Starting phenix.real_space_refine on Tue Aug 26 07:56:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqw_24638/08_2025/7rqw_24638_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqw_24638/08_2025/7rqw_24638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rqw_24638/08_2025/7rqw_24638_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqw_24638/08_2025/7rqw_24638_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rqw_24638/08_2025/7rqw_24638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqw_24638/08_2025/7rqw_24638.map" } resolution = 3.11 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= 0.013 sd= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 88 5.16 5 C 11356 2.51 5 N 2644 2.21 5 O 3080 1.98 5 H 15804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32984 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8070 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 218 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 194 Unusual residues: {'6EU': 1, '6OU': 1, 'LBN': 2, 'PCW': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Unusual residues: {'6EU': 1, '6OU': 1, 'PCW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'6OU:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Unusual residues: {'6EU': 1, '6OU': 1, 'PCW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'6OU:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, C, D Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 Time building chain proxies: 11.10, per 1000 atoms: 0.34 Number of scatterers: 32984 At special positions: 0 Unit cell: (119.88, 120.96, 109.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 12 15.00 O 3080 8.00 N 2644 7.00 C 11356 6.00 H 15804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 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: 3.45 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 4 sheets defined 67.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 removed outlier: 3.619A pdb=" N ILE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.584A pdb=" N VAL A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.634A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.901A pdb=" N GLU A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 328' Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.781A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 503 through 507 removed outlier: 4.318A pdb=" N PHE A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 removed outlier: 4.119A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 562 through 575 removed outlier: 4.164A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 599 removed outlier: 3.823A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 672 through 692 removed outlier: 3.687A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 removed outlier: 3.788A pdb=" N PHE A 720 " --> pdb=" O MET A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 removed outlier: 3.618A pdb=" N ILE B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.585A pdb=" N VAL B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.634A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.902A pdb=" N GLU B 327 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 328' Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.781A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 503 through 507 removed outlier: 4.318A pdb=" N PHE B 507 " --> pdb=" O LYS B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.120A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 562 through 575 removed outlier: 4.164A pdb=" N ALA B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 599 removed outlier: 3.823A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 692 removed outlier: 3.688A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 720 removed outlier: 3.788A pdb=" N PHE B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 3.619A pdb=" N ILE C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.584A pdb=" N VAL C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.634A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.901A pdb=" N GLU C 327 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 328' Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.782A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 503 through 507 removed outlier: 4.319A pdb=" N PHE C 507 " --> pdb=" O LYS C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 4.119A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 559 Processing helix chain 'C' and resid 562 through 575 removed outlier: 4.164A pdb=" N ALA C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.824A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 672 through 692 removed outlier: 3.687A pdb=" N ASN C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 720 removed outlier: 3.789A pdb=" N PHE C 720 " --> pdb=" O MET C 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.619A pdb=" N ILE D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.583A pdb=" N VAL D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.635A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 removed outlier: 3.901A pdb=" N GLU D 327 " --> pdb=" O LYS D 324 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 328' Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.550A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.654A pdb=" N TYR D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.782A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 429 Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 503 through 507 removed outlier: 4.318A pdb=" N PHE D 507 " --> pdb=" O LYS D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 removed outlier: 4.120A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 559 Processing helix chain 'D' and resid 562 through 575 removed outlier: 4.163A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.823A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 672 through 692 removed outlier: 3.687A pdb=" N ASN D 676 " --> pdb=" O ILE D 672 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.585A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 720 removed outlier: 3.789A pdb=" N PHE D 720 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR A 382 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 728 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR B 382 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL B 728 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 382 " --> pdb=" O PHE C 742 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 728 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 368 through 372 removed outlier: 6.848A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR D 382 " --> pdb=" O PHE D 742 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL D 728 " --> pdb=" O ASP D 737 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2832 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: 7.25 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15784 1.02 - 1.22: 52 1.22 - 1.42: 7359 1.42 - 1.61: 10017 1.61 - 1.81: 180 Bond restraints: 33392 Sorted by residual: bond pdb=" CAS 6EU D 902 " pdb=" CAX 6EU D 902 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" CAS 6EU C 902 " pdb=" CAX 6EU C 902 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" CAS 6EU B 901 " pdb=" CAX 6EU B 901 " ideal model delta sigma weight residual 1.334 1.602 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" CAW 6EU D 902 " pdb=" CBA 6EU D 902 " ideal model delta sigma weight residual 1.339 1.524 -0.185 2.00e-02 2.50e+03 8.52e+01 ... (remaining 33387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 59172 3.33 - 6.65: 388 6.65 - 9.98: 72 9.98 - 13.31: 8 13.31 - 16.63: 8 Bond angle restraints: 59648 Sorted by residual: angle pdb=" CAM 6EU A 901 " pdb=" CAV 6EU A 901 " pdb=" CBD 6EU A 901 " ideal model delta sigma weight residual 115.62 98.99 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" CAM 6EU C 902 " pdb=" CAV 6EU C 902 " pdb=" CBD 6EU C 902 " ideal model delta sigma weight residual 115.62 98.99 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" CAM 6EU B 901 " pdb=" CAV 6EU B 901 " pdb=" CBD 6EU B 901 " ideal model delta sigma weight residual 115.62 99.01 16.61 3.00e+00 1.11e-01 3.06e+01 angle pdb=" CAM 6EU D 902 " pdb=" CAV 6EU D 902 " pdb=" CBD 6EU D 902 " ideal model delta sigma weight residual 115.62 99.02 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O1 LBN B 903 " pdb=" P1 LBN B 903 " pdb=" O2 LBN B 903 " ideal model delta sigma weight residual 93.45 108.96 -15.51 3.00e+00 1.11e-01 2.67e+01 ... (remaining 59643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 15816 33.92 - 67.85: 520 67.85 - 101.77: 36 101.77 - 135.70: 8 135.70 - 169.62: 8 Dihedral angle restraints: 16388 sinusoidal: 8676 harmonic: 7712 Sorted by residual: dihedral pdb=" C1 LBN A 905 " pdb=" O1 LBN A 905 " pdb=" P1 LBN A 905 " pdb=" O3 LBN A 905 " ideal model delta sinusoidal sigma weight residual 275.40 105.78 169.62 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN A 903 " pdb=" O1 LBN A 903 " pdb=" P1 LBN A 903 " pdb=" O3 LBN A 903 " ideal model delta sinusoidal sigma weight residual 275.40 105.79 169.61 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN B 906 " pdb=" O1 LBN B 906 " pdb=" P1 LBN B 906 " pdb=" O3 LBN B 906 " ideal model delta sinusoidal sigma weight residual 275.40 105.79 169.61 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 16385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 2644 0.125 - 0.250: 16 0.250 - 0.375: 20 0.375 - 0.500: 4 0.500 - 0.624: 4 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CAO 6EU C 902 " pdb=" CAJ 6EU C 902 " pdb=" CAR 6EU C 902 " pdb=" CAW 6EU C 902 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.75e+00 chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.71e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.86 0.62 2.00e-01 2.50e+01 9.66e+00 ... (remaining 2685 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN C 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN C 687 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN B 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN B 687 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 687 " 0.100 2.00e-02 2.50e+03 9.81e-02 1.44e+02 pdb=" CG ASN A 687 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 687 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN A 687 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 687 " -0.138 2.00e-02 2.50e+03 pdb="HD22 ASN A 687 " 0.141 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2465 2.22 - 2.82: 68579 2.82 - 3.41: 85274 3.41 - 4.01: 112372 4.01 - 4.60: 176156 Nonbonded interactions: 444846 Sorted by model distance: nonbonded pdb=" O LEU D 506 " pdb=" HG SER D 510 " model vdw 1.625 2.450 nonbonded pdb=" O LEU C 506 " pdb=" HG SER C 510 " model vdw 1.625 2.450 nonbonded pdb=" O LEU B 506 " pdb=" HG SER B 510 " model vdw 1.625 2.450 nonbonded pdb=" O LEU A 506 " pdb=" HG SER A 510 " model vdw 1.625 2.450 nonbonded pdb=" HH TYR B 584 " pdb=" OG1 THR B 641 " model vdw 1.654 2.450 ... (remaining 444841 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 197 through 752 or resid 904)) selection = (chain 'B' and (resid 197 through 752 or resid 904)) selection = (chain 'C' and (resid 197 through 752 or resid 904)) selection = (chain 'D' and (resid 197 through 752 or resid 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.740 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: 0.230 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.590 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.268 17592 Z= 0.563 Angle : 0.994 16.631 23892 Z= 0.423 Chirality : 0.056 0.624 2688 Planarity : 0.003 0.038 2928 Dihedral : 17.954 169.620 6580 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 0.31 (0.18), residues: 2112 helix: 0.94 (0.14), residues: 1304 sheet: -2.12 (0.55), residues: 88 loop : -0.72 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 575 TYR 0.016 0.002 TYR D 537 PHE 0.023 0.002 PHE C 659 TRP 0.013 0.001 TRP C 549 HIS 0.002 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.01148 (17588) covalent geometry : angle 0.99415 (23884) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.21012 ( 8) hydrogen bonds : bond 0.14848 ( 972) hydrogen bonds : angle 5.56479 ( 2832) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7282 (ttpp) REVERT: A 378 HIS cc_start: 0.7408 (p90) cc_final: 0.7064 (p90) REVERT: A 445 MET cc_start: 0.7824 (mmp) cc_final: 0.7618 (mmp) REVERT: B 265 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7215 (ttpp) REVERT: B 378 HIS cc_start: 0.7417 (p90) cc_final: 0.7088 (p90) REVERT: B 445 MET cc_start: 0.7814 (mmp) cc_final: 0.7612 (mmp) REVERT: C 378 HIS cc_start: 0.7430 (p90) cc_final: 0.7141 (p90) REVERT: D 265 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7394 (ttpp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3606 time to fit residues: 97.9393 Evaluate side-chains 151 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0060 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.240908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188891 restraints weight = 47878.969| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.76 r_work: 0.3620 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17592 Z= 0.115 Angle : 0.490 4.596 23892 Z= 0.262 Chirality : 0.033 0.123 2688 Planarity : 0.003 0.029 2928 Dihedral : 16.134 163.310 3108 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.30 % Allowed : 5.08 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 0.85 (0.18), residues: 2112 helix: 1.41 (0.14), residues: 1312 sheet: -2.46 (0.51), residues: 88 loop : -0.54 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 355 TYR 0.011 0.001 TYR C 565 PHE 0.014 0.001 PHE B 659 TRP 0.007 0.001 TRP B 549 HIS 0.002 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00233 (17588) covalent geometry : angle 0.49037 (23884) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.18891 ( 8) hydrogen bonds : bond 0.05010 ( 972) hydrogen bonds : angle 4.18468 ( 2832) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7200 (ttpp) REVERT: A 378 HIS cc_start: 0.7203 (p90) cc_final: 0.6921 (p90) REVERT: A 445 MET cc_start: 0.7513 (mmp) cc_final: 0.7138 (mmp) REVERT: B 265 LYS cc_start: 0.7615 (ttmt) cc_final: 0.7136 (ttpp) REVERT: B 378 HIS cc_start: 0.7190 (p90) cc_final: 0.6925 (p90) REVERT: B 445 MET cc_start: 0.7524 (mmp) cc_final: 0.7160 (mmp) REVERT: C 378 HIS cc_start: 0.7157 (p90) cc_final: 0.6899 (p90) REVERT: C 688 LYS cc_start: 0.7515 (mptt) cc_final: 0.7075 (ttpt) REVERT: D 265 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7230 (ttpp) outliers start: 5 outliers final: 4 residues processed: 180 average time/residue: 0.3993 time to fit residues: 100.1455 Evaluate side-chains 167 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.237168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186740 restraints weight = 47881.020| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.76 r_work: 0.3552 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17592 Z= 0.203 Angle : 0.537 4.674 23892 Z= 0.286 Chirality : 0.036 0.123 2688 Planarity : 0.003 0.031 2928 Dihedral : 15.869 162.844 3108 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.66 % Allowed : 7.95 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 0.55 (0.18), residues: 2112 helix: 1.22 (0.14), residues: 1312 sheet: -2.61 (0.51), residues: 88 loop : -0.77 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 575 TYR 0.017 0.002 TYR D 530 PHE 0.018 0.001 PHE B 659 TRP 0.005 0.001 TRP D 426 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00468 (17588) covalent geometry : angle 0.53740 (23884) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.19220 ( 8) hydrogen bonds : bond 0.05290 ( 972) hydrogen bonds : angle 4.23228 ( 2832) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7658 (ttmt) cc_final: 0.7200 (ttpp) REVERT: A 378 HIS cc_start: 0.7242 (p90) cc_final: 0.6940 (p90) REVERT: A 445 MET cc_start: 0.7550 (mmp) cc_final: 0.7222 (mmp) REVERT: B 265 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7190 (ttpp) REVERT: B 378 HIS cc_start: 0.7221 (p90) cc_final: 0.6937 (p90) REVERT: C 265 LYS cc_start: 0.7566 (ttmt) cc_final: 0.7080 (ttpp) REVERT: C 378 HIS cc_start: 0.7279 (p90) cc_final: 0.7004 (p90) REVERT: C 445 MET cc_start: 0.7371 (mmp) cc_final: 0.7056 (mmp) REVERT: C 478 GLU cc_start: 0.4613 (tt0) cc_final: 0.4402 (tt0) REVERT: D 265 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7276 (ttpp) outliers start: 11 outliers final: 9 residues processed: 182 average time/residue: 0.3843 time to fit residues: 96.4782 Evaluate side-chains 169 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 204 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.238113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.185559 restraints weight = 47660.883| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.79 r_work: 0.3566 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17592 Z= 0.152 Angle : 0.480 4.645 23892 Z= 0.258 Chirality : 0.033 0.127 2688 Planarity : 0.003 0.031 2928 Dihedral : 15.647 164.074 3108 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.96 % Allowed : 9.93 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 0.69 (0.18), residues: 2112 helix: 1.35 (0.14), residues: 1312 sheet: -2.71 (0.50), residues: 88 loop : -0.72 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 575 TYR 0.011 0.001 TYR D 530 PHE 0.015 0.001 PHE D 659 TRP 0.009 0.001 TRP C 549 HIS 0.002 0.001 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00348 (17588) covalent geometry : angle 0.48041 (23884) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.17905 ( 8) hydrogen bonds : bond 0.04664 ( 972) hydrogen bonds : angle 4.02755 ( 2832) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7210 (ttpp) REVERT: A 445 MET cc_start: 0.7528 (mmp) cc_final: 0.7135 (mmp) REVERT: B 265 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7201 (ttpp) REVERT: B 378 HIS cc_start: 0.7212 (p90) cc_final: 0.6928 (p90) REVERT: C 265 LYS cc_start: 0.7585 (ttmt) cc_final: 0.7095 (ttpp) REVERT: C 378 HIS cc_start: 0.7276 (p90) cc_final: 0.6996 (p90) REVERT: D 265 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7326 (ttpp) outliers start: 16 outliers final: 14 residues processed: 183 average time/residue: 0.3878 time to fit residues: 98.0263 Evaluate side-chains 179 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 181 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.239566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187311 restraints weight = 47553.535| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.81 r_work: 0.3609 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17592 Z= 0.114 Angle : 0.437 4.592 23892 Z= 0.235 Chirality : 0.032 0.124 2688 Planarity : 0.003 0.031 2928 Dihedral : 15.030 162.476 3108 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.02 % Allowed : 11.66 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 1.04 (0.18), residues: 2112 helix: 1.69 (0.15), residues: 1308 sheet: -2.79 (0.51), residues: 88 loop : -0.67 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.009 0.001 TYR A 309 PHE 0.011 0.001 PHE D 659 TRP 0.009 0.001 TRP B 549 HIS 0.001 0.000 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00256 (17588) covalent geometry : angle 0.43732 (23884) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.20271 ( 8) hydrogen bonds : bond 0.03996 ( 972) hydrogen bonds : angle 3.74865 ( 2832) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7639 (ttmt) cc_final: 0.7242 (ttpp) REVERT: A 309 TYR cc_start: 0.6360 (t80) cc_final: 0.6115 (t80) REVERT: C 378 HIS cc_start: 0.7238 (p90) cc_final: 0.6963 (p90) REVERT: D 265 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7310 (ttpp) outliers start: 17 outliers final: 17 residues processed: 183 average time/residue: 0.3917 time to fit residues: 98.1951 Evaluate side-chains 174 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 159 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.239068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.186862 restraints weight = 47789.072| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.81 r_work: 0.3604 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17592 Z= 0.126 Angle : 0.443 4.600 23892 Z= 0.238 Chirality : 0.033 0.124 2688 Planarity : 0.003 0.031 2928 Dihedral : 14.814 160.922 3108 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.02 % Allowed : 12.20 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 1.07 (0.18), residues: 2112 helix: 1.70 (0.15), residues: 1312 sheet: -2.86 (0.50), residues: 88 loop : -0.64 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 428 TYR 0.009 0.001 TYR D 530 PHE 0.011 0.001 PHE D 659 TRP 0.007 0.001 TRP C 549 HIS 0.001 0.000 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00284 (17588) covalent geometry : angle 0.44293 (23884) SS BOND : bond 0.00032 ( 4) SS BOND : angle 0.18338 ( 8) hydrogen bonds : bond 0.04047 ( 972) hydrogen bonds : angle 3.76167 ( 2832) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7251 (ttpp) REVERT: A 309 TYR cc_start: 0.6394 (t80) cc_final: 0.6135 (t80) REVERT: C 378 HIS cc_start: 0.7247 (p90) cc_final: 0.6975 (p90) REVERT: D 265 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7316 (ttpp) outliers start: 17 outliers final: 17 residues processed: 174 average time/residue: 0.4216 time to fit residues: 99.3826 Evaluate side-chains 177 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 27 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 201 optimal weight: 0.0470 chunk 197 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.238804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.188049 restraints weight = 47564.238| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.76 r_work: 0.3578 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17592 Z= 0.127 Angle : 0.444 4.601 23892 Z= 0.238 Chirality : 0.033 0.122 2688 Planarity : 0.003 0.031 2928 Dihedral : 14.528 159.771 3108 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.08 % Allowed : 12.14 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 1.10 (0.19), residues: 2112 helix: 1.72 (0.15), residues: 1312 sheet: -2.87 (0.51), residues: 88 loop : -0.61 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 428 TYR 0.010 0.001 TYR B 530 PHE 0.012 0.001 PHE D 659 TRP 0.008 0.001 TRP D 549 HIS 0.001 0.000 HIS C 320 Details of bonding type rmsd covalent geometry : bond 0.00287 (17588) covalent geometry : angle 0.44357 (23884) SS BOND : bond 0.00014 ( 4) SS BOND : angle 0.12078 ( 8) hydrogen bonds : bond 0.04050 ( 972) hydrogen bonds : angle 3.73776 ( 2832) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7248 (ttpp) REVERT: A 309 TYR cc_start: 0.6443 (t80) cc_final: 0.6193 (t80) REVERT: A 359 GLU cc_start: 0.5184 (tm-30) cc_final: 0.4781 (mt-10) REVERT: C 308 MET cc_start: 0.8515 (tmm) cc_final: 0.8061 (tmm) REVERT: D 265 LYS cc_start: 0.7662 (ttmt) cc_final: 0.7329 (ttpp) outliers start: 18 outliers final: 18 residues processed: 181 average time/residue: 0.4319 time to fit residues: 105.4725 Evaluate side-chains 176 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 194 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.238883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.187485 restraints weight = 47223.806| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.77 r_work: 0.3607 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17592 Z= 0.123 Angle : 0.438 5.844 23892 Z= 0.236 Chirality : 0.033 0.122 2688 Planarity : 0.003 0.031 2928 Dihedral : 14.325 159.082 3108 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.08 % Allowed : 12.08 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 1.18 (0.19), residues: 2112 helix: 1.79 (0.15), residues: 1308 sheet: -2.88 (0.51), residues: 88 loop : -0.57 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.009 0.001 TYR C 565 PHE 0.011 0.001 PHE C 659 TRP 0.008 0.001 TRP C 549 HIS 0.001 0.000 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00277 (17588) covalent geometry : angle 0.43854 (23884) SS BOND : bond 0.00037 ( 4) SS BOND : angle 0.16801 ( 8) hydrogen bonds : bond 0.03930 ( 972) hydrogen bonds : angle 3.69957 ( 2832) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7253 (ttpp) REVERT: A 309 TYR cc_start: 0.6421 (t80) cc_final: 0.6177 (t80) REVERT: A 359 GLU cc_start: 0.5164 (tm-30) cc_final: 0.4770 (mt-10) REVERT: D 265 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7331 (ttpp) outliers start: 18 outliers final: 18 residues processed: 172 average time/residue: 0.4471 time to fit residues: 103.8725 Evaluate side-chains 173 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 148 optimal weight: 0.0010 chunk 105 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 36 optimal weight: 0.0270 chunk 151 optimal weight: 0.7980 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.240627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.192276 restraints weight = 47064.656| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.65 r_work: 0.3615 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17592 Z= 0.087 Angle : 0.406 4.900 23892 Z= 0.219 Chirality : 0.032 0.122 2688 Planarity : 0.003 0.030 2928 Dihedral : 13.517 156.474 3108 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.84 % Allowed : 12.50 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 1.50 (0.19), residues: 2112 helix: 2.08 (0.15), residues: 1308 sheet: -2.72 (0.52), residues: 88 loop : -0.52 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 428 TYR 0.008 0.001 TYR A 309 PHE 0.010 0.001 PHE B 489 TRP 0.010 0.001 TRP B 549 HIS 0.001 0.000 HIS D 364 Details of bonding type rmsd covalent geometry : bond 0.00185 (17588) covalent geometry : angle 0.40624 (23884) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.13784 ( 8) hydrogen bonds : bond 0.03415 ( 972) hydrogen bonds : angle 3.49052 ( 2832) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7264 (ttpp) REVERT: A 309 TYR cc_start: 0.6474 (t80) cc_final: 0.6235 (t80) REVERT: A 359 GLU cc_start: 0.5077 (tm-30) cc_final: 0.4681 (mt-10) REVERT: B 309 TYR cc_start: 0.6397 (t80) cc_final: 0.6000 (t80) REVERT: C 309 TYR cc_start: 0.6399 (t80) cc_final: 0.6012 (t80) REVERT: C 359 GLU cc_start: 0.5127 (tm-30) cc_final: 0.4800 (mt-10) REVERT: D 265 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7380 (ttpp) outliers start: 14 outliers final: 12 residues processed: 182 average time/residue: 0.4563 time to fit residues: 112.5939 Evaluate side-chains 176 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 177 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.239662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.187517 restraints weight = 47553.595| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.83 r_work: 0.3619 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17592 Z= 0.105 Angle : 0.419 4.874 23892 Z= 0.225 Chirality : 0.032 0.121 2688 Planarity : 0.003 0.030 2928 Dihedral : 13.321 155.856 3108 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.78 % Allowed : 12.68 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 1.50 (0.19), residues: 2112 helix: 2.05 (0.15), residues: 1308 sheet: -2.56 (0.57), residues: 76 loop : -0.53 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.009 0.001 TYR C 351 PHE 0.019 0.001 PHE A 559 TRP 0.006 0.001 TRP B 549 HIS 0.001 0.000 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.00233 (17588) covalent geometry : angle 0.41891 (23884) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.15788 ( 8) hydrogen bonds : bond 0.03567 ( 972) hydrogen bonds : angle 3.53511 ( 2832) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue LYS 240 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7252 (ttpp) REVERT: A 309 TYR cc_start: 0.6449 (t80) cc_final: 0.6213 (t80) REVERT: A 359 GLU cc_start: 0.5621 (tm-30) cc_final: 0.4748 (mt-10) REVERT: B 309 TYR cc_start: 0.6348 (t80) cc_final: 0.5945 (t80) REVERT: C 309 TYR cc_start: 0.6289 (t80) cc_final: 0.5877 (t80) REVERT: C 359 GLU cc_start: 0.5112 (tm-30) cc_final: 0.4795 (mt-10) REVERT: D 265 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7369 (ttpp) outliers start: 13 outliers final: 12 residues processed: 170 average time/residue: 0.4749 time to fit residues: 108.4023 Evaluate side-chains 165 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 85 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 178 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.238376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.186047 restraints weight = 47431.286| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.82 r_work: 0.3578 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17592 Z= 0.139 Angle : 0.452 4.618 23892 Z= 0.243 Chirality : 0.033 0.122 2688 Planarity : 0.003 0.030 2928 Dihedral : 13.461 155.937 3108 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.96 % Allowed : 12.62 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 aren not related in a simple way. whole: 1.29 (0.19), residues: 2112 helix: 1.86 (0.15), residues: 1312 sheet: -2.73 (0.57), residues: 76 loop : -0.58 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 428 TYR 0.011 0.001 TYR C 351 PHE 0.014 0.001 PHE D 659 TRP 0.007 0.001 TRP C 549 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00316 (17588) covalent geometry : angle 0.45219 (23884) SS BOND : bond 0.00018 ( 4) SS BOND : angle 0.07509 ( 8) hydrogen bonds : bond 0.04002 ( 972) hydrogen bonds : angle 3.67358 ( 2832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7992.65 seconds wall clock time: 136 minutes 12.31 seconds (8172.31 seconds total)