrogen planarities: 60 Chain: "I" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Unusual residues: {'6OU': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'6OU:plan-2': 8, '6OU:plan-3': 8, '6OU:plan-1': 7} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'6OU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-2': 3, '6OU:plan-3': 3} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 2, '6OU:plan-3': 2, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'6OU:plan-1': 4, '6OU:plan-2': 4, '6OU:plan-3': 4} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'6OU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 2, '6OU:plan-3': 2, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'6OU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 2, '6OU:plan-3': 2, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 8.25, per 1000 atoms: 0.24 Number of scatterers: 34989 At special positions: 0 Unit cell: (146.59, 149.8, 173.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 6 15.00 O 6179 8.00 N 5907 7.00 C 22817 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=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.3 seconds 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8272 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 21 sheets defined 65.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'J' and resid 142 through 150 removed outlier: 4.015A pdb=" N ALA J 146 " --> pdb=" O TRP J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 182 removed outlier: 4.074A pdb=" N GLU J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR J 171 " --> pdb=" O PHE J 167 " (cutoff:3.500A) Proline residue: J 172 - end of helix Processing helix chain 'J' and resid 188 through 237 removed outlier: 3.616A pdb=" N VAL J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG J 222 " --> pdb=" O HIS J 218 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE J 223 " --> pdb=" O SER J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 245 removed outlier: 3.917A pdb=" N PHE J 243 " --> pdb=" O PRO J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 266 removed outlier: 3.720A pdb=" N THR J 251 " --> pdb=" O ARG J 247 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP J 259 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 278 Processing helix chain 'J' and resid 279 through 290 Processing helix chain 'J' and resid 290 through 339 removed outlier: 3.579A pdb=" N THR J 294 " --> pdb=" O SER J 290 " (cutoff:3.500A) Proline residue: J 302 - end of helix Proline residue: J 313 - end of helix Processing helix chain 'J' and resid 339 through 346 Processing helix chain 'J' and resid 349 through 402 Processing helix chain 'J' and resid 406 through 429 Proline residue: J 423 - end of helix removed outlier: 3.614A pdb=" N GLN J 429 " --> pdb=" O ILE J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 449 Processing helix chain 'J' and resid 509 through 516 removed outlier: 4.463A pdb=" N LYS J 513 " --> pdb=" O SER J 509 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN J 516 " --> pdb=" O THR J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 544 Processing helix chain 'J' and resid 558 through 564 Processing helix chain 'J' and resid 571 through 582 removed outlier: 3.655A pdb=" N VAL J 575 " --> pdb=" O SER J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 584 through 590 removed outlier: 3.818A pdb=" N GLU J 590 " --> pdb=" O ASP J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 593 through 597 removed outlier: 3.675A pdb=" N ASN J 596 " --> pdb=" O GLU J 593 " (cutoff:3.500A) Processing helix chain 'J' and resid 607 through 622 removed outlier: 4.267A pdb=" N ASN J 622 " --> pdb=" O ARG J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 647 Processing helix chain 'J' and resid 647 through 652 Processing helix chain 'J' and resid 686 through 692 Processing helix chain 'J' and resid 696 through 706 removed outlier: 3.677A pdb=" N TYR J 700 " --> pdb=" O SER J 696 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 21 removed outlier: 3.907A pdb=" N TYR I 12 " --> pdb=" O ASP I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 35 Processing helix chain 'I' and resid 42 through 53 Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.871A pdb=" N ASN I 68 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE I 70 " --> pdb=" O LEU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 142 through 150 removed outlier: 4.084A pdb=" N ALA I 146 " --> pdb=" O TRP I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 182 removed outlier: 3.555A pdb=" N PHE I 154 " --> pdb=" O TYR I 150 " (cutoff:3.500A) Proline residue: I 172 - end of helix removed outlier: 3.907A pdb=" N PHE I 175 " --> pdb=" O THR I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 237 removed outlier: 3.551A pdb=" N ASN I 192 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 245 removed outlier: 3.811A pdb=" N PHE I 243 " --> pdb=" O PRO I 239 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER I 245 " --> pdb=" O SER I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 266 removed outlier: 3.672A pdb=" N THR I 251 " --> pdb=" O ARG I 247 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU I 258 " --> pdb=" O ARG I 254 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 278 Processing helix chain 'I' and resid 279 through 290 removed outlier: 3.752A pdb=" N PHE I 283 " --> pdb=" O SER I 279 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 284 " --> pdb=" O PHE I 280 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 339 removed outlier: 4.172A pdb=" N VAL I 296 " --> pdb=" O LYS I 292 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE I 297 " --> pdb=" O LEU I 293 " (cutoff:3.500A) Proline residue: I 302 - end of helix Proline residue: I 313 - end of helix Processing helix chain 'I' and resid 339 through 346 Processing helix chain 'I' and resid 348 through 403 Processing helix chain 'I' and resid 406 through 430 Proline residue: I 423 - end of helix removed outlier: 3.667A pdb=" N ILE I 430 " --> pdb=" O ARG I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 430 through 449 removed outlier: 3.762A pdb=" N THR I 442 " --> pdb=" O GLY I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 516 Processing helix chain 'I' and resid 537 through 543 Processing helix chain 'I' and resid 558 through 564 Processing helix chain 'I' and resid 571 through 582 removed outlier: 3.732A pdb=" N VAL I 575 " --> pdb=" O SER I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 591 Processing helix chain 'I' and resid 593 through 597 removed outlier: 3.754A pdb=" N THR I 597 " --> pdb=" O GLY I 594 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 622 removed outlier: 4.550A pdb=" N ASN I 622 " --> pdb=" O ARG I 618 " (cutoff:3.500A) Processing helix chain 'I' and resid 632 through 635 removed outlier: 4.005A pdb=" N ALA I 635 " --> pdb=" O ALA I 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 632 through 635' Processing helix chain 'I' and resid 640 through 652 removed outlier: 4.412A pdb=" N LYS I 650 " --> pdb=" O ARG I 646 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS I 652 " --> pdb=" O MET I 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 686 through 692 Processing helix chain 'I' and resid 696 through 706 Processing helix chain 'A' and resid 8 through 22 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.536A pdb=" N ASN A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 150 through 182 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 189 through 238 Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.923A pdb=" N PHE A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 257 through 268 removed outlier: 4.201A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 290 removed outlier: 3.837A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 338 Proline residue: A 302 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 348 through 403 Processing helix chain 'A' and resid 406 through 420 Processing helix chain 'A' and resid 421 through 449 removed outlier: 3.962A pdb=" N ILE A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.603A pdb=" N GLN A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.758A pdb=" N ARG A 543 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 564 Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.622A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.668A pdb=" N ASN A 596 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 637 through 652 removed outlier: 4.608A pdb=" N HIS A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LYS A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.852A pdb=" N THR A 666 " --> pdb=" O ARG A 663 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 667 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 668' Processing helix chain 'A' and resid 686 through 693 removed outlier: 4.196A pdb=" N GLU A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.814A pdb=" N ALA B 146 " --> pdb=" O TRP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 182 removed outlier: 3.671A pdb=" N PHE B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Proline residue: B 172 - end of helix Processing helix chain 'B' and resid 187 through 236 removed outlier: 3.540A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.799A pdb=" N PHE B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.644A pdb=" N LEU B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 292 through 339 removed outlier: 3.776A pdb=" N VAL B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Proline residue: B 302 - end of helix Proline residue: B 313 - end of helix Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 348 through 403 Processing helix chain 'B' and resid 406 through 427 Proline residue: B 423 - end of helix Processing helix chain 'B' and resid 427 through 449 removed outlier: 3.650A pdb=" N GLN B 435 " --> pdb=" O TRP B 431 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 516 removed outlier: 3.507A pdb=" N GLN B 516 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 536 No H-bonds generated for 'chain 'B' and resid 534 through 536' Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 558 through 564 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.708A pdb=" N VAL B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 Processing helix chain 'B' and resid 593 through 597 Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 640 through 652 removed outlier: 4.713A pdb=" N HIS B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 692 Processing helix chain 'B' and resid 696 through 706 Processing helix chain 'E' and resid 8 through 21 removed outlier: 3.821A pdb=" N TYR E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 63 through 67 removed outlier: 3.573A pdb=" N LEU E 67 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 118 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 142 through 150 removed outlier: 4.056A pdb=" N ALA E 146 " --> pdb=" O TRP E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 182 removed outlier: 3.667A pdb=" N ILE E 170 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR E 171 " --> pdb=" O PHE E 167 " (cutoff:3.500A) Proline residue: E 172 - end of helix Processing helix chain 'E' and resid 190 through 237 removed outlier: 3.537A pdb=" N ALA E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 245 removed outlier: 3.855A pdb=" N PHE E 243 " --> pdb=" O PRO E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 removed outlier: 3.591A pdb=" N THR E 251 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 278 Processing helix chain 'E' and resid 279 through 290 removed outlier: 3.571A pdb=" N VAL E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 339 removed outlier: 3.718A pdb=" N VAL E 296 " --> pdb=" O LYS E 292 " (cutoff:3.500A) Proline residue: E 302 - end of helix Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 339 through 347 Processing helix chain 'E' and resid 348 through 402 Processing helix chain 'E' and resid 406 through 429 Proline residue: E 423 - end of helix Processing helix chain 'E' and resid 430 through 449 removed outlier: 3.736A pdb=" N VAL E 447 " --> pdb=" O ARG E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 516 Processing helix chain 'E' and resid 534 through 536 No H-bonds generated for 'chain 'E' and resid 534 through 536' Processing helix chain 'E' and resid 537 through 544 removed outlier: 4.125A pdb=" N GLN E 544 " --> pdb=" O TRP E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 564 Processing helix chain 'E' and resid 571 through 582 Processing helix chain 'E' and resid 584 through 590 Processing helix chain 'E' and resid 607 through 622 removed outlier: 3.806A pdb=" N GLN E 612 " --> pdb=" O GLY E 608 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG E 613 " --> pdb=" O GLY E 609 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN E 622 " --> pdb=" O ARG E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 635 removed outlier: 4.193A pdb=" N ALA E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 632 through 635' Processing helix chain 'E' and resid 637 through 652 removed outlier: 4.575A pdb=" N HIS E 649 " --> pdb=" O MET E 645 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 663 through 668 removed outlier: 3.870A pdb=" N LYS E 668 " --> pdb=" O SER E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 692 Processing helix chain 'E' and resid 696 through 706 removed outlier: 3.840A pdb=" N TYR E 700 " --> pdb=" O SER E 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 150 removed outlier: 4.068A pdb=" N ALA F 146 " --> pdb=" O TRP F 142 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 182 Proline residue: F 172 - end of helix Processing helix chain 'F' and resid 189 through 236 removed outlier: 3.596A pdb=" N ILE F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 245 removed outlier: 3.722A pdb=" N PHE F 243 " --> pdb=" O PRO F 239 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 266 removed outlier: 3.964A pdb=" N ARG F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL F 255 " --> pdb=" O THR F 251 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 278 Processing helix chain 'F' and resid 279 through 290 removed outlier: 3.784A pdb=" N TYR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 339 Proline residue: F 302 - end of helix Proline residue: F 313 - end of helix Processing helix chain 'F' and resid 339 through 346 Processing helix chain 'F' and resid 349 through 402 Processing helix chain 'F' and resid 406 through 429 Proline residue: F 423 - end of helix removed outlier: 3.595A pdb=" N GLN F 429 " --> pdb=" O ILE F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 449 Processing helix chain 'F' and resid 506 through 510 removed outlier: 4.479A pdb=" N SER F 509 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 removed outlier: 3.724A pdb=" N GLN F 516 " --> pdb=" O THR F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 536 No H-bonds generated for 'chain 'F' and resid 534 through 536' Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 558 through 564 Processing helix chain 'F' and resid 571 through 582 removed outlier: 3.619A pdb=" N VAL F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 591 Processing helix chain 'F' and resid 593 through 597 removed outlier: 3.541A pdb=" N THR F 597 " --> pdb=" O GLY F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 604 removed outlier: 3.773A pdb=" N GLY F 603 " --> pdb=" O GLY F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 622 removed outlier: 4.883A pdb=" N ASN F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 652 removed outlier: 4.535A pdb=" N ILE F 643 " --> pdb=" O GLU F 639 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N HIS F 649 " --> pdb=" O MET F 645 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 692 Processing helix chain 'F' and resid 696 through 706 Processing helix chain 'H' and resid 10 through 25 Processing helix chain 'H' and resid 35 through 41 removed outlier: 3.593A pdb=" N PHE H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 51 removed outlier: 3.662A pdb=" N LEU H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 77 removed outlier: 3.944A pdb=" N ARG H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 25 removed outlier: 3.607A pdb=" N ILE L 25 " --> pdb=" O GLU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 41 Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 54 through 77 removed outlier: 3.925A pdb=" N ARG L 58 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 35 through 41 Processing helix chain 'D' and resid 43 through 51 removed outlier: 3.693A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 76 Processing helix chain 'C' and resid 34 through 41 removed outlier: 3.503A pdb=" N GLU C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.506A pdb=" N LEU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 78 Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 459 through 470 Proline residue: C 466 - end of helix Processing helix chain 'G' and resid 34 through 41 removed outlier: 3.535A pdb=" N PHE G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 49 Processing helix chain 'G' and resid 59 through 78 Processing helix chain 'G' and resid 373 through 380 Processing helix chain 'G' and resid 394 through 399 Processing helix chain 'G' and resid 460 through 473 Proline residue: G 466 - end of helix Processing helix chain 'K' and resid 34 through 40 removed outlier: 3.716A pdb=" N GLU K 40 " --> pdb=" O LYS K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 49 Processing helix chain 'K' and resid 58 through 76 Processing sheet with id=AA1, first strand: chain 'J' and resid 483 through 492 removed outlier: 7.074A pdb=" N ILE J 484 " --> pdb=" O ARG J 476 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ARG J 476 " --> pdb=" O ILE J 484 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP J 486 " --> pdb=" O ARG J 474 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG J 474 " --> pdb=" O ASP J 486 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE J 488 " --> pdb=" O ASN J 472 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN J 472 " --> pdb=" O ILE J 488 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE J 473 " --> pdb=" O ASN J 523 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASN J 523 " --> pdb=" O ILE J 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 545 through 548 removed outlier: 6.986A pdb=" N GLY J 546 " --> pdb=" O ILE J 628 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP J 630 " --> pdb=" O GLY J 546 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL J 548 " --> pdb=" O ASP J 630 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU J 627 " --> pdb=" O ILE J 658 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE J 660 " --> pdb=" O LEU J 627 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE J 629 " --> pdb=" O ILE J 660 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU J 683 " --> pdb=" O VAL J 675 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU J 677 " --> pdb=" O ILE J 681 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE J 681 " --> pdb=" O GLU J 677 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 55 through 61 removed outlier: 3.540A pdb=" N PHE I 84 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG I 95 " --> pdb=" O SER I 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 55 through 61 removed outlier: 3.540A pdb=" N PHE I 84 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN I 105 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 483 through 492 removed outlier: 6.763A pdb=" N ILE I 484 " --> pdb=" O ARG I 476 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ARG I 476 " --> pdb=" O ILE I 484 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP I 486 " --> pdb=" O ARG I 474 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG I 474 " --> pdb=" O ASP I 486 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE I 488 " --> pdb=" O ASN I 472 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE I 473 " --> pdb=" O ASN I 523 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN I 523 " --> pdb=" O ILE I 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 545 through 548 removed outlier: 6.505A pdb=" N GLY I 546 " --> pdb=" O ILE I 628 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP I 630 " --> pdb=" O GLY I 546 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL I 548 " --> pdb=" O ASP I 630 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU I 627 " --> pdb=" O ILE I 658 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE I 660 " --> pdb=" O LEU I 627 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE I 629 " --> pdb=" O ILE I 660 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE I 498 " --> pdb=" O ILE I 659 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY I 499 " --> pdb=" O ILE I 674 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET I 676 " --> pdb=" O GLY I 499 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL I 501 " --> pdb=" O MET I 676 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE I 673 " --> pdb=" O GLN I 684 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN I 684 " --> pdb=" O ILE I 673 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL I 675 " --> pdb=" O VAL I 682 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 61 Processing sheet with id=AA8, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.764A pdb=" N PHE A 84 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 97 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A 89 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 95 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 96 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 483 through 492 removed outlier: 6.830A pdb=" N ILE A 484 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ARG A 476 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP A 486 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG A 474 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE A 488 " --> pdb=" O ASN A 472 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.914A pdb=" N ILE A 498 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 497 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE A 674 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 499 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N MET A 676 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 501 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 683 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU A 677 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 483 through 491 removed outlier: 7.329A pdb=" N ILE B 484 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARG B 476 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASP B 486 " --> pdb=" O ARG B 474 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 474 " --> pdb=" O ASP B 486 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 488 " --> pdb=" O ASN B 472 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 472 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N PHE B 470 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 527 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN B 472 " --> pdb=" O GLN B 525 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLN B 525 " --> pdb=" O ASN B 472 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 545 through 548 removed outlier: 6.543A pdb=" N LEU B 627 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 660 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE B 629 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 498 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 672 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 683 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU B 677 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 61 removed outlier: 3.524A pdb=" N ILE E 122 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 84 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL E 89 " --> pdb=" O ARG E 95 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ARG E 95 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 483 through 492 removed outlier: 6.878A pdb=" N ILE E 484 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ARG E 476 " --> pdb=" O ILE E 484 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP E 486 " --> pdb=" O ARG E 474 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG E 474 " --> pdb=" O ASP E 486 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE E 488 " --> pdb=" O ASN E 472 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE E 473 " --> pdb=" O ASN E 523 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN E 523 " --> pdb=" O ILE E 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 545 through 548 removed outlier: 3.631A pdb=" N GLU E 683 " --> pdb=" O VAL E 675 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU E 677 " --> pdb=" O ILE E 681 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE E 681 " --> pdb=" O GLU E 677 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 485 through 492 removed outlier: 7.083A pdb=" N ASP F 486 " --> pdb=" O ARG F 474 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG F 474 " --> pdb=" O ASP F 486 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE F 488 " --> pdb=" O ASN F 472 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE F 470 " --> pdb=" O LEU F 527 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU F 527 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN F 472 " --> pdb=" O GLN F 525 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN F 525 " --> pdb=" O ASN F 472 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 545 through 548 removed outlier: 6.446A pdb=" N ILE F 498 " --> pdb=" O ILE F 659 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU F 683 " --> pdb=" O VAL F 675 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 84 removed outlier: 4.025A pdb=" N GLY C 455 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 84 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS C 453 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC2, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AC3, first strand: chain 'G' and resid 387 through 388 2134 hydrogen bonds defined for protein. 6276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.58 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5530 1.29 - 1.42: 8850 1.42 - 1.55: 20850 1.55 - 1.68: 224 1.68 - 1.81: 148 Bond restraints: 35602 Sorted by residual: bond pdb=" C40 6OU J 802 " pdb=" C41 6OU J 802 " ideal model delta sigma weight residual 1.333 1.559 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU L 401 " pdb=" C41 6OU L 401 " ideal model delta sigma weight residual 1.333 1.559 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU I 801 " pdb=" C41 6OU I 801 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU J 801 " pdb=" C41 6OU J 801 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C40 6OU A 802 " pdb=" C41 6OU A 802 " ideal model delta sigma weight residual 1.333 1.558 -0.225 2.00e-02 2.50e+03 1.26e+02 ... (remaining 35597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 47704 3.83 - 7.65: 347 7.65 - 11.48: 42 11.48 - 15.30: 1 15.30 - 19.13: 12 Bond angle restraints: 48106 Sorted by residual: angle pdb=" N GLY F 403 " pdb=" CA GLY F 403 " pdb=" C GLY F 403 " ideal model delta sigma weight residual 115.30 125.45 -10.15 1.39e+00 5.18e-01 5.33e+01 angle pdb=" C40 6OU L 401 " pdb=" C41 6OU L 401 " pdb=" C42 6OU L 401 " ideal model delta sigma weight residual 127.56 108.43 19.13 3.00e+00 1.11e-01 4.07e+01 angle pdb=" C40 6OU J 802 " pdb=" C41 6OU J 802 " pdb=" C42 6OU J 802 " ideal model delta sigma weight residual 127.56 109.24 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C40 6OU F 802 " pdb=" C41 6OU F 802 " pdb=" C42 6OU F 802 " ideal model delta sigma weight residual 127.56 109.26 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C40 6OU J 801 " pdb=" C41 6OU J 801 " pdb=" C42 6OU J 801 " ideal model delta sigma weight residual 127.56 109.95 17.61 3.00e+00 1.11e-01 3.45e+01 ... (remaining 48101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 20931 33.71 - 67.42: 458 67.42 - 101.13: 67 101.13 - 134.84: 3 134.84 - 168.55: 8 Dihedral angle restraints: 21467 sinusoidal: 8691 harmonic: 12776 Sorted by residual: dihedral pdb=" CA VAL F 348 " pdb=" C VAL F 348 " pdb=" N SER F 349 " pdb=" CA SER F 349 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C19 6OU A 801 " pdb=" C20 6OU A 801 " pdb=" C21 6OU A 801 " pdb=" O22 6OU A 801 " ideal model delta sinusoidal sigma weight residual 301.00 132.45 168.55 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C19 6OU K 401 " pdb=" C20 6OU K 401 " pdb=" C21 6OU K 401 " pdb=" O22 6OU K 401 " ideal model delta sinusoidal sigma weight residual -59.00 108.54 -167.54 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 21464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5427 0.098 - 0.196: 212 0.196 - 0.294: 7 0.294 - 0.392: 1 0.392 - 0.491: 2 Chirality restraints: 5649 Sorted by residual: chirality pdb=" CA LEU A 301 " pdb=" N LEU A 301 " pdb=" C LEU A 301 " pdb=" CB LEU A 301 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA PHE A 299 " pdb=" N PHE A 299 " pdb=" C PHE A 299 " pdb=" CB PHE A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ASP F 404 " pdb=" N ASP F 404 " pdb=" C ASP F 404 " pdb=" CB ASP F 404 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 5646 not shown) Planarity restraints: 6007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C39 6OU L 401 " -0.262 2.00e-02 2.50e+03 2.94e-01 8.64e+02 pdb=" C40 6OU L 401 " 0.477 2.00e-02 2.50e+03 pdb=" C41 6OU L 401 " -0.222 2.00e-02 2.50e+03 pdb=" C42 6OU L 401 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU F 802 " 0.241 2.00e-02 2.50e+03 2.91e-01 8.45e+02 pdb=" C40 6OU F 802 " -0.459 2.00e-02 2.50e+03 pdb=" C41 6OU F 802 " 0.259 2.00e-02 2.50e+03 pdb=" C42 6OU F 802 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU A 802 " 0.227 2.00e-02 2.50e+03 2.88e-01 8.29e+02 pdb=" C40 6OU A 802 " -0.444 2.00e-02 2.50e+03 pdb=" C41 6OU A 802 " 0.281 2.00e-02 2.50e+03 pdb=" C42 6OU A 802 " -0.063 2.00e-02 2.50e+03 ... (remaining 6004 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2935 2.74 - 3.28: 35020 3.28 - 3.82: 56968 3.82 - 4.36: 65957 4.36 - 4.90: 117400 Nonbonded interactions: 278280 Sorted by model distance: nonbonded pdb=" OE1 GLU I 257 " pdb=" OG SER I 440 " model vdw 2.202 3.040 nonbonded pdb=" O LEU E 41 " pdb=" OG SER E 45 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLU E 257 " pdb=" OG SER E 440 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLN J 176 " pdb=" OH TYR J 289 " model vdw 2.232 3.040 nonbonded pdb=" OG SER E 692 " pdb=" OE2 GLU E 693 " model vdw 2.238 3.040 ... (remaining 278275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 130 or (resid 131 through 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 454 or (resid 455 th \ rough 456 and (name N or name CA or name C or name O or name CB )) or resid 457 \ or (resid 458 and (name N or name CA or name C or name O or name CB )) or resid \ 459 through 706)) selection = (chain 'E' and (resid 7 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 136 or (resid 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 706)) selection = (chain 'I' and (resid 7 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 130 or (resid 131 through 132 and ( \ name N or name CA or name C or name O or name CB )) or (resid 133 through 137 an \ d (name N or name CA or name C or name O or name CB )) or resid 138 through 454 \ or (resid 455 through 456 and (name N or name CA or name C or name O or name CB \ )) or resid 457 through 706)) } ncs_group { reference = (chain 'B' and (resid 137 through 687 or (resid 688 and (name N or name CA or na \ me C or name O or name CB )) or resid 689 through 801)) selection = (chain 'F' and (resid 137 through 687 or (resid 688 and (name N or name CA or na \ me C or name O or name CB )) or resid 689 through 706 or (resid 801 and (name C3 \ 1 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45))) \ ) selection = (chain 'J' and (resid 137 through 706 or (resid 801 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44 or name C45)))) } ncs_group { reference = (chain 'C' and (resid 29 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 363 through 471)) selection = (chain 'G' and resid 29 through 471) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 9 through 77) selection = (chain 'L' and resid 9 through 77) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 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: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 32.780 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 0.226 35602 Z= 0.343 Angle : 0.792 19.128 48106 Z= 0.385 Chirality : 0.043 0.491 5649 Planarity : 0.009 0.294 6007 Dihedral : 15.212 168.546 13195 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.13), residues: 4369 helix: 1.80 (0.10), residues: 2658 sheet: -0.94 (0.29), residues: 346 loop : -1.43 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 517 TYR 0.013 0.001 TYR C 462 PHE 0.030 0.001 PHE A 278 TRP 0.069 0.001 TRP B 431 HIS 0.004 0.001 HIS E 662 Details of bonding type rmsd covalent geometry : bond 0.00658 (35602) covalent geometry : angle 0.79236 (48106) hydrogen bonds : bond 0.14471 ( 2121) hydrogen bonds : angle 5.58219 ( 6276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 702 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: J 467 ASN cc_start: 0.6908 (m-40) cc_final: 0.6689 (t0) REVERT: J 550 GLN cc_start: 0.7729 (tt0) cc_final: 0.7387 (tt0) REVERT: J 630 ASP cc_start: 0.6874 (t70) cc_final: 0.6609 (t0) REVERT: J 673 ILE cc_start: 0.7760 (mp) cc_final: 0.7464 (mp) REVERT: I 69 PHE cc_start: 0.8286 (m-80) cc_final: 0.7975 (m-10) REVERT: I 328 ASP cc_start: 0.7578 (m-30) cc_final: 0.7327 (m-30) REVERT: I 369 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7861 (mttt) REVERT: I 498 ILE cc_start: 0.8208 (mm) cc_final: 0.7882 (mm) REVERT: I 663 ARG cc_start: 0.6401 (mpt180) cc_final: 0.5994 (mpt180) REVERT: A 8 ASP cc_start: 0.5433 (p0) cc_final: 0.5101 (p0) REVERT: A 358 LYS cc_start: 0.7093 (mttt) cc_final: 0.6883 (mppt) REVERT: A 433 ASP cc_start: 0.7073 (m-30) cc_final: 0.6453 (m-30) REVERT: A 645 MET cc_start: 0.8393 (mmm) cc_final: 0.8009 (mmm) REVERT: A 646 ARG cc_start: 0.7246 (mpt180) cc_final: 0.6991 (mpt180) REVERT: A 684 GLN cc_start: 0.8434 (pt0) cc_final: 0.8189 (pt0) REVERT: A 704 LEU cc_start: 0.8788 (tt) cc_final: 0.8560 (tp) REVERT: B 181 LYS cc_start: 0.8348 (mmtp) cc_final: 0.8115 (mmtp) REVERT: B 259 ASP cc_start: 0.7681 (t0) cc_final: 0.7230 (t70) REVERT: B 316 ARG cc_start: 0.7634 (tpm-80) cc_final: 0.7379 (tpm170) REVERT: B 474 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7616 (mtp-110) REVERT: B 512 THR cc_start: 0.8692 (t) cc_final: 0.8328 (m) REVERT: B 523 ASN cc_start: 0.7135 (t0) cc_final: 0.6912 (t0) REVERT: B 678 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7734 (tptp) REVERT: E 31 LYS cc_start: 0.8095 (tttt) cc_final: 0.7810 (tttm) REVERT: E 224 ASP cc_start: 0.7885 (t70) cc_final: 0.7570 (t0) REVERT: E 663 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7613 (ttm110) REVERT: F 346 MET cc_start: 0.7809 (mtp) cc_final: 0.7605 (mtm) REVERT: F 586 ASP cc_start: 0.7283 (m-30) cc_final: 0.6783 (m-30) REVERT: F 601 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6276 (tt0) REVERT: F 625 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7888 (mmtm) REVERT: F 639 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6881 (tm-30) REVERT: F 645 MET cc_start: 0.7889 (mmm) cc_final: 0.7578 (mtp) REVERT: F 678 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7644 (mptt) REVERT: H 24 LYS cc_start: 0.7831 (mmtm) cc_final: 0.7535 (mmmt) REVERT: H 27 LYS cc_start: 0.8361 (mtmt) cc_final: 0.7930 (mtpp) REVERT: L 16 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6640 (mmpt) REVERT: L 25 ILE cc_start: 0.7949 (tp) cc_final: 0.7722 (tp) REVERT: D 65 MET cc_start: 0.7392 (mtm) cc_final: 0.7173 (mtp) REVERT: K 37 ASP cc_start: 0.7705 (m-30) cc_final: 0.7464 (m-30) outliers start: 0 outliers final: 1 residues processed: 702 average time/residue: 0.6688 time to fit residues: 561.7873 Evaluate side-chains 454 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 398 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 0.0770 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.5980 chunk 424 optimal weight: 50.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 435 GLN I 185 HIS I 385 GLN I 662 HIS ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN A 467 ASN A 523 ASN B 192 ASN B 472 ASN E 19 GLN E 268 GLN E 525 GLN E 539 ASN E 552 ASN E 622 ASN ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.153879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116206 restraints weight = 44500.323| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.31 r_work: 0.3259 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35602 Z= 0.125 Angle : 0.526 12.277 48106 Z= 0.275 Chirality : 0.041 0.216 5649 Planarity : 0.004 0.062 6007 Dihedral : 11.381 165.060 5262 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.94 % Allowed : 11.08 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4369 helix: 2.00 (0.10), residues: 2693 sheet: -0.76 (0.28), residues: 352 loop : -1.30 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 256 TYR 0.019 0.001 TYR E 700 PHE 0.020 0.001 PHE J 587 TRP 0.036 0.001 TRP B 431 HIS 0.003 0.001 HIS F 649 Details of bonding type rmsd covalent geometry : bond 0.00249 (35602) covalent geometry : angle 0.52578 (48106) hydrogen bonds : bond 0.05034 ( 2121) hydrogen bonds : angle 4.29567 ( 6276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 491 time to evaluate : 1.178 Fit side-chains REVERT: J 262 ARG cc_start: 0.7001 (ttp80) cc_final: 0.6637 (ttp-110) REVERT: J 335 GLU cc_start: 0.7854 (tt0) cc_final: 0.7458 (tt0) REVERT: J 467 ASN cc_start: 0.6704 (m-40) cc_final: 0.6431 (t0) REVERT: J 550 GLN cc_start: 0.7829 (tt0) cc_final: 0.7600 (tt0) REVERT: J 570 MET cc_start: 0.8625 (ptm) cc_final: 0.8298 (ptm) REVERT: I 33 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7533 (ttt180) REVERT: I 88 LYS cc_start: 0.8418 (tptm) cc_final: 0.8006 (tptp) REVERT: I 97 LEU cc_start: 0.7852 (tp) cc_final: 0.7469 (tm) REVERT: I 328 ASP cc_start: 0.8005 (m-30) cc_final: 0.7799 (m-30) REVERT: I 369 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8064 (mttt) REVERT: I 680 LYS cc_start: 0.8257 (mttm) cc_final: 0.7958 (mttp) REVERT: I 693 GLU cc_start: 0.7497 (mp0) cc_final: 0.7223 (mp0) REVERT: A 8 ASP cc_start: 0.5587 (p0) cc_final: 0.5218 (p0) REVERT: A 259 ASP cc_start: 0.7018 (p0) cc_final: 0.6747 (t0) REVERT: A 278 PHE cc_start: 0.7076 (m-10) cc_final: 0.6607 (t80) REVERT: A 330 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: A 358 LYS cc_start: 0.7504 (mttt) cc_final: 0.7078 (mppt) REVERT: A 433 ASP cc_start: 0.7211 (m-30) cc_final: 0.6468 (m-30) REVERT: A 645 MET cc_start: 0.8523 (mmm) cc_final: 0.8119 (mmm) REVERT: A 646 ARG cc_start: 0.7247 (mpt180) cc_final: 0.6924 (mpt180) REVERT: A 684 GLN cc_start: 0.8687 (pt0) cc_final: 0.8436 (pt0) REVERT: A 690 LEU cc_start: 0.8326 (mt) cc_final: 0.7944 (mp) REVERT: B 181 LYS cc_start: 0.8374 (mmtp) cc_final: 0.8094 (mmtp) REVERT: B 259 ASP cc_start: 0.7275 (t0) cc_final: 0.6879 (t70) REVERT: B 358 LYS cc_start: 0.8117 (mttp) cc_final: 0.7737 (mmmt) REVERT: B 373 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 474 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7124 (mtp-110) REVERT: B 488 ILE cc_start: 0.8243 (pp) cc_final: 0.7956 (pp) REVERT: E 31 LYS cc_start: 0.8437 (tttt) cc_final: 0.8176 (tttp) REVERT: E 95 ARG cc_start: 0.7320 (ptp-110) cc_final: 0.6685 (mtt180) REVERT: E 570 MET cc_start: 0.6683 (mmt) cc_final: 0.6223 (mpt) REVERT: E 631 GLU cc_start: 0.8054 (mp0) cc_final: 0.7231 (mp0) REVERT: E 680 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7817 (mptt) REVERT: F 346 MET cc_start: 0.8326 (mtp) cc_final: 0.8085 (mtm) REVERT: F 493 LYS cc_start: 0.8170 (mttt) cc_final: 0.7911 (mmpt) REVERT: F 586 ASP cc_start: 0.7029 (m-30) cc_final: 0.6668 (m-30) REVERT: F 601 GLU cc_start: 0.7160 (mm-30) cc_final: 0.5659 (tt0) REVERT: F 625 LYS cc_start: 0.8690 (mmmt) cc_final: 0.7989 (mmtm) REVERT: F 639 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7066 (tm-30) REVERT: F 645 MET cc_start: 0.8072 (mmm) cc_final: 0.7670 (mtp) REVERT: F 646 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6688 (ptp-170) REVERT: F 678 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7408 (mptt) REVERT: F 683 GLU cc_start: 0.7931 (pm20) cc_final: 0.7489 (pm20) REVERT: F 688 LYS cc_start: 0.7077 (tppp) cc_final: 0.6763 (tptp) REVERT: H 24 LYS cc_start: 0.7214 (mmtm) cc_final: 0.6926 (mmmt) REVERT: H 27 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7847 (mtpp) REVERT: L 16 LYS cc_start: 0.6972 (mmmt) cc_final: 0.6278 (mmpt) REVERT: L 25 ILE cc_start: 0.7786 (tp) cc_final: 0.7449 (tp) REVERT: D 65 MET cc_start: 0.7134 (mtm) cc_final: 0.6922 (mtp) REVERT: G 456 MET cc_start: 0.7975 (mtp) cc_final: 0.7668 (mtp) REVERT: G 465 SER cc_start: 0.7933 (t) cc_final: 0.7719 (p) REVERT: G 472 THR cc_start: 0.7147 (m) cc_final: 0.6869 (m) REVERT: G 473 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5105 (tp30) REVERT: K 37 ASP cc_start: 0.7901 (m-30) cc_final: 0.7561 (m-30) outliers start: 71 outliers final: 17 residues processed: 529 average time/residue: 0.6548 time to fit residues: 417.2784 Evaluate side-chains 461 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 439 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 680 LYS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 646 ARG Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain K residue 36 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 370 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 323 optimal weight: 10.0000 chunk 304 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 185 HIS I 185 HIS I 385 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 467 ASN A 523 ASN E 121 HIS E 398 HIS E 552 ASN E 622 ASN F 585 HIS F 612 GLN C 39 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110524 restraints weight = 44972.399| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.33 r_work: 0.3183 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35602 Z= 0.156 Angle : 0.538 13.441 48106 Z= 0.281 Chirality : 0.042 0.213 5649 Planarity : 0.004 0.048 6007 Dihedral : 10.273 168.037 5260 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.62 % Allowed : 13.10 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.13), residues: 4369 helix: 1.98 (0.10), residues: 2688 sheet: -0.59 (0.27), residues: 350 loop : -1.26 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 517 TYR 0.022 0.001 TYR E 700 PHE 0.023 0.002 PHE L 41 TRP 0.025 0.001 TRP B 431 HIS 0.005 0.001 HIS F 218 Details of bonding type rmsd covalent geometry : bond 0.00359 (35602) covalent geometry : angle 0.53842 (48106) hydrogen bonds : bond 0.05669 ( 2121) hydrogen bonds : angle 4.20259 ( 6276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 476 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: J 262 ARG cc_start: 0.7569 (ttp80) cc_final: 0.7167 (ttp-110) REVERT: J 321 ASP cc_start: 0.8203 (m-30) cc_final: 0.7983 (m-30) REVERT: J 346 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8391 (mtm) REVERT: J 467 ASN cc_start: 0.7052 (m-40) cc_final: 0.6655 (t0) REVERT: J 511 LEU cc_start: 0.8787 (mt) cc_final: 0.8488 (mt) REVERT: J 550 GLN cc_start: 0.8188 (tt0) cc_final: 0.7920 (tt0) REVERT: J 570 MET cc_start: 0.8636 (ptm) cc_final: 0.8250 (ptm) REVERT: I 97 LEU cc_start: 0.7839 (tp) cc_final: 0.7449 (tm) REVERT: I 394 TRP cc_start: 0.7396 (t60) cc_final: 0.7133 (t60) REVERT: I 602 GLN cc_start: 0.8512 (mt0) cc_final: 0.8209 (mt0) REVERT: A 259 ASP cc_start: 0.7088 (p0) cc_final: 0.6708 (t70) REVERT: A 260 GLN cc_start: 0.7336 (tt0) cc_final: 0.7076 (tt0) REVERT: A 278 PHE cc_start: 0.7049 (m-10) cc_final: 0.6692 (t80) REVERT: A 330 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: A 433 ASP cc_start: 0.7175 (m-30) cc_final: 0.6462 (m-30) REVERT: A 446 ASP cc_start: 0.8521 (t0) cc_final: 0.8263 (t0) REVERT: A 645 MET cc_start: 0.8570 (mmm) cc_final: 0.8203 (mmm) REVERT: A 646 ARG cc_start: 0.7245 (mpt180) cc_final: 0.6960 (mpt180) REVERT: B 181 LYS cc_start: 0.8360 (mmtp) cc_final: 0.8084 (mmtp) REVERT: B 256 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7722 (mtm110) REVERT: B 259 ASP cc_start: 0.7381 (t0) cc_final: 0.7065 (t70) REVERT: B 474 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7267 (ttp80) REVERT: B 476 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6714 (ptp90) REVERT: B 488 ILE cc_start: 0.8199 (pp) cc_final: 0.7930 (pp) REVERT: B 574 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7827 (mtpp) REVERT: B 688 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7361 (mptt) REVERT: B 704 LEU cc_start: 0.7341 (mp) cc_final: 0.7062 (mt) REVERT: E 31 LYS cc_start: 0.8576 (tttt) cc_final: 0.8308 (tttp) REVERT: E 111 GLN cc_start: 0.7691 (tt0) cc_final: 0.7382 (tt0) REVERT: E 631 GLU cc_start: 0.8128 (mp0) cc_final: 0.7318 (mp0) REVERT: E 648 MET cc_start: 0.8241 (tpt) cc_final: 0.8026 (mmt) REVERT: F 321 ASP cc_start: 0.7858 (t0) cc_final: 0.7316 (m-30) REVERT: F 456 HIS cc_start: 0.4851 (m-70) cc_final: 0.4593 (m-70) REVERT: F 586 ASP cc_start: 0.7206 (m-30) cc_final: 0.6757 (m-30) REVERT: F 590 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7176 (mm-30) REVERT: F 592 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.7141 (tpp-160) REVERT: F 593 GLU cc_start: 0.8143 (mp0) cc_final: 0.7925 (mp0) REVERT: F 601 GLU cc_start: 0.7303 (mm-30) cc_final: 0.5841 (tt0) REVERT: F 639 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7004 (tm-30) REVERT: F 645 MET cc_start: 0.8115 (mmm) cc_final: 0.7787 (mtp) REVERT: F 646 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6858 (ptp-170) REVERT: F 678 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7479 (mptt) REVERT: H 24 LYS cc_start: 0.7236 (mmtm) cc_final: 0.6878 (mmmt) REVERT: H 27 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7905 (mtpp) REVERT: H 40 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8592 (mt-10) REVERT: L 25 ILE cc_start: 0.7830 (tp) cc_final: 0.7543 (tp) REVERT: L 67 PHE cc_start: 0.7747 (t80) cc_final: 0.7536 (t80) REVERT: C 35 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7892 (mm-30) REVERT: C 39 ASN cc_start: 0.8143 (m-40) cc_final: 0.7701 (m110) REVERT: C 47 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: G 36 LYS cc_start: 0.7770 (ptmt) cc_final: 0.7513 (pttm) REVERT: G 456 MET cc_start: 0.7925 (mtp) cc_final: 0.7570 (mtp) REVERT: G 472 THR cc_start: 0.7300 (m) cc_final: 0.7026 (m) REVERT: G 473 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5338 (tp30) REVERT: K 37 ASP cc_start: 0.7840 (m-30) cc_final: 0.7481 (m-30) outliers start: 96 outliers final: 41 residues processed: 527 average time/residue: 0.6275 time to fit residues: 401.6853 Evaluate side-chains 467 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 419 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 346 MET Chi-restraints excluded: chain J residue 387 THR Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 553 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 646 ARG Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 473 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 198 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 325 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 423 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS I 329 ASN I 385 GLN A 185 HIS A 330 GLN A 467 ASN B 185 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN E 429 GLN E 552 ASN E 567 ASN E 622 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113189 restraints weight = 44684.641| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.39 r_work: 0.3206 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35602 Z= 0.121 Angle : 0.491 12.555 48106 Z= 0.258 Chirality : 0.041 0.223 5649 Planarity : 0.003 0.049 6007 Dihedral : 9.609 165.247 5260 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.48 % Allowed : 15.26 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.13), residues: 4369 helix: 2.12 (0.10), residues: 2682 sheet: -0.53 (0.27), residues: 350 loop : -1.19 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 128 TYR 0.018 0.001 TYR J 700 PHE 0.017 0.001 PHE F 587 TRP 0.014 0.001 TRP B 431 HIS 0.004 0.001 HIS F 218 Details of bonding type rmsd covalent geometry : bond 0.00262 (35602) covalent geometry : angle 0.49065 (48106) hydrogen bonds : bond 0.05055 ( 2121) hydrogen bonds : angle 4.05628 ( 6276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 447 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 262 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7067 (ttp-110) REVERT: J 346 MET cc_start: 0.8641 (mtp) cc_final: 0.8337 (mtm) REVERT: J 467 ASN cc_start: 0.7046 (m-40) cc_final: 0.6642 (t0) REVERT: J 511 LEU cc_start: 0.8769 (mt) cc_final: 0.8461 (mt) REVERT: J 550 GLN cc_start: 0.8165 (tt0) cc_final: 0.7856 (tt0) REVERT: J 570 MET cc_start: 0.8637 (ptm) cc_final: 0.8237 (ptm) REVERT: I 97 LEU cc_start: 0.7817 (tp) cc_final: 0.7455 (tm) REVERT: I 394 TRP cc_start: 0.7395 (t60) cc_final: 0.7151 (t60) REVERT: I 419 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7775 (mt0) REVERT: I 602 GLN cc_start: 0.8423 (mt0) cc_final: 0.8057 (mt0) REVERT: A 259 ASP cc_start: 0.6963 (p0) cc_final: 0.6629 (t70) REVERT: A 260 GLN cc_start: 0.7274 (tt0) cc_final: 0.7028 (tt0) REVERT: A 330 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7318 (mp-120) REVERT: A 433 ASP cc_start: 0.7161 (m-30) cc_final: 0.6456 (m-30) REVERT: A 446 ASP cc_start: 0.8559 (t0) cc_final: 0.8301 (t0) REVERT: A 550 GLN cc_start: 0.8170 (pt0) cc_final: 0.7847 (tt0) REVERT: A 645 MET cc_start: 0.8538 (mmm) cc_final: 0.8150 (mmm) REVERT: A 646 ARG cc_start: 0.7227 (mpt180) cc_final: 0.6893 (mpt180) REVERT: B 181 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8064 (mmtp) REVERT: B 256 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7800 (mtm110) REVERT: B 259 ASP cc_start: 0.7360 (t0) cc_final: 0.7041 (t70) REVERT: B 373 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8099 (mt) REVERT: B 474 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7199 (tmm-80) REVERT: B 476 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6638 (ptp90) REVERT: B 535 LEU cc_start: 0.8524 (mt) cc_final: 0.8061 (pp) REVERT: B 574 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7731 (mtpp) REVERT: B 704 LEU cc_start: 0.7264 (mp) cc_final: 0.7049 (mt) REVERT: E 31 LYS cc_start: 0.8515 (tttt) cc_final: 0.8213 (tttp) REVERT: E 95 ARG cc_start: 0.7392 (ptp-110) cc_final: 0.6567 (mtm180) REVERT: E 152 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7640 (mmmm) REVERT: E 557 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6721 (mtm180) REVERT: E 631 GLU cc_start: 0.8126 (mp0) cc_final: 0.7325 (mp0) REVERT: E 688 LYS cc_start: 0.7970 (mppt) cc_final: 0.7619 (mmtm) REVERT: F 268 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6826 (mm110) REVERT: F 321 ASP cc_start: 0.7797 (t0) cc_final: 0.7287 (m-30) REVERT: F 593 GLU cc_start: 0.8117 (mp0) cc_final: 0.7899 (mp0) REVERT: F 601 GLU cc_start: 0.7278 (mm-30) cc_final: 0.5737 (tt0) REVERT: F 639 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7708 (mp0) REVERT: F 645 MET cc_start: 0.8032 (mmm) cc_final: 0.7770 (mtp) REVERT: F 678 LYS cc_start: 0.7676 (mtmm) cc_final: 0.7429 (mptt) REVERT: H 24 LYS cc_start: 0.7157 (mmtm) cc_final: 0.6795 (mmmt) REVERT: L 25 ILE cc_start: 0.7736 (tp) cc_final: 0.7458 (tp) REVERT: L 67 PHE cc_start: 0.7703 (t80) cc_final: 0.7496 (t80) REVERT: C 39 ASN cc_start: 0.8003 (m-40) cc_final: 0.7559 (m110) REVERT: C 47 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: G 35 GLU cc_start: 0.7304 (tp30) cc_final: 0.6995 (tp30) REVERT: G 36 LYS cc_start: 0.7723 (ptmt) cc_final: 0.7417 (pttm) REVERT: G 39 ASN cc_start: 0.7744 (m-40) cc_final: 0.7423 (m-40) REVERT: G 456 MET cc_start: 0.8141 (mtp) cc_final: 0.7732 (ttm) REVERT: G 472 THR cc_start: 0.7365 (m) cc_final: 0.7093 (m) REVERT: G 473 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5417 (tp30) REVERT: K 37 ASP cc_start: 0.7806 (m-30) cc_final: 0.7429 (m-30) outliers start: 91 outliers final: 38 residues processed: 494 average time/residue: 0.6410 time to fit residues: 383.6077 Evaluate side-chains 471 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 424 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 419 GLN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain F residue 268 GLN Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 473 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 284 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 351 optimal weight: 3.9990 chunk 233 optimal weight: 0.0670 chunk 124 optimal weight: 0.0170 chunk 157 optimal weight: 0.9980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS I 385 GLN A 19 GLN A 165 GLN A 467 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 552 ASN E 622 ASN F 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114467 restraints weight = 44703.463| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.39 r_work: 0.3222 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35602 Z= 0.113 Angle : 0.476 10.189 48106 Z= 0.250 Chirality : 0.040 0.239 5649 Planarity : 0.003 0.049 6007 Dihedral : 9.134 164.661 5260 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.43 % Allowed : 15.89 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.13), residues: 4369 helix: 2.21 (0.10), residues: 2683 sheet: -0.44 (0.27), residues: 352 loop : -1.13 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 256 TYR 0.020 0.001 TYR G 62 PHE 0.016 0.001 PHE F 587 TRP 0.014 0.001 TRP A 431 HIS 0.003 0.001 HIS F 218 Details of bonding type rmsd covalent geometry : bond 0.00235 (35602) covalent geometry : angle 0.47633 (48106) hydrogen bonds : bond 0.04804 ( 2121) hydrogen bonds : angle 3.95897 ( 6276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 447 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 262 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7054 (ttp-110) REVERT: J 467 ASN cc_start: 0.7162 (m-40) cc_final: 0.6705 (t0) REVERT: J 511 LEU cc_start: 0.8763 (mt) cc_final: 0.8456 (mt) REVERT: J 550 GLN cc_start: 0.8180 (tt0) cc_final: 0.7875 (tt0) REVERT: J 570 MET cc_start: 0.8634 (ptm) cc_final: 0.8207 (ptm) REVERT: I 88 LYS cc_start: 0.8351 (tptm) cc_final: 0.7955 (tptp) REVERT: I 97 LEU cc_start: 0.7834 (tp) cc_final: 0.7489 (tm) REVERT: I 111 GLN cc_start: 0.6979 (tt0) cc_final: 0.6644 (tp40) REVERT: I 175 PHE cc_start: 0.8096 (m-80) cc_final: 0.7893 (m-10) REVERT: I 394 TRP cc_start: 0.7352 (t60) cc_final: 0.7103 (t60) REVERT: I 419 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: I 602 GLN cc_start: 0.8393 (mt0) cc_final: 0.8045 (mt0) REVERT: A 257 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 433 ASP cc_start: 0.7227 (m-30) cc_final: 0.6483 (m-30) REVERT: A 446 ASP cc_start: 0.8596 (t0) cc_final: 0.8318 (t0) REVERT: A 645 MET cc_start: 0.8561 (mmm) cc_final: 0.8170 (mmm) REVERT: A 646 ARG cc_start: 0.7229 (mpt180) cc_final: 0.6926 (mpt180) REVERT: B 181 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8070 (mmtp) REVERT: B 256 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7790 (mtm110) REVERT: B 259 ASP cc_start: 0.7317 (t0) cc_final: 0.7008 (t70) REVERT: B 373 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8073 (mt) REVERT: B 474 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7183 (ttp80) REVERT: B 476 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6619 (ptp90) REVERT: B 574 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7719 (mtpp) REVERT: B 704 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7055 (mt) REVERT: E 31 LYS cc_start: 0.8505 (tttt) cc_final: 0.8214 (tttp) REVERT: E 95 ARG cc_start: 0.7373 (ptp-110) cc_final: 0.6604 (mtm180) REVERT: E 152 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7524 (mmmm) REVERT: E 247 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7106 (mtm180) REVERT: E 557 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6696 (mtm180) REVERT: E 631 GLU cc_start: 0.8143 (mp0) cc_final: 0.7372 (mp0) REVERT: E 688 LYS cc_start: 0.7948 (mppt) cc_final: 0.7612 (mmtt) REVERT: F 321 ASP cc_start: 0.7788 (t0) cc_final: 0.7284 (m-30) REVERT: F 601 GLU cc_start: 0.7161 (mm-30) cc_final: 0.5592 (tt0) REVERT: F 639 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7629 (mp0) REVERT: F 645 MET cc_start: 0.8026 (mmm) cc_final: 0.7763 (mtp) REVERT: F 678 LYS cc_start: 0.7687 (mtmm) cc_final: 0.7424 (mptt) REVERT: H 24 LYS cc_start: 0.6881 (mmtm) cc_final: 0.6492 (mmmt) REVERT: L 25 ILE cc_start: 0.7658 (tp) cc_final: 0.7378 (tp) REVERT: L 48 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8713 (mp) REVERT: C 39 ASN cc_start: 0.7980 (m-40) cc_final: 0.7556 (m110) REVERT: C 47 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: G 36 LYS cc_start: 0.7729 (ptmt) cc_final: 0.7498 (pttm) REVERT: G 456 MET cc_start: 0.8138 (mtp) cc_final: 0.7715 (ttm) REVERT: G 473 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5384 (tp30) REVERT: K 37 ASP cc_start: 0.7820 (m-30) cc_final: 0.7448 (m-30) outliers start: 89 outliers final: 44 residues processed: 499 average time/residue: 0.6374 time to fit residues: 384.9489 Evaluate side-chains 477 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 423 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 512 THR Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 419 GLN Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 473 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 393 optimal weight: 7.9990 chunk 355 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 325 optimal weight: 0.5980 chunk 309 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 380 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 400 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS I 385 GLN A 260 GLN A 330 GLN A 467 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 GLN E 552 ASN E 602 GLN E 622 ASN F 185 HIS ** F 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 649 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112559 restraints weight = 44571.522| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.38 r_work: 0.3211 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35602 Z= 0.123 Angle : 0.492 14.404 48106 Z= 0.257 Chirality : 0.041 0.238 5649 Planarity : 0.003 0.048 6007 Dihedral : 8.802 163.145 5260 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.62 % Allowed : 16.49 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.13), residues: 4369 helix: 2.22 (0.10), residues: 2675 sheet: -0.34 (0.27), residues: 352 loop : -1.08 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 256 TYR 0.020 0.001 TYR J 700 PHE 0.017 0.001 PHE D 67 TRP 0.018 0.001 TRP A 431 HIS 0.004 0.001 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00271 (35602) covalent geometry : angle 0.49217 (48106) hydrogen bonds : bond 0.04945 ( 2121) hydrogen bonds : angle 3.95336 ( 6276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 446 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 262 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7116 (ttp-110) REVERT: J 467 ASN cc_start: 0.7242 (m-40) cc_final: 0.6739 (t0) REVERT: J 511 LEU cc_start: 0.8790 (mt) cc_final: 0.8493 (mt) REVERT: J 550 GLN cc_start: 0.8212 (tt0) cc_final: 0.7905 (tt0) REVERT: J 570 MET cc_start: 0.8650 (ptm) cc_final: 0.8313 (ptm) REVERT: J 638 TYR cc_start: 0.7550 (t80) cc_final: 0.6887 (t80) REVERT: J 643 ILE cc_start: 0.7327 (mm) cc_final: 0.7076 (mp) REVERT: I 97 LEU cc_start: 0.7884 (tp) cc_final: 0.7525 (tm) REVERT: I 111 GLN cc_start: 0.6969 (tt0) cc_final: 0.6650 (tp40) REVERT: I 602 GLN cc_start: 0.8316 (mt0) cc_final: 0.7976 (mt0) REVERT: A 257 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 259 ASP cc_start: 0.7067 (p0) cc_final: 0.6679 (t70) REVERT: A 260 GLN cc_start: 0.7273 (tt0) cc_final: 0.7008 (tt0) REVERT: A 330 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7473 (mp-120) REVERT: A 433 ASP cc_start: 0.7220 (m-30) cc_final: 0.6463 (m-30) REVERT: A 446 ASP cc_start: 0.8648 (t0) cc_final: 0.8339 (t0) REVERT: A 645 MET cc_start: 0.8549 (mmm) cc_final: 0.8142 (mmm) REVERT: A 646 ARG cc_start: 0.7237 (mpt180) cc_final: 0.6937 (mpt180) REVERT: B 181 LYS cc_start: 0.8345 (mmtp) cc_final: 0.8071 (mmtp) REVERT: B 256 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7808 (mtm110) REVERT: B 259 ASP cc_start: 0.7387 (t0) cc_final: 0.7072 (t70) REVERT: B 373 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 474 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7203 (ttp80) REVERT: B 476 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6852 (ptp90) REVERT: B 574 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7711 (mtpp) REVERT: B 704 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7084 (mt) REVERT: E 31 LYS cc_start: 0.8494 (tttt) cc_final: 0.8201 (tttp) REVERT: E 152 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7528 (mmmm) REVERT: E 247 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7141 (mtm180) REVERT: E 557 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6765 (mtm180) REVERT: E 570 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5965 (mpt) REVERT: E 688 LYS cc_start: 0.7980 (mppt) cc_final: 0.7587 (mmtt) REVERT: F 321 ASP cc_start: 0.7776 (t0) cc_final: 0.7246 (m-30) REVERT: F 456 HIS cc_start: 0.4738 (m-70) cc_final: 0.4526 (m-70) REVERT: F 601 GLU cc_start: 0.7188 (mm-30) cc_final: 0.5604 (tt0) REVERT: F 639 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7648 (mp0) REVERT: F 645 MET cc_start: 0.8028 (mmm) cc_final: 0.7768 (mtp) REVERT: F 678 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7412 (mptt) REVERT: H 24 LYS cc_start: 0.6942 (mmtm) cc_final: 0.6556 (mmmt) REVERT: L 16 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6669 (mmpt) REVERT: L 25 ILE cc_start: 0.7643 (tp) cc_final: 0.7371 (tp) REVERT: C 39 ASN cc_start: 0.7998 (m-40) cc_final: 0.7572 (m110) REVERT: G 36 LYS cc_start: 0.7728 (ptmt) cc_final: 0.7457 (pttm) REVERT: G 456 MET cc_start: 0.8117 (mtp) cc_final: 0.7693 (ttm) REVERT: G 473 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5510 (tp30) REVERT: K 37 ASP cc_start: 0.7807 (m-30) cc_final: 0.7475 (m-30) outliers start: 96 outliers final: 54 residues processed: 508 average time/residue: 0.6247 time to fit residues: 385.4272 Evaluate side-chains 489 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 425 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 512 THR Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 570 MET Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 274 optimal weight: 0.5980 chunk 409 optimal weight: 30.0000 chunk 212 optimal weight: 0.6980 chunk 358 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 318 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 185 HIS I 385 GLN A 19 GLN A 467 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN E 552 ASN E 622 ASN F 263 ASN F 612 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113075 restraints weight = 44632.448| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.34 r_work: 0.3213 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35602 Z= 0.124 Angle : 0.495 12.362 48106 Z= 0.257 Chirality : 0.041 0.187 5649 Planarity : 0.003 0.053 6007 Dihedral : 8.667 162.128 5260 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.43 % Allowed : 17.09 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.13), residues: 4369 helix: 2.22 (0.10), residues: 2676 sheet: -0.32 (0.27), residues: 354 loop : -1.04 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 95 TYR 0.020 0.001 TYR J 700 PHE 0.015 0.001 PHE H 63 TRP 0.019 0.001 TRP A 431 HIS 0.004 0.001 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00274 (35602) covalent geometry : angle 0.49494 (48106) hydrogen bonds : bond 0.04954 ( 2121) hydrogen bonds : angle 3.94388 ( 6276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 448 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 262 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7172 (ttp-110) REVERT: J 268 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7945 (mm-40) REVERT: J 320 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7963 (m-30) REVERT: J 467 ASN cc_start: 0.7198 (m-40) cc_final: 0.6758 (t0) REVERT: J 511 LEU cc_start: 0.8869 (mt) cc_final: 0.8587 (mt) REVERT: J 550 GLN cc_start: 0.8137 (tt0) cc_final: 0.7904 (tt0) REVERT: J 570 MET cc_start: 0.8664 (ptm) cc_final: 0.8278 (ptm) REVERT: J 638 TYR cc_start: 0.7567 (t80) cc_final: 0.6896 (t80) REVERT: J 643 ILE cc_start: 0.7398 (mm) cc_final: 0.7143 (mp) REVERT: I 97 LEU cc_start: 0.7932 (tp) cc_final: 0.7572 (tm) REVERT: I 111 GLN cc_start: 0.7004 (tt0) cc_final: 0.6694 (tp40) REVERT: I 175 PHE cc_start: 0.8069 (m-80) cc_final: 0.7844 (m-10) REVERT: I 602 GLN cc_start: 0.8333 (mt0) cc_final: 0.8002 (mt0) REVERT: A 257 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: A 259 ASP cc_start: 0.7049 (p0) cc_final: 0.6669 (t70) REVERT: A 260 GLN cc_start: 0.7265 (tt0) cc_final: 0.6999 (tt0) REVERT: A 433 ASP cc_start: 0.7253 (m-30) cc_final: 0.6498 (m-30) REVERT: A 446 ASP cc_start: 0.8674 (t0) cc_final: 0.8367 (t0) REVERT: A 645 MET cc_start: 0.8584 (mmm) cc_final: 0.8171 (mmm) REVERT: A 646 ARG cc_start: 0.7255 (mpt180) cc_final: 0.6916 (mpt180) REVERT: B 181 LYS cc_start: 0.8347 (mmtp) cc_final: 0.8071 (mmtp) REVERT: B 373 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8125 (mt) REVERT: B 439 ILE cc_start: 0.7675 (mt) cc_final: 0.7336 (tt) REVERT: B 474 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7245 (ttp80) REVERT: B 476 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6746 (ptp90) REVERT: B 561 ASP cc_start: 0.8319 (m-30) cc_final: 0.8031 (m-30) REVERT: B 704 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7136 (mt) REVERT: E 31 LYS cc_start: 0.8519 (tttt) cc_final: 0.8228 (tttp) REVERT: E 95 ARG cc_start: 0.7412 (ptp-110) cc_final: 0.6432 (mtm-85) REVERT: E 152 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7520 (mmmm) REVERT: E 247 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7318 (mtm180) REVERT: E 557 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6775 (mtm180) REVERT: E 570 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.6005 (mpt) REVERT: E 688 LYS cc_start: 0.8016 (mppt) cc_final: 0.7631 (mmtt) REVERT: F 321 ASP cc_start: 0.7800 (t0) cc_final: 0.7282 (m-30) REVERT: F 601 GLU cc_start: 0.7297 (mm-30) cc_final: 0.5738 (tt0) REVERT: F 639 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7653 (mp0) REVERT: F 645 MET cc_start: 0.8037 (mmm) cc_final: 0.7790 (mtp) REVERT: F 678 LYS cc_start: 0.7709 (mtmm) cc_final: 0.7434 (mptt) REVERT: H 24 LYS cc_start: 0.6959 (mmtm) cc_final: 0.6560 (mmmt) REVERT: L 16 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6716 (mmpt) REVERT: L 25 ILE cc_start: 0.7706 (tp) cc_final: 0.7443 (tp) REVERT: L 67 PHE cc_start: 0.7714 (t80) cc_final: 0.7494 (t80) REVERT: D 34 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6117 (mtt-85) REVERT: C 39 ASN cc_start: 0.8021 (m-40) cc_final: 0.7590 (m110) REVERT: C 47 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: G 36 LYS cc_start: 0.7750 (ptmt) cc_final: 0.7492 (pttm) REVERT: G 456 MET cc_start: 0.8174 (mtp) cc_final: 0.7792 (ttm) REVERT: G 468 GLU cc_start: 0.6028 (mt-10) cc_final: 0.5809 (mt-10) REVERT: G 473 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5793 (tp30) outliers start: 89 outliers final: 55 residues processed: 500 average time/residue: 0.6328 time to fit residues: 384.2858 Evaluate side-chains 497 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 429 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 268 GLN Chi-restraints excluded: chain J residue 320 ASP Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 512 THR Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 398 HIS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 570 MET Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 289 TYR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 473 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 225 optimal weight: 2.9990 chunk 387 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 410 optimal weight: 50.0000 chunk 241 optimal weight: 2.9990 chunk 278 optimal weight: 0.3980 chunk 424 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 121 HIS I 185 HIS I 385 GLN A 467 ASN A 649 HIS B 456 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN B 612 GLN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 HIS E 429 GLN E 552 ASN E 622 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108164 restraints weight = 45073.027| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.33 r_work: 0.3145 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35602 Z= 0.203 Angle : 0.570 11.626 48106 Z= 0.298 Chirality : 0.044 0.299 5649 Planarity : 0.004 0.059 6007 Dihedral : 9.137 161.775 5260 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.51 % Allowed : 17.20 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4369 helix: 1.93 (0.10), residues: 2686 sheet: -0.41 (0.27), residues: 358 loop : -1.11 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 95 TYR 0.020 0.001 TYR J 700 PHE 0.021 0.002 PHE J 587 TRP 0.029 0.002 TRP F 431 HIS 0.006 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00494 (35602) covalent geometry : angle 0.57012 (48106) hydrogen bonds : bond 0.06205 ( 2121) hydrogen bonds : angle 4.17452 ( 6276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 432 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 262 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7196 (ttp-110) REVERT: J 283 PHE cc_start: 0.8290 (m-80) cc_final: 0.7710 (m-10) REVERT: J 320 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: J 358 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8472 (mtmt) REVERT: J 437 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8503 (p) REVERT: J 467 ASN cc_start: 0.7544 (m-40) cc_final: 0.7018 (t0) REVERT: J 550 GLN cc_start: 0.8250 (tt0) cc_final: 0.8003 (tt0) REVERT: J 570 MET cc_start: 0.8652 (ptm) cc_final: 0.8310 (ptm) REVERT: J 638 TYR cc_start: 0.7639 (t80) cc_final: 0.6977 (t80) REVERT: I 97 LEU cc_start: 0.7953 (tp) cc_final: 0.7545 (tm) REVERT: I 111 GLN cc_start: 0.7041 (tt0) cc_final: 0.6736 (tp40) REVERT: I 570 MET cc_start: 0.8525 (ptm) cc_final: 0.8112 (ptm) REVERT: I 602 GLN cc_start: 0.8538 (mt0) cc_final: 0.8206 (mt0) REVERT: A 179 MET cc_start: 0.8365 (tpp) cc_final: 0.8128 (ttm) REVERT: A 257 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 259 ASP cc_start: 0.7044 (p0) cc_final: 0.6658 (t70) REVERT: A 433 ASP cc_start: 0.7343 (m-30) cc_final: 0.6924 (m-30) REVERT: A 446 ASP cc_start: 0.8681 (t0) cc_final: 0.8408 (t0) REVERT: A 645 MET cc_start: 0.8409 (mmm) cc_final: 0.7971 (mmm) REVERT: B 181 LYS cc_start: 0.8347 (mmtp) cc_final: 0.8063 (mmtp) REVERT: B 205 GLU cc_start: 0.7669 (tt0) cc_final: 0.7194 (tm-30) REVERT: B 259 ASP cc_start: 0.7400 (t70) cc_final: 0.6972 (t70) REVERT: B 373 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8252 (mt) REVERT: B 439 ILE cc_start: 0.7885 (mt) cc_final: 0.7642 (tt) REVERT: B 474 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7311 (tmm-80) REVERT: B 476 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6994 (ptp90) REVERT: B 561 ASP cc_start: 0.8338 (m-30) cc_final: 0.7894 (m-30) REVERT: B 704 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7124 (mt) REVERT: E 31 LYS cc_start: 0.8583 (tttt) cc_final: 0.8279 (tttp) REVERT: E 247 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7281 (mtm180) REVERT: E 557 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6657 (mtm180) REVERT: E 648 MET cc_start: 0.8198 (tpt) cc_final: 0.7979 (mmt) REVERT: E 688 LYS cc_start: 0.8048 (mppt) cc_final: 0.7677 (mmtt) REVERT: F 295 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8003 (mm) REVERT: F 321 ASP cc_start: 0.7932 (t0) cc_final: 0.7336 (m-30) REVERT: F 601 GLU cc_start: 0.7364 (mm-30) cc_final: 0.5813 (tt0) REVERT: F 639 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7609 (mp0) REVERT: F 645 MET cc_start: 0.8133 (mmm) cc_final: 0.7840 (mtp) REVERT: F 678 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7438 (mptt) REVERT: H 24 LYS cc_start: 0.7206 (mmtm) cc_final: 0.6805 (mmmt) REVERT: L 25 ILE cc_start: 0.7800 (tp) cc_final: 0.7543 (tp) REVERT: D 34 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6175 (mtt-85) REVERT: C 47 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: G 36 LYS cc_start: 0.7730 (ptmt) cc_final: 0.7498 (pttm) REVERT: G 456 MET cc_start: 0.8085 (mtp) cc_final: 0.7666 (ttm) REVERT: G 473 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5924 (tp30) REVERT: K 38 GLU cc_start: 0.8185 (tt0) cc_final: 0.7923 (mt-10) outliers start: 92 outliers final: 55 residues processed: 486 average time/residue: 0.6462 time to fit residues: 379.4119 Evaluate side-chains 486 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 320 ASP Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain J residue 512 THR Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 373 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 473 GLU Chi-restraints excluded: chain K residue 54 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 163 optimal weight: 0.7980 chunk 365 optimal weight: 0.9980 chunk 428 optimal weight: 40.0000 chunk 416 optimal weight: 0.6980 chunk 368 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 413 optimal weight: 0.0970 chunk 189 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 HIS I 121 HIS I 185 HIS I 385 GLN A 467 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 552 ASN E 622 ASN E 662 HIS C 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112715 restraints weight = 44348.403| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.34 r_work: 0.3215 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35602 Z= 0.118 Angle : 0.502 11.545 48106 Z= 0.260 Chirality : 0.041 0.302 5649 Planarity : 0.003 0.053 6007 Dihedral : 8.618 160.869 5260 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.94 % Allowed : 18.15 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.13), residues: 4369 helix: 2.18 (0.10), residues: 2676 sheet: -0.29 (0.27), residues: 354 loop : -1.02 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 95 TYR 0.021 0.001 TYR G 62 PHE 0.015 0.001 PHE H 63 TRP 0.023 0.001 TRP F 431 HIS 0.005 0.001 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00246 (35602) covalent geometry : angle 0.50154 (48106) hydrogen bonds : bond 0.04982 ( 2121) hydrogen bonds : angle 3.97897 ( 6276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 446 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: J 262 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7072 (ttp-110) REVERT: J 467 ASN cc_start: 0.7370 (m-40) cc_final: 0.6927 (t0) REVERT: J 476 ARG cc_start: 0.6984 (mtp85) cc_final: 0.5893 (mtp85) REVERT: J 550 GLN cc_start: 0.8068 (tt0) cc_final: 0.7832 (tt0) REVERT: J 570 MET cc_start: 0.8710 (ptm) cc_final: 0.8300 (ptm) REVERT: J 638 TYR cc_start: 0.7529 (t80) cc_final: 0.6825 (t80) REVERT: I 88 LYS cc_start: 0.8376 (tptm) cc_final: 0.7960 (tptp) REVERT: I 97 LEU cc_start: 0.7951 (tp) cc_final: 0.7587 (tm) REVERT: I 111 GLN cc_start: 0.6971 (tt0) cc_final: 0.6693 (tp40) REVERT: I 175 PHE cc_start: 0.8089 (m-80) cc_final: 0.7870 (m-10) REVERT: I 570 MET cc_start: 0.8406 (ptm) cc_final: 0.8004 (ptm) REVERT: I 602 GLN cc_start: 0.8419 (mt0) cc_final: 0.8135 (mt0) REVERT: A 259 ASP cc_start: 0.6961 (p0) cc_final: 0.6601 (t70) REVERT: A 260 GLN cc_start: 0.7193 (tt0) cc_final: 0.6933 (tt0) REVERT: A 433 ASP cc_start: 0.7159 (m-30) cc_final: 0.6705 (m-30) REVERT: A 446 ASP cc_start: 0.8679 (t0) cc_final: 0.8408 (t0) REVERT: A 645 MET cc_start: 0.8356 (mmm) cc_final: 0.7935 (mmm) REVERT: B 169 LEU cc_start: 0.7785 (tt) cc_final: 0.7538 (tp) REVERT: B 181 LYS cc_start: 0.8289 (mmtp) cc_final: 0.8012 (mmtp) REVERT: B 205 GLU cc_start: 0.7489 (tt0) cc_final: 0.7025 (tm-30) REVERT: B 259 ASP cc_start: 0.7353 (t70) cc_final: 0.6924 (t70) REVERT: B 373 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 439 ILE cc_start: 0.7684 (mt) cc_final: 0.7342 (tt) REVERT: B 474 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7178 (tmm-80) REVERT: B 476 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6684 (ptp90) REVERT: B 561 ASP cc_start: 0.8319 (m-30) cc_final: 0.7890 (m-30) REVERT: B 704 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7168 (mt) REVERT: E 31 LYS cc_start: 0.8468 (tttt) cc_final: 0.8168 (tttp) REVERT: E 95 ARG cc_start: 0.7404 (ptp-110) cc_final: 0.6313 (mtm-85) REVERT: E 247 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7360 (mtm180) REVERT: E 557 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6574 (mtm110) REVERT: E 570 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.5596 (mpt) REVERT: E 688 LYS cc_start: 0.8125 (mppt) cc_final: 0.7828 (mmtt) REVERT: F 295 LEU cc_start: 0.8210 (mp) cc_final: 0.7988 (mm) REVERT: F 321 ASP cc_start: 0.7777 (t0) cc_final: 0.7261 (m-30) REVERT: F 601 GLU cc_start: 0.7300 (mm-30) cc_final: 0.5724 (tt0) REVERT: F 639 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7611 (mp0) REVERT: F 645 MET cc_start: 0.8041 (mmm) cc_final: 0.7771 (mtp) REVERT: F 678 LYS cc_start: 0.7622 (mtmm) cc_final: 0.7391 (mptt) REVERT: H 24 LYS cc_start: 0.7098 (mmtm) cc_final: 0.6706 (mmmt) REVERT: L 16 LYS cc_start: 0.6916 (mmmt) cc_final: 0.6661 (mmpt) REVERT: L 25 ILE cc_start: 0.7646 (tp) cc_final: 0.7383 (tp) REVERT: C 47 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8289 (tp30) REVERT: C 62 TYR cc_start: 0.7282 (t80) cc_final: 0.6952 (t80) REVERT: G 36 LYS cc_start: 0.7627 (ptmt) cc_final: 0.7425 (pttm) REVERT: G 456 MET cc_start: 0.8109 (mtp) cc_final: 0.7694 (ttm) REVERT: G 462 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6941 (m-10) REVERT: G 473 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5976 (tp30) REVERT: K 38 GLU cc_start: 0.8200 (tt0) cc_final: 0.7875 (mt-10) outliers start: 71 outliers final: 43 residues processed: 491 average time/residue: 0.6238 time to fit residues: 371.6443 Evaluate side-chains 479 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 428 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 263 ASN Chi-restraints excluded: chain J residue 389 MET Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain J residue 535 LEU Chi-restraints excluded: chain J residue 689 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 103 GLN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 570 MET Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain G residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 328 optimal weight: 0.0070 chunk 159 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 116 optimal weight: 0.0030 chunk 381 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 121 HIS I 185 HIS I 385 GLN A 19 GLN A 165 GLN A 467 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN E 68 ASN E 429 GLN E 552 ASN E 567 ASN E 622 ASN C 39 ASN G 45 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.154164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114706 restraints weight = 44637.960| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.40 r_work: 0.3233 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35602 Z= 0.113 Angle : 0.499 11.344 48106 Z= 0.259 Chirality : 0.041 0.290 5649 Planarity : 0.003 0.060 6007 Dihedral : 8.237 157.985 5260 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.72 % Allowed : 18.73 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.13), residues: 4369 helix: 2.27 (0.10), residues: 2680 sheet: -0.21 (0.27), residues: 354 loop : -0.94 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 95 TYR 0.021 0.001 TYR J 700 PHE 0.018 0.001 PHE A 278 TRP 0.023 0.001 TRP A 431 HIS 0.005 0.001 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00236 (35602) covalent geometry : angle 0.49923 (48106) hydrogen bonds : bond 0.04661 ( 2121) hydrogen bonds : angle 3.88206 ( 6276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8738 Ramachandran restraints generated. 4369 Oldfield, 0 Emsley, 4369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 448 time to evaluate : 1.179 Fit side-chains REVERT: J 262 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7104 (ttp-110) REVERT: J 467 ASN cc_start: 0.7392 (m-40) cc_final: 0.6939 (t0) REVERT: J 550 GLN cc_start: 0.8063 (tt0) cc_final: 0.7828 (tt0) REVERT: J 570 MET cc_start: 0.8741 (ptm) cc_final: 0.8366 (ptm) REVERT: J 638 TYR cc_start: 0.7513 (t80) cc_final: 0.6752 (t80) REVERT: I 88 LYS cc_start: 0.8388 (tptm) cc_final: 0.8019 (tptp) REVERT: I 97 LEU cc_start: 0.7975 (tp) cc_final: 0.7640 (tm) REVERT: I 111 GLN cc_start: 0.7061 (tt0) cc_final: 0.6779 (tp40) REVERT: I 175 PHE cc_start: 0.8075 (m-80) cc_final: 0.7870 (m-10) REVERT: I 526 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8476 (t) REVERT: I 570 MET cc_start: 0.8362 (ptm) cc_final: 0.7903 (ptm) REVERT: I 602 GLN cc_start: 0.8265 (mt0) cc_final: 0.7978 (mt0) REVERT: A 259 ASP cc_start: 0.6972 (p0) cc_final: 0.6623 (t70) REVERT: A 260 GLN cc_start: 0.7308 (tt0) cc_final: 0.7052 (tt0) REVERT: A 433 ASP cc_start: 0.7221 (m-30) cc_final: 0.6718 (m-30) REVERT: A 446 ASP cc_start: 0.8603 (t0) cc_final: 0.8347 (t0) REVERT: A 645 MET cc_start: 0.8379 (mmm) cc_final: 0.8037 (mmm) REVERT: B 169 LEU cc_start: 0.7786 (tt) cc_final: 0.7560 (tp) REVERT: B 181 LYS cc_start: 0.8347 (mmtp) cc_final: 0.8063 (mmtp) REVERT: B 256 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7882 (mtt180) REVERT: B 259 ASP cc_start: 0.7370 (t70) cc_final: 0.6909 (t70) REVERT: B 373 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8112 (mt) REVERT: B 439 ILE cc_start: 0.7577 (mt) cc_final: 0.7342 (tt) REVERT: B 474 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7190 (tmm-80) REVERT: B 476 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6670 (ptp90) REVERT: B 561 ASP cc_start: 0.8221 (m-30) cc_final: 0.7781 (m-30) REVERT: B 643 ILE cc_start: 0.8154 (mt) cc_final: 0.7898 (mp) REVERT: B 645 MET cc_start: 0.8225 (mmm) cc_final: 0.7906 (mmm) REVERT: E 95 ARG cc_start: 0.7448 (ptp-110) cc_final: 0.6393 (mtm-85) REVERT: E 247 ARG cc_start: 0.7601 (mtm180) cc_final: 0.7333 (mtm180) REVERT: E 522 GLU cc_start: 0.8600 (tt0) cc_final: 0.8314 (pt0) REVERT: E 557 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6583 (mtm180) REVERT: E 567 ASN cc_start: 0.7507 (t0) cc_final: 0.7145 (t0) REVERT: E 570 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5308 (mpt) REVERT: E 688 LYS cc_start: 0.8146 (mppt) cc_final: 0.7842 (mmtt) REVERT: F 295 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7968 (mm) REVERT: F 321 ASP cc_start: 0.7764 (t0) cc_final: 0.7240 (m-30) REVERT: F 601 GLU cc_start: 0.7222 (mm-30) cc_final: 0.5711 (tt0) REVERT: F 639 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7598 (mp0) REVERT: F 645 MET cc_start: 0.8033 (mmm) cc_final: 0.7748 (mtp) REVERT: F 678 LYS cc_start: 0.7593 (mtmm) cc_final: 0.7366 (mptt) REVERT: F 703 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8620 (tt0) REVERT: H 24 LYS cc_start: 0.7386 (mmtm) cc_final: 0.6982 (mmmt) REVERT: L 16 LYS cc_start: 0.6858 (mmmt) cc_final: 0.6585 (mmpt) REVERT: L 25 ILE cc_start: 0.7628 (tp) cc_final: 0.7378 (tp) REVERT: C 47 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: C 62 TYR cc_start: 0.7204 (t80) cc_final: 0.6985 (t80) REVERT: G 36 LYS cc_start: 0.7659 (ptmt) cc_final: 0.7445 (pttm) REVERT: G 456 MET cc_start: 0.8075 (mtp) cc_final: 0.7725 (ttm) REVERT: G 462 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6920 (m-10) REVERT: G 468 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5865 (pt0) REVERT: G 473 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6143 (tp30) REVERT: K 38 GLU cc_start: 0.8193 (tt0) cc_final: 0.7881 (mt-10) outliers start: 63 outliers final: 34 residues processed: 487 average time/residue: 0.6175 time to fit residues: 365.3256 Evaluate side-chains 465 residues out of total 3838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 422 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 398 HIS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 643 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 308 SER Chi-restraints excluded: chain E residue 398 HIS Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 570 MET Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 398 HIS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 665 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 462 TYR Chi-restraints excluded: chain G residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 322 optimal weight: 7.9990 chunk 316 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 121 HIS I 185 HIS I 385 GLN A 165 GLN A 467 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 ASN E 622 ASN C 39 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111588 restraints weight = 44519.196| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.35 r_work: 0.3196 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35602 Z= 0.141 Angle : 0.522 10.923 48106 Z= 0.271 Chirality : 0.042 0.283 5649 Planarity : 0.004 0.061 6007 Dihedral : 8.334 156.654 5260 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.69 % Allowed : 19.00 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.13), residues: 4369 helix: 2.19 (0.10), residues: 2680 sheet: -0.26 (0.27), residues: 354 loop : -0.96 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 95 TYR 0.022 0.001 TYR F 577 PHE 0.027 0.001 PHE A 278 TRP 0.030 0.001 TRP F 431 HIS 0.007 0.001 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00324 (35602) covalent geometry : angle 0.52190 (48106) hydrogen bonds : bond 0.05206 ( 2121) hydrogen bonds : angle 3.95876 ( 6276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13105.95 seconds wall clock time: 222 minutes 54.38 seconds (13374.38 seconds total)