Starting phenix.real_space_refine on Sun Aug 9 21:52:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf9_29982/08_2026/8gf9_29982_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf9_29982/08_2026/8gf9_29982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gf9_29982/08_2026/8gf9_29982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf9_29982/08_2026/8gf9_29982.map" model { file = "/net/cci-nas-00/data/ceres_data/8gf9_29982/08_2026/8gf9_29982_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf9_29982/08_2026/8gf9_29982_neut_trim.cif" } resolution = 2.58 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= 0.008 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 36 5.49 5 S 112 5.16 5 Na 2 4.78 5 C 12700 2.51 5 N 2756 2.21 5 O 3420 1.98 5 H 17068 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36094 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 8512 Classifications: {'peptide': 523} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 509} Chain breaks: 2 Chain: "B" Number of atoms: 8512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 8512 Classifications: {'peptide': 523} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 509} Chain breaks: 2 Chain: "D" Number of atoms: 8512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 8512 Classifications: {'peptide': 523} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 509} Chain breaks: 2 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 490 Unusual residues: {' NA': 2, '8IJ': 1, 'POV': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 488 Unusual residues: {'8IJ': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 488 Unusual residues: {'8IJ': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Restraints were copied for chains: C Time building chain proxies: 12.39, per 1000 atoms: 0.34 Number of scatterers: 36094 At special positions: 0 Unit cell: (116.965, 116.965, 110.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 112 16.00 P 36 15.00 Na 2 11.00 O 3420 8.00 N 2756 7.00 C 12700 6.00 H 17068 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 391 " distance=2.04 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 391 " distance=2.04 Simple disulfide: pdb=" SG CYS C 258 " - pdb=" SG CYS C 258 " distance=0.00 Simple disulfide: pdb=" SG CYS C 363 " - pdb=" SG CYS C 363 " distance=0.00 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.04 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 387 " distance=0.00 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 387 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 391 " distance=0.00 Simple disulfide: pdb=" SG CYS C 443 " - pdb=" SG CYS C 443 " distance=0.00 Simple disulfide: pdb=" SG CYS C 578 " - pdb=" SG CYS C 578 " distance=0.00 Simple disulfide: pdb=" SG CYS C 635 " - pdb=" SG CYS C 635 " distance=0.00 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 742 " distance=0.00 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.04 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: 3.11 Conformation dependent library (CDL) restraints added in 771.1 milliseconds 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3944 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 61.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.547A pdb=" N ILE A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.785A pdb=" N VAL A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 264 through 270 removed outlier: 3.745A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 299 through 320 removed outlier: 3.563A pdb=" N PHE A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 418 through 431 removed outlier: 3.608A pdb=" N VAL A 431 " --> pdb=" O TRP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 455 Processing helix chain 'A' and resid 469 through 496 removed outlier: 3.798A pdb=" N THR A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 510 through 532 removed outlier: 3.796A pdb=" N VAL A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.743A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 556 removed outlier: 4.045A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'A' and resid 576 through 599 removed outlier: 3.581A pdb=" N LEU A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 674 through 712 removed outlier: 3.836A pdb=" N VAL A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.547A pdb=" N ILE B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.785A pdb=" N VAL B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 264 through 270 removed outlier: 3.745A pdb=" N LEU B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.563A pdb=" N PHE B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 314 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 418 through 431 removed outlier: 3.608A pdb=" N VAL B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 455 Processing helix chain 'B' and resid 469 through 496 removed outlier: 3.798A pdb=" N THR B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.796A pdb=" N VAL B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.744A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 556 removed outlier: 4.044A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'B' and resid 576 through 599 removed outlier: 3.580A pdb=" N LEU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 674 through 712 removed outlier: 3.836A pdb=" N VAL B 687 " --> pdb=" O MET B 683 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 695 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.547A pdb=" N ILE C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 224 removed outlier: 3.785A pdb=" N VAL C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 264 through 270 removed outlier: 3.744A pdb=" N LEU C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 299 through 320 removed outlier: 3.562A pdb=" N PHE C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 418 through 431 removed outlier: 3.608A pdb=" N VAL C 431 " --> pdb=" O TRP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 455 Processing helix chain 'C' and resid 469 through 496 removed outlier: 3.797A pdb=" N THR C 476 " --> pdb=" O TYR C 472 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 507 Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.797A pdb=" N VAL C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 530 " --> pdb=" O THR C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.744A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 556 removed outlier: 4.045A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 576 through 599 removed outlier: 3.580A pdb=" N LEU C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 638 Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 674 through 712 removed outlier: 3.835A pdb=" N VAL C 687 " --> pdb=" O MET C 683 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 688 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 700 " --> pdb=" O ASN C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.547A pdb=" N ILE D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 3.785A pdb=" N VAL D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 264 through 270 removed outlier: 3.744A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 320 removed outlier: 3.563A pdb=" N PHE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 314 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 418 through 431 removed outlier: 3.608A pdb=" N VAL D 431 " --> pdb=" O TRP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 455 Processing helix chain 'D' and resid 469 through 496 removed outlier: 3.797A pdb=" N THR D 476 " --> pdb=" O TYR D 472 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 507 Processing helix chain 'D' and resid 510 through 532 removed outlier: 3.796A pdb=" N VAL D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 530 " --> pdb=" O THR D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.744A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 556 removed outlier: 4.044A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 574 Processing helix chain 'D' and resid 576 through 599 removed outlier: 3.580A pdb=" N LEU D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 638 Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 674 through 712 removed outlier: 3.835A pdb=" N VAL D 687 " --> pdb=" O MET D 683 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLN D 692 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS D 695 " --> pdb=" O ALA D 691 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 700 " --> pdb=" O ASN D 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 374 removed outlier: 6.866A pdb=" N SER A 380 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 374 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP A 738 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 729 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 371 through 374 removed outlier: 6.867A pdb=" N SER B 380 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA B 374 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP B 738 " --> pdb=" O VAL B 729 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 729 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 371 through 374 removed outlier: 6.866A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA C 374 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP C 738 " --> pdb=" O VAL C 729 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 729 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 371 through 374 removed outlier: 6.867A pdb=" N SER D 380 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA D 374 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 729 " --> pdb=" O ASP D 738 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2568 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: 8.07 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.40: 24536 1.40 - 1.99: 11808 1.99 - 2.57: 4 2.57 - 3.15: 8 3.15 - 3.73: 12 Bond restraints: 36368 Sorted by residual: bond pdb=" CA ASN A 754 " pdb=" HA ASN A 754 " ideal model delta sigma weight residual 0.970 3.732 -2.762 2.00e-02 2.50e+03 1.91e+04 bond pdb=" CA ASN B 754 " pdb=" HA ASN B 754 " ideal model delta sigma weight residual 0.970 3.727 -2.757 2.00e-02 2.50e+03 1.90e+04 bond pdb=" CA ASN C 754 " pdb=" HA ASN C 754 " ideal model delta sigma weight residual 0.970 3.726 -2.756 2.00e-02 2.50e+03 1.90e+04 bond pdb=" CA ASN D 754 " pdb=" HA ASN D 754 " ideal model delta sigma weight residual 0.970 3.718 -2.748 2.00e-02 2.50e+03 1.89e+04 bond pdb=" CB ASN D 754 " pdb=" HB3 ASN D 754 " ideal model delta sigma weight residual 0.970 3.322 -2.352 2.00e-02 2.50e+03 1.38e+04 ... (remaining 36363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 64181 5.40 - 10.80: 135 10.80 - 16.20: 18 16.20 - 21.60: 6 21.60 - 27.00: 4 Bond angle restraints: 64344 Sorted by residual: angle pdb="HD21 ASN D 754 " pdb=" ND2 ASN D 754 " pdb="HD22 ASN D 754 " ideal model delta sigma weight residual 120.00 93.00 27.00 3.00e+00 1.11e-01 8.10e+01 angle pdb="HD21 ASN B 754 " pdb=" ND2 ASN B 754 " pdb="HD22 ASN B 754 " ideal model delta sigma weight residual 120.00 93.80 26.20 3.00e+00 1.11e-01 7.63e+01 angle pdb="HD21 ASN A 754 " pdb=" ND2 ASN A 754 " pdb="HD22 ASN A 754 " ideal model delta sigma weight residual 120.00 93.91 26.09 3.00e+00 1.11e-01 7.56e+01 angle pdb="HD21 ASN C 754 " pdb=" ND2 ASN C 754 " pdb="HD22 ASN C 754 " ideal model delta sigma weight residual 120.00 94.35 25.65 3.00e+00 1.11e-01 7.31e+01 angle pdb=" HB2 ASN D 754 " pdb=" CB ASN D 754 " pdb=" HB3 ASN D 754 " ideal model delta sigma weight residual 110.00 91.17 18.83 3.00e+00 1.11e-01 3.94e+01 ... (remaining 64339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 17186 35.65 - 71.30: 631 71.30 - 106.95: 92 106.95 - 142.60: 16 142.60 - 178.25: 28 Dihedral angle restraints: 17953 sinusoidal: 10301 harmonic: 7652 Sorted by residual: dihedral pdb=" CA LEU D 324 " pdb=" C LEU D 324 " pdb=" N LYS D 325 " pdb=" CA LYS D 325 " ideal model delta harmonic sigma weight residual 180.00 -132.85 -47.15 0 5.00e+00 4.00e-02 8.89e+01 dihedral pdb=" CA LEU B 324 " pdb=" C LEU B 324 " pdb=" N LYS B 325 " pdb=" CA LYS B 325 " ideal model delta harmonic sigma weight residual -180.00 -132.89 -47.11 0 5.00e+00 4.00e-02 8.88e+01 dihedral pdb=" CA LEU C 324 " pdb=" C LEU C 324 " pdb=" N LYS C 325 " pdb=" CA LYS C 325 " ideal model delta harmonic sigma weight residual -180.00 -132.90 -47.10 0 5.00e+00 4.00e-02 8.87e+01 ... (remaining 17950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1565 0.041 - 0.082: 796 0.082 - 0.123: 250 0.123 - 0.164: 80 0.164 - 0.205: 17 Chirality restraints: 2708 Sorted by residual: chirality pdb=" CB THR D 642 " pdb=" CA THR D 642 " pdb=" OG1 THR D 642 " pdb=" CG2 THR D 642 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU C 682 " pdb=" CB LEU C 682 " pdb=" CD1 LEU C 682 " pdb=" CD2 LEU C 682 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB THR C 642 " pdb=" CA THR C 642 " pdb=" OG1 THR C 642 " pdb=" CG2 THR C 642 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2705 not shown) Planarity restraints: 5040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 754 " -0.207 2.00e-02 2.50e+03 1.83e-01 5.03e+02 pdb=" CG ASN C 754 " 0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN C 754 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN C 754 " 0.352 2.00e-02 2.50e+03 pdb="HD21 ASN C 754 " -0.039 2.00e-02 2.50e+03 pdb="HD22 ASN C 754 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 754 " -0.194 2.00e-02 2.50e+03 1.75e-01 4.58e+02 pdb=" CG ASN B 754 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN B 754 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 754 " 0.339 2.00e-02 2.50e+03 pdb="HD21 ASN B 754 " -0.039 2.00e-02 2.50e+03 pdb="HD22 ASN B 754 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 754 " 0.195 2.00e-02 2.50e+03 1.73e-01 4.47e+02 pdb=" CG ASN D 754 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN D 754 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 754 " -0.333 2.00e-02 2.50e+03 pdb="HD21 ASN D 754 " 0.036 2.00e-02 2.50e+03 pdb="HD22 ASN D 754 " 0.160 2.00e-02 2.50e+03 ... (remaining 5037 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4004 2.26 - 2.84: 80519 2.84 - 3.43: 95487 3.43 - 4.01: 135144 4.01 - 4.60: 211161 Nonbonded interactions: 526315 Sorted by model distance: nonbonded pdb=" OD1 ASP B 576 " pdb="HH21 ARG B 579 " model vdw 1.671 2.450 nonbonded pdb=" OD1 ASP D 576 " pdb="HH21 ARG D 579 " model vdw 1.671 2.450 nonbonded pdb=" OD1 ASP A 576 " pdb="HH21 ARG A 579 " model vdw 1.671 2.450 nonbonded pdb=" OD1 ASP C 576 " pdb="HH21 ARG C 579 " model vdw 1.671 2.450 nonbonded pdb=" O LYS D 640 " pdb=" H MET D 645 " model vdw 1.688 2.450 ... (remaining 526310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 199 through 1201 or (resid 1205 through 1206 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1207 through 1210)) selection = (chain 'B' and (resid 199 through 1201 or (resid 1205 through 1206 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1207 through 1210)) selection = (chain 'C' and (resid 199 through 1201 or (resid 1205 through 1206 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1207 through 1210)) selection = (chain 'D' and (resid 199 through 1201 or (resid 1205 through 1206 and (name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or nam \ e C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or res \ id 1207 through 1210)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.170 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 38.360 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 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 : 0.012 0.082 19303 Z= 0.517 Angle : 1.129 12.838 25758 Z= 0.530 Chirality : 0.055 0.205 2708 Planarity : 0.005 0.052 3012 Dihedral : 21.330 178.248 7988 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.93 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.15 (0.14), residues: 2068 helix: -3.40 (0.10), residues: 1196 sheet: -3.71 (0.45), residues: 76 loop : -3.15 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 499 TYR 0.017 0.003 TYR D 383 PHE 0.022 0.003 PHE A 522 TRP 0.018 0.002 TRP C 698 HIS 0.015 0.003 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.01222 / 0.52 (19300) covalent geometry : angle 1.12877 / 0.53 (25744) SS BOND : bond 0.00482 / 0.24 ( 3) SS BOND : angle 0.45705 / 0.28 ( 14) hydrogen bonds : bond 0.26986 / 17.88 ( 884) hydrogen bonds : angle 10.32510 / 7.23 ( 2568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 0.784 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 201 LYS cc_start: 0.4748 (tptp) cc_final: 0.4423 (mmtm) REVERT: A 364 ARG cc_start: 0.6041 (ppt-90) cc_final: 0.5040 (ttt-90) REVERT: A 367 SER cc_start: 0.7378 (m) cc_final: 0.7026 (m) REVERT: A 446 MET cc_start: 0.8249 (mmp) cc_final: 0.7618 (mmp) REVERT: A 503 MET cc_start: 0.5588 (mpt) cc_final: 0.5279 (mpm) REVERT: A 704 ILE cc_start: 0.8054 (mt) cc_final: 0.7706 (mt) REVERT: B 201 LYS cc_start: 0.4795 (tptp) cc_final: 0.4461 (mptt) REVERT: B 364 ARG cc_start: 0.6055 (ppt-90) cc_final: 0.5086 (ttt-90) REVERT: B 367 SER cc_start: 0.7417 (m) cc_final: 0.7063 (m) REVERT: B 503 MET cc_start: 0.5669 (mpt) cc_final: 0.5431 (mpm) REVERT: B 704 ILE cc_start: 0.7909 (mt) cc_final: 0.7561 (mt) REVERT: C 201 LYS cc_start: 0.4816 (tptp) cc_final: 0.4487 (mptt) REVERT: C 364 ARG cc_start: 0.6104 (ppt-90) cc_final: 0.5135 (ttt-90) REVERT: C 367 SER cc_start: 0.7405 (m) cc_final: 0.7064 (m) REVERT: C 503 MET cc_start: 0.5706 (mpt) cc_final: 0.5474 (mpm) REVERT: C 704 ILE cc_start: 0.7954 (mt) cc_final: 0.7602 (mt) REVERT: D 201 LYS cc_start: 0.4567 (tptp) cc_final: 0.4144 (mptt) REVERT: D 235 ASP cc_start: 0.5343 (m-30) cc_final: 0.4944 (m-30) REVERT: D 364 ARG cc_start: 0.5682 (ppt-90) cc_final: 0.5328 (ptm160) REVERT: D 367 SER cc_start: 0.7306 (m) cc_final: 0.7037 (m) REVERT: D 503 MET cc_start: 0.5478 (mpt) cc_final: 0.5155 (mpm) REVERT: D 704 ILE cc_start: 0.7929 (mt) cc_final: 0.7590 (mt) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 1.2935 time to fit residues: 522.6481 Evaluate side-chains 218 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN A 394 ASN A 754 ASN B 298 ASN B 394 ASN B 754 ASN C 298 ASN C 394 ASN C 754 ASN D 298 ASN D 394 ASN D 754 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.219968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168472 restraints weight = 52892.823| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.83 r_work: 0.3809 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19303 Z= 0.148 Angle : 0.676 8.479 25758 Z= 0.352 Chirality : 0.038 0.138 2708 Planarity : 0.005 0.045 3012 Dihedral : 25.132 178.065 4020 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.67 % Favored : 92.94 % Rotamer: Outliers : 0.87 % Allowed : 10.22 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.15), residues: 2068 helix: -1.99 (0.11), residues: 1284 sheet: -2.83 (0.52), residues: 76 loop : -3.09 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 575 TYR 0.021 0.001 TYR D 352 PHE 0.015 0.001 PHE D 580 TRP 0.013 0.001 TRP C 698 HIS 0.004 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (19300) covalent geometry : angle 0.67662 / 0.35 (25744) SS BOND : bond 0.00083 / 0.04 ( 3) SS BOND : angle 0.25297 / 0.16 ( 14) hydrogen bonds : bond 0.05478 / 3.61 ( 884) hydrogen bonds : angle 5.67652 / 3.99 ( 2568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.939 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 201 LYS cc_start: 0.4260 (tptp) cc_final: 0.3911 (mmtt) REVERT: A 235 ASP cc_start: 0.4507 (m-30) cc_final: 0.4157 (m-30) REVERT: A 364 ARG cc_start: 0.5574 (ppt-90) cc_final: 0.4591 (ttt-90) REVERT: A 367 SER cc_start: 0.6699 (m) cc_final: 0.6272 (m) REVERT: A 446 MET cc_start: 0.8105 (mmp) cc_final: 0.7781 (mmp) REVERT: A 494 GLN cc_start: 0.6526 (mt0) cc_final: 0.5995 (mm-40) REVERT: A 503 MET cc_start: 0.5326 (mpt) cc_final: 0.5029 (mpm) REVERT: A 708 ASP cc_start: 0.7224 (m-30) cc_final: 0.6921 (m-30) REVERT: B 201 LYS cc_start: 0.4251 (tptp) cc_final: 0.3859 (mptt) REVERT: B 235 ASP cc_start: 0.4421 (m-30) cc_final: 0.4069 (m-30) REVERT: B 364 ARG cc_start: 0.5570 (ppt-90) cc_final: 0.4558 (ttt-90) REVERT: B 494 GLN cc_start: 0.6559 (mt0) cc_final: 0.6011 (mm-40) REVERT: B 503 MET cc_start: 0.5321 (mpt) cc_final: 0.5021 (mpm) REVERT: B 708 ASP cc_start: 0.7226 (m-30) cc_final: 0.6924 (m-30) REVERT: C 201 LYS cc_start: 0.4252 (tptp) cc_final: 0.3861 (mptt) REVERT: C 235 ASP cc_start: 0.4436 (m-30) cc_final: 0.4085 (m-30) REVERT: C 364 ARG cc_start: 0.5612 (ppt-90) cc_final: 0.4584 (ttt-90) REVERT: C 367 SER cc_start: 0.6758 (m) cc_final: 0.6334 (m) REVERT: C 494 GLN cc_start: 0.6542 (mt0) cc_final: 0.6010 (mm-40) REVERT: C 503 MET cc_start: 0.5379 (mpt) cc_final: 0.5099 (mpm) REVERT: C 708 ASP cc_start: 0.7236 (m-30) cc_final: 0.6923 (m-30) REVERT: C 725 LYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5559 (mtmm) REVERT: D 201 LYS cc_start: 0.4121 (tptp) cc_final: 0.3703 (mptt) REVERT: D 235 ASP cc_start: 0.4463 (m-30) cc_final: 0.4089 (m-30) REVERT: D 364 ARG cc_start: 0.5521 (ppt-90) cc_final: 0.5110 (ptm160) REVERT: D 494 GLN cc_start: 0.6554 (mt0) cc_final: 0.6008 (mm-40) REVERT: D 503 MET cc_start: 0.5263 (mpt) cc_final: 0.4983 (mpm) REVERT: D 708 ASP cc_start: 0.7242 (m-30) cc_final: 0.6933 (m-30) outliers start: 16 outliers final: 4 residues processed: 259 average time/residue: 1.1068 time to fit residues: 327.5808 Evaluate side-chains 220 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 ASN A 688 ASN B 653 ASN B 688 ASN C 653 ASN C 688 ASN D 653 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.210402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156845 restraints weight = 53517.534| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.88 r_work: 0.3677 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19303 Z= 0.242 Angle : 0.652 7.344 25758 Z= 0.338 Chirality : 0.040 0.166 2708 Planarity : 0.005 0.042 3012 Dihedral : 24.035 173.209 4020 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 2.12 % Allowed : 9.08 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.17), residues: 2068 helix: -0.96 (0.13), residues: 1252 sheet: -2.48 (0.57), residues: 76 loop : -2.96 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 474 TYR 0.014 0.002 TYR B 584 PHE 0.019 0.002 PHE B 639 TRP 0.015 0.002 TRP C 698 HIS 0.004 0.001 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (19300) covalent geometry : angle 0.65202 / 0.34 (25744) SS BOND : bond 0.00039 / 0.02 ( 3) SS BOND : angle 0.22258 / 0.14 ( 14) hydrogen bonds : bond 0.05171 / 3.41 ( 884) hydrogen bonds : angle 5.20612 / 3.64 ( 2568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.886 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 201 LYS cc_start: 0.4155 (tptp) cc_final: 0.3727 (mmpt) REVERT: A 235 ASP cc_start: 0.4179 (m-30) cc_final: 0.3817 (m-30) REVERT: A 301 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.7011 (t70) REVERT: A 364 ARG cc_start: 0.5836 (ppt-90) cc_final: 0.4899 (ttt90) REVERT: A 417 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: A 494 GLN cc_start: 0.6521 (mt0) cc_final: 0.5987 (mm-40) REVERT: A 503 MET cc_start: 0.5316 (mpt) cc_final: 0.5030 (mpm) REVERT: A 600 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6520 (mt-10) REVERT: A 725 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5404 (mtmm) REVERT: B 201 LYS cc_start: 0.4126 (tptp) cc_final: 0.3686 (mmpt) REVERT: B 235 ASP cc_start: 0.4246 (m-30) cc_final: 0.3872 (m-30) REVERT: B 364 ARG cc_start: 0.5842 (ppt-90) cc_final: 0.4910 (ttt90) REVERT: B 494 GLN cc_start: 0.6499 (mt0) cc_final: 0.5950 (mm-40) REVERT: B 503 MET cc_start: 0.5331 (mpt) cc_final: 0.5042 (mpm) REVERT: B 725 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5445 (mtmm) REVERT: C 201 LYS cc_start: 0.4112 (tptp) cc_final: 0.3671 (mmpt) REVERT: C 235 ASP cc_start: 0.4215 (m-30) cc_final: 0.3854 (m-30) REVERT: C 364 ARG cc_start: 0.5860 (ppt-90) cc_final: 0.4959 (ttt90) REVERT: C 494 GLN cc_start: 0.6491 (mt0) cc_final: 0.5953 (mm-40) REVERT: C 503 MET cc_start: 0.5331 (mpt) cc_final: 0.5042 (mpm) REVERT: C 725 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5572 (mtmm) REVERT: D 201 LYS cc_start: 0.4106 (tptp) cc_final: 0.3607 (mmpt) REVERT: D 235 ASP cc_start: 0.4461 (m-30) cc_final: 0.4107 (m-30) REVERT: D 332 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7102 (mmmt) REVERT: D 364 ARG cc_start: 0.5641 (ppt-90) cc_final: 0.4745 (ttt90) REVERT: D 494 GLN cc_start: 0.6423 (mt0) cc_final: 0.5877 (mm-40) REVERT: D 503 MET cc_start: 0.5257 (mpt) cc_final: 0.4971 (mpm) REVERT: D 600 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6602 (mt-10) REVERT: D 725 LYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5471 (mtmm) outliers start: 39 outliers final: 16 residues processed: 244 average time/residue: 1.2111 time to fit residues: 335.2435 Evaluate side-chains 225 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 140 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN A 394 ASN B 311 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 394 ASN D 311 ASN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.212681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159932 restraints weight = 53452.366| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.82 r_work: 0.3718 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19303 Z= 0.134 Angle : 0.541 6.154 25758 Z= 0.286 Chirality : 0.035 0.126 2708 Planarity : 0.004 0.039 3012 Dihedral : 22.455 163.297 4020 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.86 % Rotamer: Outliers : 2.28 % Allowed : 9.35 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.17), residues: 2068 helix: -0.38 (0.14), residues: 1248 sheet: -2.73 (0.51), residues: 76 loop : -2.72 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 474 TYR 0.012 0.001 TYR B 511 PHE 0.014 0.002 PHE A 248 TRP 0.011 0.001 TRP A 698 HIS 0.002 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (19300) covalent geometry : angle 0.54057 / 0.29 (25744) SS BOND : bond 0.00052 / 0.03 ( 3) SS BOND : angle 0.39677 / 0.25 ( 14) hydrogen bonds : bond 0.04263 / 2.79 ( 884) hydrogen bonds : angle 4.74693 / 3.32 ( 2568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.643 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 201 LYS cc_start: 0.4102 (tptp) cc_final: 0.3691 (mmpt) REVERT: A 235 ASP cc_start: 0.4241 (m-30) cc_final: 0.3845 (m-30) REVERT: A 301 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6974 (t70) REVERT: A 364 ARG cc_start: 0.5781 (ppt-90) cc_final: 0.4875 (ttt90) REVERT: A 478 GLU cc_start: 0.6741 (mt-10) cc_final: 0.5914 (mp0) REVERT: A 494 GLN cc_start: 0.6330 (mt0) cc_final: 0.5770 (mm110) REVERT: A 503 MET cc_start: 0.5294 (mpt) cc_final: 0.5010 (mpm) REVERT: A 708 ASP cc_start: 0.7956 (m-30) cc_final: 0.7650 (m-30) REVERT: A 725 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5475 (mtmm) REVERT: B 201 LYS cc_start: 0.4081 (tptp) cc_final: 0.3659 (mmpt) REVERT: B 235 ASP cc_start: 0.4217 (m-30) cc_final: 0.3817 (m-30) REVERT: B 364 ARG cc_start: 0.5750 (ppt-90) cc_final: 0.4862 (ttt90) REVERT: B 478 GLU cc_start: 0.6757 (mt-10) cc_final: 0.5928 (mp0) REVERT: B 494 GLN cc_start: 0.6364 (mt0) cc_final: 0.5818 (mm-40) REVERT: B 503 MET cc_start: 0.5292 (mpt) cc_final: 0.5003 (mpm) REVERT: B 725 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5427 (mtmm) REVERT: C 201 LYS cc_start: 0.4027 (tptp) cc_final: 0.3605 (mmpt) REVERT: C 235 ASP cc_start: 0.4237 (m-30) cc_final: 0.3839 (m-30) REVERT: C 364 ARG cc_start: 0.5798 (ppt-90) cc_final: 0.4946 (ttt90) REVERT: C 478 GLU cc_start: 0.6742 (mt-10) cc_final: 0.5924 (mp0) REVERT: C 494 GLN cc_start: 0.6345 (mt0) cc_final: 0.5799 (mm-40) REVERT: C 503 MET cc_start: 0.5293 (mpt) cc_final: 0.5008 (mpm) REVERT: C 708 ASP cc_start: 0.7967 (m-30) cc_final: 0.7663 (m-30) REVERT: C 725 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5533 (mtmm) REVERT: D 201 LYS cc_start: 0.4076 (tptp) cc_final: 0.3613 (mmpt) REVERT: D 235 ASP cc_start: 0.4339 (m-30) cc_final: 0.3926 (m-30) REVERT: D 364 ARG cc_start: 0.5554 (ppt-90) cc_final: 0.4714 (ttt90) REVERT: D 478 GLU cc_start: 0.6655 (mt-10) cc_final: 0.5844 (mp0) REVERT: D 494 GLN cc_start: 0.6328 (mt0) cc_final: 0.5796 (mm-40) REVERT: D 503 MET cc_start: 0.5270 (mpt) cc_final: 0.4978 (mpm) REVERT: D 725 LYS cc_start: 0.6059 (OUTLIER) cc_final: 0.5583 (mtmm) outliers start: 42 outliers final: 17 residues processed: 241 average time/residue: 1.0743 time to fit residues: 296.0348 Evaluate side-chains 225 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 131 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 311 ASN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 311 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 311 ASN ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 394 ASN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.206249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152250 restraints weight = 53792.172| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.83 r_work: 0.3636 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19303 Z= 0.272 Angle : 0.662 6.718 25758 Z= 0.339 Chirality : 0.041 0.141 2708 Planarity : 0.005 0.042 3012 Dihedral : 22.528 155.405 4020 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.11 % Favored : 92.70 % Rotamer: Outliers : 2.61 % Allowed : 10.49 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.17), residues: 2068 helix: -0.33 (0.14), residues: 1244 sheet: -2.93 (0.50), residues: 76 loop : -2.74 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 474 TYR 0.019 0.002 TYR D 511 PHE 0.025 0.003 PHE B 248 TRP 0.013 0.002 TRP B 698 HIS 0.005 0.002 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.27 (19300) covalent geometry : angle 0.66170 / 0.34 (25744) SS BOND : bond 0.00070 / 0.04 ( 3) SS BOND : angle 0.22455 / 0.14 ( 14) hydrogen bonds : bond 0.04887 / 3.21 ( 884) hydrogen bonds : angle 4.93208 / 3.45 ( 2568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.776 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 201 LYS cc_start: 0.4178 (tptp) cc_final: 0.3697 (mmpt) REVERT: A 235 ASP cc_start: 0.4207 (m-30) cc_final: 0.3801 (m-30) REVERT: A 312 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.4432 (mp0) REVERT: A 364 ARG cc_start: 0.5960 (ppt-90) cc_final: 0.5178 (ttt90) REVERT: A 404 SER cc_start: 0.7210 (m) cc_final: 0.6680 (p) REVERT: A 494 GLN cc_start: 0.6325 (mt0) cc_final: 0.5806 (mm-40) REVERT: A 503 MET cc_start: 0.5337 (mpt) cc_final: 0.5044 (mpm) REVERT: A 504 LYS cc_start: 0.6956 (tttt) cc_final: 0.6745 (tppt) REVERT: A 600 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 636 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7584 (tm) REVERT: A 725 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5395 (mtmm) REVERT: B 201 LYS cc_start: 0.4240 (tptp) cc_final: 0.3731 (mmpt) REVERT: B 235 ASP cc_start: 0.4201 (m-30) cc_final: 0.3768 (m-30) REVERT: B 312 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.4413 (mp0) REVERT: B 364 ARG cc_start: 0.5979 (ppt-90) cc_final: 0.5131 (ttt90) REVERT: B 404 SER cc_start: 0.7127 (m) cc_final: 0.6596 (p) REVERT: B 494 GLN cc_start: 0.6306 (mt0) cc_final: 0.5794 (mm-40) REVERT: B 503 MET cc_start: 0.5366 (mpt) cc_final: 0.5064 (mpm) REVERT: B 504 LYS cc_start: 0.6988 (tttt) cc_final: 0.6772 (tppt) REVERT: B 636 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7574 (tm) REVERT: B 725 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5417 (mtmm) REVERT: C 201 LYS cc_start: 0.4226 (tptp) cc_final: 0.3717 (mmpt) REVERT: C 235 ASP cc_start: 0.4205 (m-30) cc_final: 0.3796 (m-30) REVERT: C 364 ARG cc_start: 0.6006 (ppt-90) cc_final: 0.5157 (ttt90) REVERT: C 404 SER cc_start: 0.7162 (m) cc_final: 0.6633 (p) REVERT: C 494 GLN cc_start: 0.6329 (mt0) cc_final: 0.5813 (mm-40) REVERT: C 503 MET cc_start: 0.5321 (mpt) cc_final: 0.5025 (mpm) REVERT: C 504 LYS cc_start: 0.6962 (tttt) cc_final: 0.6751 (tppt) REVERT: C 636 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7599 (tm) REVERT: C 725 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5517 (mtmm) REVERT: D 201 LYS cc_start: 0.4098 (tptp) cc_final: 0.3560 (mmpt) REVERT: D 332 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7160 (mmmt) REVERT: D 364 ARG cc_start: 0.5842 (ppt-90) cc_final: 0.5013 (ttt90) REVERT: D 404 SER cc_start: 0.7200 (m) cc_final: 0.6635 (p) REVERT: D 494 GLN cc_start: 0.6301 (mt0) cc_final: 0.5790 (mm-40) REVERT: D 503 MET cc_start: 0.5368 (mpt) cc_final: 0.5072 (mpm) REVERT: D 504 LYS cc_start: 0.6985 (tttt) cc_final: 0.6757 (tppt) REVERT: D 600 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6614 (mt-10) REVERT: D 636 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7575 (tm) REVERT: D 725 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.5398 (mtmm) outliers start: 48 outliers final: 15 residues processed: 261 average time/residue: 1.0765 time to fit residues: 322.2415 Evaluate side-chains 233 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 190 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 394 ASN ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.208311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154636 restraints weight = 53868.299| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.83 r_work: 0.3658 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19303 Z= 0.171 Angle : 0.549 5.668 25758 Z= 0.290 Chirality : 0.036 0.123 2708 Planarity : 0.004 0.040 3012 Dihedral : 21.328 149.074 4020 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.24 % Favored : 93.57 % Rotamer: Outliers : 2.61 % Allowed : 11.09 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.18), residues: 2068 helix: -0.01 (0.14), residues: 1256 sheet: -2.89 (0.49), residues: 76 loop : -2.75 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 474 TYR 0.015 0.002 TYR D 511 PHE 0.019 0.002 PHE A 248 TRP 0.013 0.001 TRP C 698 HIS 0.003 0.001 HIS B 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (19300) covalent geometry : angle 0.54925 / 0.29 (25744) SS BOND : bond 0.00004 / 0.00 ( 3) SS BOND : angle 0.38451 / 0.25 ( 14) hydrogen bonds : bond 0.04268 / 2.80 ( 884) hydrogen bonds : angle 4.61941 / 3.23 ( 2568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4210 (tptp) cc_final: 0.3725 (mmpt) REVERT: A 235 ASP cc_start: 0.4245 (m-30) cc_final: 0.3781 (m-30) REVERT: A 312 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.4369 (mp0) REVERT: A 364 ARG cc_start: 0.5992 (ppt-90) cc_final: 0.5137 (ttt90) REVERT: A 404 SER cc_start: 0.7164 (m) cc_final: 0.6612 (p) REVERT: A 494 GLN cc_start: 0.6344 (mt0) cc_final: 0.5822 (mm-40) REVERT: A 503 MET cc_start: 0.5443 (mpt) cc_final: 0.5158 (mpm) REVERT: A 636 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7600 (tm) REVERT: A 725 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.5390 (mtmm) REVERT: B 201 LYS cc_start: 0.4232 (tptp) cc_final: 0.3709 (mmpt) REVERT: B 235 ASP cc_start: 0.4288 (m-30) cc_final: 0.3817 (m-30) REVERT: B 281 ARG cc_start: 0.5304 (mpt-90) cc_final: 0.4626 (mtm180) REVERT: B 312 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.4357 (mp0) REVERT: B 364 ARG cc_start: 0.5997 (ppt-90) cc_final: 0.5138 (ttt90) REVERT: B 404 SER cc_start: 0.7183 (m) cc_final: 0.6628 (p) REVERT: B 494 GLN cc_start: 0.6325 (mt0) cc_final: 0.5818 (mm-40) REVERT: B 503 MET cc_start: 0.5454 (mpt) cc_final: 0.5168 (mpm) REVERT: B 636 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7591 (tm) REVERT: B 725 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5426 (mtmm) REVERT: C 201 LYS cc_start: 0.4231 (tptp) cc_final: 0.3721 (mmpt) REVERT: C 235 ASP cc_start: 0.4231 (m-30) cc_final: 0.3786 (m-30) REVERT: C 281 ARG cc_start: 0.5347 (mpt-90) cc_final: 0.4670 (mtm180) REVERT: C 364 ARG cc_start: 0.5975 (ppt-90) cc_final: 0.5121 (ttt90) REVERT: C 404 SER cc_start: 0.7236 (m) cc_final: 0.6676 (p) REVERT: C 417 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: C 494 GLN cc_start: 0.6343 (mt0) cc_final: 0.5833 (mm-40) REVERT: C 503 MET cc_start: 0.5408 (mpt) cc_final: 0.5129 (mpm) REVERT: C 636 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7609 (tm) REVERT: C 725 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5501 (mtmm) REVERT: D 201 LYS cc_start: 0.4062 (tptp) cc_final: 0.3515 (mmpt) REVERT: D 281 ARG cc_start: 0.5310 (mpt-90) cc_final: 0.4655 (mtm180) REVERT: D 332 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7165 (mmmt) REVERT: D 364 ARG cc_start: 0.5840 (ppt-90) cc_final: 0.4984 (ttt90) REVERT: D 404 SER cc_start: 0.7229 (m) cc_final: 0.6651 (p) REVERT: D 417 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: D 494 GLN cc_start: 0.6321 (mt0) cc_final: 0.5810 (mm-40) REVERT: D 503 MET cc_start: 0.5361 (mpt) cc_final: 0.5084 (mpm) REVERT: D 600 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6644 (mt-10) REVERT: D 636 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7614 (tm) REVERT: D 725 LYS cc_start: 0.5855 (OUTLIER) cc_final: 0.5415 (mtmm) outliers start: 48 outliers final: 14 residues processed: 248 average time/residue: 1.1041 time to fit residues: 312.7708 Evaluate side-chains 217 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 417 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 6 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.204642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150273 restraints weight = 54202.219| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.86 r_work: 0.3615 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19303 Z= 0.271 Angle : 0.632 6.428 25758 Z= 0.328 Chirality : 0.040 0.143 2708 Planarity : 0.005 0.044 3012 Dihedral : 21.561 149.407 4020 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 2.45 % Allowed : 12.12 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 2068 helix: -0.09 (0.14), residues: 1264 sheet: -2.81 (0.52), residues: 76 loop : -2.77 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 421 TYR 0.015 0.002 TYR D 383 PHE 0.019 0.002 PHE A 439 TRP 0.011 0.002 TRP D 698 HIS 0.005 0.002 HIS A 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.27 (19300) covalent geometry : angle 0.63216 / 0.33 (25744) SS BOND : bond 0.00131 / 0.07 ( 3) SS BOND : angle 0.21536 / 0.14 ( 14) hydrogen bonds : bond 0.04725 / 3.11 ( 884) hydrogen bonds : angle 4.77714 / 3.33 ( 2568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4139 (tptp) cc_final: 0.3600 (mmpt) REVERT: A 235 ASP cc_start: 0.4311 (m-30) cc_final: 0.3843 (m-30) REVERT: A 281 ARG cc_start: 0.5287 (mpt-90) cc_final: 0.4777 (mpp-170) REVERT: A 312 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.4442 (mp0) REVERT: A 364 ARG cc_start: 0.6031 (ppt-90) cc_final: 0.5218 (ttt90) REVERT: A 404 SER cc_start: 0.7280 (m) cc_final: 0.6665 (p) REVERT: A 494 GLN cc_start: 0.6314 (mt0) cc_final: 0.5814 (mm-40) REVERT: A 503 MET cc_start: 0.5311 (mpt) cc_final: 0.4979 (mpm) REVERT: A 600 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6607 (mt-10) REVERT: A 636 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7559 (tm) REVERT: A 725 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.5401 (mtmm) REVERT: B 201 LYS cc_start: 0.4173 (tptp) cc_final: 0.3637 (mmtt) REVERT: B 281 ARG cc_start: 0.5330 (mpt-90) cc_final: 0.4811 (mpp-170) REVERT: B 312 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.4454 (mp0) REVERT: B 364 ARG cc_start: 0.6034 (ppt-90) cc_final: 0.5213 (ttt90) REVERT: B 404 SER cc_start: 0.7276 (m) cc_final: 0.6674 (p) REVERT: B 494 GLN cc_start: 0.6308 (mt0) cc_final: 0.5810 (mm-40) REVERT: B 503 MET cc_start: 0.5331 (mpt) cc_final: 0.5040 (mpm) REVERT: B 636 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7561 (tm) REVERT: B 725 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.5428 (mtmm) REVERT: C 201 LYS cc_start: 0.4177 (tptp) cc_final: 0.3643 (mmtt) REVERT: C 281 ARG cc_start: 0.5319 (mpt-90) cc_final: 0.4804 (mpp-170) REVERT: C 364 ARG cc_start: 0.6030 (ppt-90) cc_final: 0.5196 (ttt90) REVERT: C 404 SER cc_start: 0.7278 (m) cc_final: 0.6667 (p) REVERT: C 494 GLN cc_start: 0.6320 (mt0) cc_final: 0.5816 (mm-40) REVERT: C 503 MET cc_start: 0.5305 (mpt) cc_final: 0.5035 (mpm) REVERT: C 512 SER cc_start: 0.8348 (t) cc_final: 0.7863 (p) REVERT: C 636 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7561 (tm) REVERT: C 725 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5456 (mtmm) REVERT: D 201 LYS cc_start: 0.4201 (tptp) cc_final: 0.3605 (mmtt) REVERT: D 281 ARG cc_start: 0.5344 (mpt-90) cc_final: 0.4762 (mpp-170) REVERT: D 332 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7144 (mmmt) REVERT: D 364 ARG cc_start: 0.5914 (ppt-90) cc_final: 0.5108 (ttt90) REVERT: D 404 SER cc_start: 0.7288 (m) cc_final: 0.6667 (p) REVERT: D 406 GLU cc_start: 0.6895 (pm20) cc_final: 0.6684 (pm20) REVERT: D 494 GLN cc_start: 0.6298 (mt0) cc_final: 0.5799 (mm-40) REVERT: D 503 MET cc_start: 0.5349 (mpt) cc_final: 0.5079 (mpm) REVERT: D 512 SER cc_start: 0.8356 (t) cc_final: 0.7858 (p) REVERT: D 600 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6659 (mt-10) REVERT: D 636 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7555 (tm) REVERT: D 725 LYS cc_start: 0.5804 (OUTLIER) cc_final: 0.5400 (mtmm) outliers start: 45 outliers final: 18 residues processed: 235 average time/residue: 1.1385 time to fit residues: 304.6773 Evaluate side-chains 220 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 108 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.206154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152429 restraints weight = 54193.102| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.84 r_work: 0.3639 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19303 Z= 0.189 Angle : 0.552 5.679 25758 Z= 0.292 Chirality : 0.036 0.122 2708 Planarity : 0.004 0.040 3012 Dihedral : 20.915 145.626 4020 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.04 % Favored : 93.76 % Rotamer: Outliers : 1.85 % Allowed : 12.45 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2068 helix: 0.21 (0.14), residues: 1256 sheet: -2.92 (0.50), residues: 76 loop : -2.66 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.013 0.002 TYR D 511 PHE 0.015 0.002 PHE D 439 TRP 0.013 0.001 TRP A 698 HIS 0.003 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (19300) covalent geometry : angle 0.55246 / 0.29 (25744) SS BOND : bond 0.00042 / 0.02 ( 3) SS BOND : angle 0.38067 / 0.24 ( 14) hydrogen bonds : bond 0.04255 / 2.80 ( 884) hydrogen bonds : angle 4.56046 / 3.18 ( 2568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.793 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 201 LYS cc_start: 0.4096 (tptp) cc_final: 0.3591 (mmtt) REVERT: A 235 ASP cc_start: 0.4250 (m-30) cc_final: 0.3824 (m-30) REVERT: A 281 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4665 (mtm180) REVERT: A 312 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.4321 (mp0) REVERT: A 364 ARG cc_start: 0.6017 (ppt-90) cc_final: 0.5163 (ttt90) REVERT: A 404 SER cc_start: 0.7165 (m) cc_final: 0.6565 (p) REVERT: A 406 GLU cc_start: 0.6896 (pm20) cc_final: 0.6643 (pm20) REVERT: A 494 GLN cc_start: 0.6268 (mt0) cc_final: 0.5795 (mm-40) REVERT: A 503 MET cc_start: 0.5298 (mpt) cc_final: 0.5016 (mpm) REVERT: A 600 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 636 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7475 (tm) REVERT: A 725 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5395 (mtmm) REVERT: B 201 LYS cc_start: 0.4099 (tptp) cc_final: 0.3558 (mmtt) REVERT: B 281 ARG cc_start: 0.5285 (OUTLIER) cc_final: 0.4643 (mtm180) REVERT: B 312 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.4325 (mp0) REVERT: B 364 ARG cc_start: 0.5997 (ppt-90) cc_final: 0.5147 (ttt90) REVERT: B 404 SER cc_start: 0.7189 (m) cc_final: 0.6579 (p) REVERT: B 494 GLN cc_start: 0.6261 (mt0) cc_final: 0.5791 (mm-40) REVERT: B 503 MET cc_start: 0.5329 (mpt) cc_final: 0.5040 (mpm) REVERT: B 636 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7471 (tm) REVERT: B 725 LYS cc_start: 0.5779 (OUTLIER) cc_final: 0.5369 (mtmm) REVERT: C 201 LYS cc_start: 0.4096 (tptp) cc_final: 0.3559 (mmtt) REVERT: C 281 ARG cc_start: 0.5300 (OUTLIER) cc_final: 0.4650 (mtm180) REVERT: C 364 ARG cc_start: 0.5974 (ppt-90) cc_final: 0.5145 (ttt90) REVERT: C 404 SER cc_start: 0.7194 (m) cc_final: 0.6583 (p) REVERT: C 406 GLU cc_start: 0.6876 (pm20) cc_final: 0.6611 (pm20) REVERT: C 494 GLN cc_start: 0.6302 (mt0) cc_final: 0.5823 (mm-40) REVERT: C 503 MET cc_start: 0.5326 (mpt) cc_final: 0.5044 (mpm) REVERT: C 636 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7470 (tm) REVERT: C 725 LYS cc_start: 0.5704 (OUTLIER) cc_final: 0.5303 (mtmm) REVERT: D 201 LYS cc_start: 0.4164 (tptp) cc_final: 0.3562 (mmtt) REVERT: D 281 ARG cc_start: 0.5333 (OUTLIER) cc_final: 0.4691 (mtm180) REVERT: D 332 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7148 (mmmt) REVERT: D 364 ARG cc_start: 0.5886 (ppt-90) cc_final: 0.5013 (ttt90) REVERT: D 404 SER cc_start: 0.7235 (m) cc_final: 0.6643 (p) REVERT: D 494 GLN cc_start: 0.6264 (mt0) cc_final: 0.5795 (mm-40) REVERT: D 503 MET cc_start: 0.5341 (mpt) cc_final: 0.5058 (mpm) REVERT: D 600 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6651 (mt-10) REVERT: D 636 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7470 (tm) REVERT: D 725 LYS cc_start: 0.5812 (OUTLIER) cc_final: 0.5371 (mtmm) outliers start: 34 outliers final: 14 residues processed: 223 average time/residue: 1.1270 time to fit residues: 286.0245 Evaluate side-chains 221 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 725 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 120 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.206306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152810 restraints weight = 53969.396| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.83 r_work: 0.3648 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19303 Z= 0.173 Angle : 0.537 5.328 25758 Z= 0.284 Chirality : 0.036 0.119 2708 Planarity : 0.004 0.045 3012 Dihedral : 20.429 143.017 4020 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.43 % Favored : 93.38 % Rotamer: Outliers : 1.74 % Allowed : 12.93 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.18), residues: 2068 helix: 0.46 (0.14), residues: 1232 sheet: -3.02 (0.49), residues: 76 loop : -2.52 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.012 0.002 TYR D 383 PHE 0.015 0.002 PHE C 248 TRP 0.013 0.001 TRP B 698 HIS 0.004 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (19300) covalent geometry : angle 0.53756 / 0.28 (25744) SS BOND : bond 0.00044 / 0.02 ( 3) SS BOND : angle 0.28915 / 0.19 ( 14) hydrogen bonds : bond 0.04142 / 2.72 ( 884) hydrogen bonds : angle 4.47247 / 3.12 ( 2568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.585 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 201 LYS cc_start: 0.4134 (tptp) cc_final: 0.3610 (mmtt) REVERT: A 235 ASP cc_start: 0.4330 (m-30) cc_final: 0.3885 (m-30) REVERT: A 281 ARG cc_start: 0.5315 (OUTLIER) cc_final: 0.4598 (mtm180) REVERT: A 364 ARG cc_start: 0.6042 (ppt-90) cc_final: 0.5179 (ttt90) REVERT: A 404 SER cc_start: 0.7282 (m) cc_final: 0.6701 (p) REVERT: A 466 MET cc_start: 0.6330 (mtp) cc_final: 0.5938 (mpp) REVERT: A 494 GLN cc_start: 0.6343 (mt0) cc_final: 0.5864 (mm-40) REVERT: A 503 MET cc_start: 0.5343 (mpt) cc_final: 0.5052 (mpm) REVERT: A 600 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6650 (mt-10) REVERT: A 636 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7555 (tm) REVERT: B 201 LYS cc_start: 0.4172 (tptp) cc_final: 0.3616 (mmtt) REVERT: B 281 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.4580 (mtm180) REVERT: B 312 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.4314 (mp0) REVERT: B 364 ARG cc_start: 0.6002 (ppt-90) cc_final: 0.5147 (ttt90) REVERT: B 404 SER cc_start: 0.7228 (m) cc_final: 0.6637 (p) REVERT: B 494 GLN cc_start: 0.6336 (mt0) cc_final: 0.5849 (mm-40) REVERT: B 503 MET cc_start: 0.5388 (mpt) cc_final: 0.5090 (mpm) REVERT: B 636 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7553 (tm) REVERT: B 725 LYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5451 (mtmm) REVERT: C 201 LYS cc_start: 0.4200 (tptp) cc_final: 0.3657 (mmtt) REVERT: C 281 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.4600 (mtm180) REVERT: C 364 ARG cc_start: 0.6011 (ppt-90) cc_final: 0.5172 (ttt90) REVERT: C 404 SER cc_start: 0.7314 (m) cc_final: 0.6708 (p) REVERT: C 466 MET cc_start: 0.6332 (mtp) cc_final: 0.5966 (mpp) REVERT: C 494 GLN cc_start: 0.6323 (mt0) cc_final: 0.5837 (mm-40) REVERT: C 503 MET cc_start: 0.5354 (mpt) cc_final: 0.5063 (mpm) REVERT: C 636 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7552 (tm) REVERT: C 725 LYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5350 (mtmm) REVERT: D 201 LYS cc_start: 0.4248 (tptp) cc_final: 0.3590 (mmpt) REVERT: D 281 ARG cc_start: 0.5312 (OUTLIER) cc_final: 0.4675 (mtm180) REVERT: D 332 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7175 (mmmt) REVERT: D 364 ARG cc_start: 0.5891 (ppt-90) cc_final: 0.5031 (ttt90) REVERT: D 404 SER cc_start: 0.7325 (m) cc_final: 0.6714 (p) REVERT: D 494 GLN cc_start: 0.6315 (mt0) cc_final: 0.5833 (mm-40) REVERT: D 503 MET cc_start: 0.5370 (mpt) cc_final: 0.5092 (mpm) REVERT: D 600 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6699 (mt-10) REVERT: D 636 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7555 (tm) outliers start: 32 outliers final: 15 residues processed: 221 average time/residue: 1.1158 time to fit residues: 281.3383 Evaluate side-chains 219 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 725 LYS Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 83 optimal weight: 3.9990 chunk 178 optimal weight: 0.4980 chunk 198 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.206405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152531 restraints weight = 54122.976| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.85 r_work: 0.3642 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19303 Z= 0.179 Angle : 0.537 5.306 25758 Z= 0.283 Chirality : 0.036 0.118 2708 Planarity : 0.004 0.040 3012 Dihedral : 20.107 141.260 4020 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.00 % Favored : 93.81 % Rotamer: Outliers : 1.68 % Allowed : 13.10 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2068 helix: 0.57 (0.14), residues: 1232 sheet: -3.08 (0.48), residues: 76 loop : -2.46 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.013 0.002 TYR D 511 PHE 0.014 0.002 PHE A 439 TRP 0.012 0.001 TRP C 698 HIS 0.004 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (19300) covalent geometry : angle 0.53754 / 0.28 (25744) SS BOND : bond 0.00040 / 0.02 ( 3) SS BOND : angle 0.31258 / 0.20 ( 14) hydrogen bonds : bond 0.04120 / 2.71 ( 884) hydrogen bonds : angle 4.44410 / 3.10 ( 2568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4136 Ramachandran restraints generated. 2068 Oldfield, 0 Emsley, 2068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.794 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 201 LYS cc_start: 0.4223 (tptp) cc_final: 0.3678 (mmtt) REVERT: A 235 ASP cc_start: 0.4434 (m-30) cc_final: 0.3978 (m-30) REVERT: A 281 ARG cc_start: 0.5298 (OUTLIER) cc_final: 0.4641 (mtm180) REVERT: A 364 ARG cc_start: 0.6057 (ppt-90) cc_final: 0.5190 (ttt90) REVERT: A 404 SER cc_start: 0.7306 (m) cc_final: 0.6717 (p) REVERT: A 494 GLN cc_start: 0.6394 (mt0) cc_final: 0.5909 (mm-40) REVERT: A 503 MET cc_start: 0.5383 (mpt) cc_final: 0.5091 (mpm) REVERT: A 636 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7521 (tm) REVERT: B 201 LYS cc_start: 0.4250 (tptp) cc_final: 0.3678 (mmtt) REVERT: B 281 ARG cc_start: 0.5351 (OUTLIER) cc_final: 0.4698 (mtm180) REVERT: B 364 ARG cc_start: 0.6068 (ppt-90) cc_final: 0.5200 (ttt90) REVERT: B 404 SER cc_start: 0.7286 (m) cc_final: 0.6712 (p) REVERT: B 494 GLN cc_start: 0.6352 (mt0) cc_final: 0.5872 (mm-40) REVERT: B 503 MET cc_start: 0.5387 (mpt) cc_final: 0.5089 (mpm) REVERT: B 636 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7531 (tm) REVERT: C 201 LYS cc_start: 0.4262 (tptp) cc_final: 0.3691 (mmtt) REVERT: C 281 ARG cc_start: 0.5317 (OUTLIER) cc_final: 0.4667 (mtm180) REVERT: C 364 ARG cc_start: 0.6079 (ppt-90) cc_final: 0.5190 (ttt90) REVERT: C 404 SER cc_start: 0.7244 (m) cc_final: 0.6669 (p) REVERT: C 494 GLN cc_start: 0.6371 (mt0) cc_final: 0.5890 (mm-40) REVERT: C 503 MET cc_start: 0.5361 (mpt) cc_final: 0.5070 (mpm) REVERT: C 636 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7526 (tm) REVERT: C 725 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.5378 (mtmm) REVERT: D 201 LYS cc_start: 0.4256 (tptp) cc_final: 0.3581 (mmpt) REVERT: D 281 ARG cc_start: 0.5388 (OUTLIER) cc_final: 0.4751 (mtm180) REVERT: D 364 ARG cc_start: 0.5977 (ppt-90) cc_final: 0.5100 (ttt90) REVERT: D 404 SER cc_start: 0.7489 (m) cc_final: 0.6899 (p) REVERT: D 413 MET cc_start: 0.8500 (ttm) cc_final: 0.8152 (mtp) REVERT: D 466 MET cc_start: 0.6408 (mtp) cc_final: 0.5998 (mpp) REVERT: D 494 GLN cc_start: 0.6309 (mt0) cc_final: 0.5826 (mm-40) REVERT: D 503 MET cc_start: 0.5353 (mpt) cc_final: 0.5060 (mpm) REVERT: D 600 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6717 (mt-10) REVERT: D 636 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7532 (tm) outliers start: 31 outliers final: 15 residues processed: 220 average time/residue: 1.1520 time to fit residues: 288.6602 Evaluate side-chains 218 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 725 LYS Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 636 LEU Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 196 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.205410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.151554 restraints weight = 53894.111| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.84 r_work: 0.3632 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19303 Z= 0.213 Angle : 0.565 5.866 25758 Z= 0.295 Chirality : 0.038 0.201 2708 Planarity : 0.004 0.045 3012 Dihedral : 20.145 142.706 4020 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 1.90 % Allowed : 13.32 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.18), residues: 2068 helix: 0.46 (0.14), residues: 1232 sheet: -3.03 (0.49), residues: 76 loop : -2.43 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.013 0.002 TYR A 383 PHE 0.019 0.002 PHE A 248 TRP 0.011 0.001 TRP D 698 HIS 0.005 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (19300) covalent geometry : angle 0.56503 / 0.30 (25744) SS BOND : bond 0.00059 / 0.03 ( 3) SS BOND : angle 0.25971 / 0.17 ( 14) hydrogen bonds : bond 0.04226 / 2.78 ( 884) hydrogen bonds : angle 4.51819 / 3.16 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13468.59 seconds wall clock time: 227 minutes 56.91 seconds (13676.91 seconds total)