Starting phenix.real_space_refine on Mon Jul 6 20:09:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf9_29982/07_2026/8gf9_29982_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf9_29982/07_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_29982/07_2026/8gf9_29982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf9_29982/07_2026/8gf9_29982.map" model { file = "/net/cci-nas-00/data/ceres_data/8gf9_29982/07_2026/8gf9_29982_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf9_29982/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 488 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'8IJ': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 2 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: 13.62, per 1000 atoms: 0.38 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: 3.26 Conformation dependent library (CDL) restraints added in 751.4 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: 0.70 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: 7.75 Time building geometry restraints manager: 4.26 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: 1.080 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: 0.220 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 38.620 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.070 ------------------------------------------------------------------------------- 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 : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 1.2505 time to fit residues: 504.4015 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 : 0.664 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.219760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.168909 restraints weight = 53042.163| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.80 r_work: 0.3810 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19303 Z= 0.158 Angle : 0.678 8.635 25758 Z= 0.352 Chirality : 0.038 0.138 2708 Planarity : 0.005 0.045 3012 Dihedral : 25.202 178.184 4020 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.58 % Favored : 93.04 % 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: -3.71 (0.15), residues: 2068 helix: -2.01 (0.12), residues: 1256 sheet: -2.89 (0.52), residues: 76 loop : -3.00 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 575 TYR 0.020 0.001 TYR D 352 PHE 0.015 0.001 PHE A 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 0.00320 / 0.16 (19300) covalent geometry : angle 0.67817 / 0.35 (25744) SS BOND : bond 0.00080 / 0.04 ( 3) SS BOND : angle 0.28564 / 0.18 ( 14) hydrogen bonds : bond 0.05876 / 3.88 ( 884) hydrogen bonds : angle 5.74797 / 4.04 ( 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 263 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 247 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4285 (tptp) cc_final: 0.3899 (mmtt) REVERT: A 235 ASP cc_start: 0.4615 (m-30) cc_final: 0.4260 (m-30) REVERT: A 364 ARG cc_start: 0.5598 (ppt-90) cc_final: 0.4605 (ttt-90) REVERT: A 367 SER cc_start: 0.6750 (m) cc_final: 0.6325 (m) REVERT: A 446 MET cc_start: 0.8113 (mmp) cc_final: 0.7774 (mmp) REVERT: A 494 GLN cc_start: 0.6550 (mt0) cc_final: 0.6019 (mm-40) REVERT: A 503 MET cc_start: 0.5314 (mpt) cc_final: 0.5019 (mpm) REVERT: A 708 ASP cc_start: 0.7189 (m-30) cc_final: 0.6895 (m-30) REVERT: B 201 LYS cc_start: 0.4274 (tptp) cc_final: 0.3884 (mptt) REVERT: B 235 ASP cc_start: 0.4509 (m-30) cc_final: 0.4149 (m-30) REVERT: B 364 ARG cc_start: 0.5592 (ppt-90) cc_final: 0.4593 (ttt-90) REVERT: B 367 SER cc_start: 0.6721 (m) cc_final: 0.6312 (m) REVERT: B 494 GLN cc_start: 0.6569 (mt0) cc_final: 0.6027 (mm-40) REVERT: B 503 MET cc_start: 0.5357 (mpt) cc_final: 0.5057 (mpm) REVERT: B 708 ASP cc_start: 0.7193 (m-30) cc_final: 0.6905 (m-30) REVERT: C 201 LYS cc_start: 0.4281 (tptp) cc_final: 0.3892 (mptt) REVERT: C 235 ASP cc_start: 0.4523 (m-30) cc_final: 0.4165 (m-30) REVERT: C 364 ARG cc_start: 0.5634 (ppt-90) cc_final: 0.4596 (ttt-90) REVERT: C 367 SER cc_start: 0.6807 (m) cc_final: 0.6377 (m) REVERT: C 494 GLN cc_start: 0.6540 (mt0) cc_final: 0.6004 (mm-40) REVERT: C 503 MET cc_start: 0.5348 (mpt) cc_final: 0.5068 (mpm) REVERT: C 708 ASP cc_start: 0.7181 (m-30) cc_final: 0.6877 (m-30) REVERT: C 725 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5573 (mtmm) REVERT: D 201 LYS cc_start: 0.4189 (tptp) cc_final: 0.3774 (mptt) REVERT: D 235 ASP cc_start: 0.4565 (m-30) cc_final: 0.4212 (m-30) REVERT: D 364 ARG cc_start: 0.5545 (ppt-90) cc_final: 0.5137 (ptm160) REVERT: D 494 GLN cc_start: 0.6545 (mt0) cc_final: 0.5966 (mm-40) REVERT: D 503 MET cc_start: 0.5272 (mpt) cc_final: 0.4988 (mpm) REVERT: D 708 ASP cc_start: 0.7249 (m-30) cc_final: 0.6960 (m-30) outliers start: 16 outliers final: 4 residues processed: 258 average time/residue: 1.1250 time to fit residues: 330.7562 Evaluate side-chains 218 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 213 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 ASN B 653 ASN C 653 ASN D 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.209087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.155593 restraints weight = 53626.528| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.82 r_work: 0.3664 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19303 Z= 0.262 Angle : 0.678 7.296 25758 Z= 0.350 Chirality : 0.041 0.137 2708 Planarity : 0.005 0.042 3012 Dihedral : 24.300 175.384 4020 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.11 % Favored : 92.70 % Rotamer: Outliers : 2.28 % Allowed : 8.86 % Favored : 88.86 % 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: -2.82 (0.16), residues: 2068 helix: -1.13 (0.13), residues: 1252 sheet: -2.58 (0.56), residues: 76 loop : -2.98 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 474 TYR 0.015 0.002 TYR D 584 PHE 0.021 0.002 PHE A 639 TRP 0.015 0.002 TRP C 698 HIS 0.004 0.001 HIS D 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.26 (19300) covalent geometry : angle 0.67768 / 0.35 (25744) SS BOND : bond 0.00017 / 0.01 ( 3) SS BOND : angle 0.22696 / 0.15 ( 14) hydrogen bonds : bond 0.05396 / 3.57 ( 884) hydrogen bonds : angle 5.27887 / 3.69 ( 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 265 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 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: 0.4179 (tptp) cc_final: 0.3767 (mmpt) REVERT: A 235 ASP cc_start: 0.4285 (m-30) cc_final: 0.3916 (m-30) REVERT: A 301 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.7033 (t70) REVERT: A 364 ARG cc_start: 0.5883 (ppt-90) cc_final: 0.4921 (ttt90) REVERT: A 417 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: A 494 GLN cc_start: 0.6531 (mt0) cc_final: 0.6000 (mm-40) REVERT: A 503 MET cc_start: 0.5330 (mpt) cc_final: 0.5037 (mpm) REVERT: A 600 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6527 (mt-10) REVERT: B 201 LYS cc_start: 0.4196 (tptp) cc_final: 0.3747 (mmpt) REVERT: B 235 ASP cc_start: 0.4252 (m-30) cc_final: 0.3881 (m-30) REVERT: B 364 ARG cc_start: 0.5853 (ppt-90) cc_final: 0.4917 (ttt90) REVERT: B 494 GLN cc_start: 0.6556 (mt0) cc_final: 0.6028 (mm-40) REVERT: B 503 MET cc_start: 0.5349 (mpt) cc_final: 0.5053 (mpm) REVERT: B 725 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5492 (mtmm) REVERT: C 201 LYS cc_start: 0.4200 (tptp) cc_final: 0.3770 (mmtt) REVERT: C 235 ASP cc_start: 0.4246 (m-30) cc_final: 0.3890 (m-30) REVERT: C 364 ARG cc_start: 0.5908 (ppt-90) cc_final: 0.5005 (ttt90) REVERT: C 494 GLN cc_start: 0.6553 (mt0) cc_final: 0.6023 (mm-40) REVERT: C 503 MET cc_start: 0.5333 (mpt) cc_final: 0.5041 (mpm) REVERT: C 725 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5623 (mtmm) REVERT: D 201 LYS cc_start: 0.4170 (tptp) cc_final: 0.3687 (mptt) REVERT: D 235 ASP cc_start: 0.4536 (m-30) cc_final: 0.4159 (m-30) REVERT: D 332 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7126 (mmmt) REVERT: D 364 ARG cc_start: 0.5724 (ppt-90) cc_final: 0.4811 (ttt90) REVERT: D 494 GLN cc_start: 0.6436 (mt0) cc_final: 0.5913 (mm-40) REVERT: D 503 MET cc_start: 0.5210 (mpt) cc_final: 0.4920 (mpm) REVERT: D 600 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6578 (mt-10) REVERT: D 725 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5540 (mtmm) outliers start: 42 outliers final: 16 residues processed: 252 average time/residue: 1.2130 time to fit residues: 345.5217 Evaluate side-chains 226 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 483 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 483 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 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 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: 0.8980 chunk 137 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN A 394 ASN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 394 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 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 = 0.4381 r_free = 0.4381 target = 0.212002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158484 restraints weight = 53223.934| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.83 r_work: 0.3704 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3533 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= 0.139 Angle : 0.550 6.288 25758 Z= 0.290 Chirality : 0.035 0.125 2708 Planarity : 0.004 0.039 3012 Dihedral : 22.554 163.965 4020 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.04 % Favored : 93.76 % Rotamer: Outliers : 2.55 % Allowed : 8.97 % Favored : 88.48 % 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: -2.07 (0.17), residues: 2068 helix: -0.46 (0.13), residues: 1256 sheet: -2.74 (0.51), residues: 76 loop : -2.77 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 474 TYR 0.013 0.001 TYR A 511 PHE 0.015 0.001 PHE A 248 TRP 0.012 0.001 TRP A 698 HIS 0.002 0.001 HIS B 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (19300) covalent geometry : angle 0.55040 / 0.29 (25744) SS BOND : bond 0.00088 / 0.04 ( 3) SS BOND : angle 0.43443 / 0.28 ( 14) hydrogen bonds : bond 0.04362 / 2.86 ( 884) hydrogen bonds : angle 4.76333 / 3.33 ( 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 259 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4018 (tptp) cc_final: 0.3608 (mmpt) REVERT: A 235 ASP cc_start: 0.4299 (m-30) cc_final: 0.3909 (m-30) REVERT: A 364 ARG cc_start: 0.5829 (ppt-90) cc_final: 0.4904 (ttt90) REVERT: A 494 GLN cc_start: 0.6367 (mt0) cc_final: 0.5823 (mm-40) REVERT: A 503 MET cc_start: 0.5230 (mpt) cc_final: 0.4946 (mpm) REVERT: A 600 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6458 (mt-10) REVERT: A 725 LYS cc_start: 0.5912 (OUTLIER) cc_final: 0.5466 (mtmm) REVERT: B 201 LYS cc_start: 0.4049 (tptp) cc_final: 0.3624 (mmpt) REVERT: B 235 ASP cc_start: 0.4264 (m-30) cc_final: 0.3863 (m-30) REVERT: B 364 ARG cc_start: 0.5793 (ppt-90) cc_final: 0.4891 (ttt90) REVERT: B 494 GLN cc_start: 0.6374 (mt0) cc_final: 0.5819 (mm110) REVERT: B 503 MET cc_start: 0.5226 (mpt) cc_final: 0.4940 (mpm) REVERT: B 725 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5515 (mtmm) REVERT: C 201 LYS cc_start: 0.4012 (tptp) cc_final: 0.3584 (mmpt) REVERT: C 235 ASP cc_start: 0.4322 (m-30) cc_final: 0.3928 (m-30) REVERT: C 364 ARG cc_start: 0.5793 (ppt-90) cc_final: 0.4911 (ttt90) REVERT: C 478 GLU cc_start: 0.6771 (mt-10) cc_final: 0.5928 (mp0) REVERT: C 494 GLN cc_start: 0.6367 (mt0) cc_final: 0.5838 (mm-40) REVERT: C 503 MET cc_start: 0.5193 (mpt) cc_final: 0.4913 (mpm) REVERT: C 725 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5520 (mtmm) REVERT: D 201 LYS cc_start: 0.4041 (tptp) cc_final: 0.3570 (mmpt) REVERT: D 235 ASP cc_start: 0.4195 (m-30) cc_final: 0.3791 (m-30) REVERT: D 364 ARG cc_start: 0.5579 (ppt-90) cc_final: 0.4738 (ttt90) REVERT: D 421 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7602 (mtt-85) REVERT: D 478 GLU cc_start: 0.6688 (mt-10) cc_final: 0.5857 (mp0) REVERT: D 494 GLN cc_start: 0.6373 (mt0) cc_final: 0.5845 (mm-40) REVERT: D 503 MET cc_start: 0.5278 (mpt) cc_final: 0.4990 (mpm) REVERT: D 725 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5578 (mtmm) outliers start: 47 outliers final: 18 residues processed: 246 average time/residue: 1.1156 time to fit residues: 315.2916 Evaluate side-chains 229 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 483 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 483 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 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 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: 5.9990 chunk 186 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 168 optimal weight: 0.0870 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 GLN B 311 ASN ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.212656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.159828 restraints weight = 53595.303| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.81 r_work: 0.3719 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19303 Z= 0.123 Angle : 0.517 5.748 25758 Z= 0.271 Chirality : 0.035 0.124 2708 Planarity : 0.004 0.041 3012 Dihedral : 20.950 151.271 4020 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.86 % Rotamer: Outliers : 2.01 % Allowed : 10.54 % Favored : 87.45 % 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: -1.35 (0.18), residues: 2068 helix: 0.22 (0.14), residues: 1236 sheet: -2.74 (0.52), residues: 76 loop : -2.59 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 474 TYR 0.011 0.001 TYR D 511 PHE 0.022 0.001 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 0.00257 / 0.12 (19300) covalent geometry : angle 0.51662 / 0.27 (25744) SS BOND : bond 0.00053 / 0.03 ( 3) SS BOND : angle 0.33039 / 0.21 ( 14) hydrogen bonds : bond 0.04004 / 2.62 ( 884) hydrogen bonds : angle 4.47657 / 3.13 ( 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 255 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 1.000 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: 0.3999 (tptp) cc_final: 0.3590 (mmpt) REVERT: A 235 ASP cc_start: 0.4295 (m-30) cc_final: 0.3884 (m-30) REVERT: A 364 ARG cc_start: 0.5833 (ppt-90) cc_final: 0.5007 (ttt90) REVERT: A 494 GLN cc_start: 0.6319 (mt0) cc_final: 0.5778 (mm-40) REVERT: A 503 MET cc_start: 0.5249 (mpt) cc_final: 0.4951 (mpm) REVERT: A 725 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5377 (mtmm) REVERT: B 201 LYS cc_start: 0.4008 (tptp) cc_final: 0.3581 (mmpt) REVERT: B 235 ASP cc_start: 0.4390 (m-30) cc_final: 0.3941 (m-30) REVERT: B 364 ARG cc_start: 0.5817 (ppt-90) cc_final: 0.4977 (ttt90) REVERT: B 393 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7383 (ptpp) REVERT: B 494 GLN cc_start: 0.6326 (mt0) cc_final: 0.5801 (mm-40) REVERT: B 503 MET cc_start: 0.5350 (mpt) cc_final: 0.5042 (mpm) REVERT: B 725 LYS cc_start: 0.5808 (OUTLIER) cc_final: 0.5348 (mtmm) REVERT: C 201 LYS cc_start: 0.3994 (tptp) cc_final: 0.3571 (mmpt) REVERT: C 235 ASP cc_start: 0.4352 (m-30) cc_final: 0.3932 (m-30) REVERT: C 364 ARG cc_start: 0.5831 (ppt-90) cc_final: 0.4985 (ttt90) REVERT: C 494 GLN cc_start: 0.6337 (mt0) cc_final: 0.5820 (mm-40) REVERT: C 503 MET cc_start: 0.5211 (mpt) cc_final: 0.4924 (mpm) REVERT: C 725 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5430 (mtmm) REVERT: D 201 LYS cc_start: 0.3987 (tptp) cc_final: 0.3545 (mmpt) REVERT: D 235 ASP cc_start: 0.4176 (m-30) cc_final: 0.3732 (m-30) REVERT: D 364 ARG cc_start: 0.5652 (ppt-90) cc_final: 0.4821 (ttt90) REVERT: D 421 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7586 (mtt-85) REVERT: D 478 GLU cc_start: 0.6694 (mt-10) cc_final: 0.5862 (mp0) REVERT: D 494 GLN cc_start: 0.6325 (mt0) cc_final: 0.5726 (pt0) REVERT: D 503 MET cc_start: 0.5327 (mpt) cc_final: 0.5033 (mpm) REVERT: D 725 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5484 (mtmm) outliers start: 37 outliers final: 18 residues processed: 244 average time/residue: 1.1546 time to fit residues: 321.9398 Evaluate side-chains 226 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 483 LEU 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 393 LYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 483 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 190 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.210327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157238 restraints weight = 53777.653| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.82 r_work: 0.3685 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19303 Z= 0.160 Angle : 0.530 5.161 25758 Z= 0.280 Chirality : 0.036 0.121 2708 Planarity : 0.004 0.040 3012 Dihedral : 20.430 145.584 4020 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 2.72 % Allowed : 10.60 % Favored : 86.68 % 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: -1.19 (0.18), residues: 2068 helix: 0.36 (0.14), residues: 1244 sheet: -2.81 (0.51), residues: 76 loop : -2.55 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 474 TYR 0.013 0.002 TYR D 511 PHE 0.024 0.002 PHE A 248 TRP 0.009 0.001 TRP C 698 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (19300) covalent geometry : angle 0.53014 / 0.28 (25744) SS BOND : bond 0.00019 / 0.01 ( 3) SS BOND : angle 0.29496 / 0.19 ( 14) hydrogen bonds : bond 0.04086 / 2.68 ( 884) hydrogen bonds : angle 4.42398 / 3.09 ( 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 267 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.777 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: 0.4044 (tptp) cc_final: 0.3618 (mmpt) REVERT: A 235 ASP cc_start: 0.4443 (m-30) cc_final: 0.3975 (m-30) REVERT: A 312 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.4261 (mp0) REVERT: A 364 ARG cc_start: 0.5919 (ppt-90) cc_final: 0.5091 (ttt90) REVERT: A 494 GLN cc_start: 0.6414 (mt0) cc_final: 0.5871 (mm-40) REVERT: A 503 MET cc_start: 0.5381 (mpt) cc_final: 0.5055 (mpm) REVERT: A 725 LYS cc_start: 0.5799 (OUTLIER) cc_final: 0.5363 (mtmm) REVERT: B 201 LYS cc_start: 0.4110 (tptp) cc_final: 0.3657 (mmpt) REVERT: B 235 ASP cc_start: 0.4363 (m-30) cc_final: 0.3866 (m-30) REVERT: B 364 ARG cc_start: 0.5907 (ppt-90) cc_final: 0.5062 (ttt90) REVERT: B 393 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7435 (ptpp) REVERT: B 404 SER cc_start: 0.7175 (m) cc_final: 0.6641 (p) REVERT: B 494 GLN cc_start: 0.6427 (mt0) cc_final: 0.5904 (mm-40) REVERT: B 503 MET cc_start: 0.5416 (mpt) cc_final: 0.5110 (mpm) REVERT: B 504 LYS cc_start: 0.7008 (tttt) cc_final: 0.6802 (tppt) REVERT: B 725 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5367 (mtmm) REVERT: C 201 LYS cc_start: 0.4111 (tptp) cc_final: 0.3662 (mmpt) REVERT: C 235 ASP cc_start: 0.4371 (m-30) cc_final: 0.3899 (m-30) REVERT: C 364 ARG cc_start: 0.5923 (ppt-90) cc_final: 0.5092 (ttt90) REVERT: C 404 SER cc_start: 0.7176 (m) cc_final: 0.6648 (p) REVERT: C 494 GLN cc_start: 0.6437 (mt0) cc_final: 0.5909 (mm-40) REVERT: C 503 MET cc_start: 0.5397 (mpt) cc_final: 0.5089 (mpm) REVERT: C 725 LYS cc_start: 0.5812 (OUTLIER) cc_final: 0.5393 (mtmm) REVERT: D 201 LYS cc_start: 0.4070 (tptp) cc_final: 0.3595 (mmpt) REVERT: D 235 ASP cc_start: 0.4170 (m-30) cc_final: 0.3745 (m-30) REVERT: D 364 ARG cc_start: 0.5739 (ppt-90) cc_final: 0.4908 (ttt90) REVERT: D 387 CYS cc_start: 0.8454 (m) cc_final: 0.8225 (m) REVERT: D 404 SER cc_start: 0.7117 (m) cc_final: 0.6581 (p) REVERT: D 417 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: D 421 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7713 (mtt-85) REVERT: D 494 GLN cc_start: 0.6343 (mt0) cc_final: 0.5756 (pt0) REVERT: D 503 MET cc_start: 0.5388 (mpt) cc_final: 0.5086 (mpm) REVERT: D 600 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6664 (mt-10) REVERT: D 725 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5561 (mtmm) outliers start: 50 outliers final: 19 residues processed: 251 average time/residue: 1.1771 time to fit residues: 335.8978 Evaluate side-chains 226 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 483 LEU 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 312 GLU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 483 LEU 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 417 GLU Chi-restraints excluded: chain D residue 475 VAL 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: 10.0000 chunk 115 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 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 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153177 restraints weight = 53992.829| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.84 r_work: 0.3648 rms_B_bonded: 2.58 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: 0.7508 moved from start: 0.4390 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= 0.217 Angle : 0.581 5.912 25758 Z= 0.304 Chirality : 0.038 0.118 2708 Planarity : 0.004 0.045 3012 Dihedral : 20.562 144.232 4020 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 2.88 % Allowed : 10.49 % Favored : 86.63 % 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: -1.25 (0.18), residues: 2068 helix: 0.32 (0.14), residues: 1244 sheet: -2.81 (0.50), residues: 76 loop : -2.61 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 474 TYR 0.015 0.002 TYR C 375 PHE 0.021 0.002 PHE A 248 TRP 0.009 0.001 TRP A 698 HIS 0.004 0.001 HIS B 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (19300) covalent geometry : angle 0.58137 / 0.30 (25744) SS BOND : bond 0.00031 / 0.02 ( 3) SS BOND : angle 0.23556 / 0.15 ( 14) hydrogen bonds : bond 0.04380 / 2.88 ( 884) hydrogen bonds : angle 4.55031 / 3.18 ( 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 260 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.859 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: 0.4140 (tptp) cc_final: 0.3672 (mmpt) REVERT: A 235 ASP cc_start: 0.4278 (m-30) cc_final: 0.3814 (m-30) REVERT: A 281 ARG cc_start: 0.5296 (mpt-90) cc_final: 0.4603 (mtm180) REVERT: A 312 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.4281 (mp0) REVERT: A 364 ARG cc_start: 0.5971 (ppt-90) cc_final: 0.5138 (ttt90) REVERT: A 404 SER cc_start: 0.7534 (m) cc_final: 0.6920 (p) REVERT: A 406 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: A 494 GLN cc_start: 0.6254 (mt0) cc_final: 0.5747 (mm-40) REVERT: A 503 MET cc_start: 0.5331 (mpt) cc_final: 0.5045 (mpm) REVERT: A 725 LYS cc_start: 0.5695 (OUTLIER) cc_final: 0.5270 (mtmm) REVERT: B 201 LYS cc_start: 0.4176 (tptp) cc_final: 0.3678 (mmpt) REVERT: B 235 ASP cc_start: 0.4280 (m-30) cc_final: 0.3814 (m-30) REVERT: B 281 ARG cc_start: 0.5254 (mpt-90) cc_final: 0.4568 (mtm180) REVERT: B 312 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.4303 (mp0) REVERT: B 364 ARG cc_start: 0.5972 (ppt-90) cc_final: 0.5132 (ttt90) REVERT: B 404 SER cc_start: 0.7356 (m) cc_final: 0.6788 (p) REVERT: B 494 GLN cc_start: 0.6282 (mt0) cc_final: 0.5780 (mm-40) REVERT: B 503 MET cc_start: 0.5358 (mpt) cc_final: 0.5064 (mpm) REVERT: B 725 LYS cc_start: 0.5716 (OUTLIER) cc_final: 0.5295 (mtmm) REVERT: C 201 LYS cc_start: 0.4202 (tptp) cc_final: 0.3717 (mmpt) REVERT: C 235 ASP cc_start: 0.4298 (m-30) cc_final: 0.3830 (m-30) REVERT: C 281 ARG cc_start: 0.5299 (mpt-90) cc_final: 0.4618 (mtm180) REVERT: C 364 ARG cc_start: 0.5935 (ppt-90) cc_final: 0.5110 (ttt90) REVERT: C 404 SER cc_start: 0.7368 (m) cc_final: 0.6796 (p) REVERT: C 494 GLN cc_start: 0.6294 (mt0) cc_final: 0.5790 (mm-40) REVERT: C 503 MET cc_start: 0.5304 (mpt) cc_final: 0.5017 (mpm) REVERT: C 725 LYS cc_start: 0.5741 (OUTLIER) cc_final: 0.5346 (mtmm) REVERT: D 201 LYS cc_start: 0.4075 (tptp) cc_final: 0.3547 (mmpt) REVERT: D 281 ARG cc_start: 0.5281 (mpt-90) cc_final: 0.4619 (mtm180) REVERT: D 364 ARG cc_start: 0.5838 (ppt-90) cc_final: 0.5046 (ttt90) REVERT: D 404 SER cc_start: 0.7385 (m) cc_final: 0.6810 (p) REVERT: D 417 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: D 494 GLN cc_start: 0.6268 (mt0) cc_final: 0.5696 (pt0) REVERT: D 503 MET cc_start: 0.5359 (mpt) cc_final: 0.5083 (mpm) REVERT: D 600 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6637 (mt-10) REVERT: D 708 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7869 (t0) REVERT: D 725 LYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5307 (mtmm) outliers start: 53 outliers final: 15 residues processed: 250 average time/residue: 1.1548 time to fit residues: 329.7839 Evaluate side-chains 214 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 406 GLU Chi-restraints excluded: chain A residue 475 VAL 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 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 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 417 GLU Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 708 ASP 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: 6.9990 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 171 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 311 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.208608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.155200 restraints weight = 53939.997| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.84 r_work: 0.3666 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19303 Z= 0.147 Angle : 0.518 5.141 25758 Z= 0.276 Chirality : 0.035 0.123 2708 Planarity : 0.004 0.039 3012 Dihedral : 19.880 140.238 4020 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.14 % Favored : 93.67 % Rotamer: Outliers : 2.01 % Allowed : 11.90 % Favored : 86.09 % 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: -1.02 (0.18), residues: 2068 helix: 0.53 (0.14), residues: 1240 sheet: -2.84 (0.50), residues: 76 loop : -2.54 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 421 TYR 0.013 0.001 TYR D 511 PHE 0.015 0.001 PHE C 248 TRP 0.012 0.001 TRP C 698 HIS 0.002 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (19300) covalent geometry : angle 0.51812 / 0.28 (25744) SS BOND : bond 0.00010 / 0.01 ( 3) SS BOND : angle 0.32529 / 0.21 ( 14) hydrogen bonds : bond 0.04027 / 2.64 ( 884) hydrogen bonds : angle 4.37032 / 3.05 ( 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 235 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.895 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: 0.4209 (tptp) cc_final: 0.3747 (mmpt) REVERT: A 235 ASP cc_start: 0.4408 (m-30) cc_final: 0.3920 (m-30) REVERT: A 281 ARG cc_start: 0.5395 (mpt-90) cc_final: 0.4686 (mtm180) REVERT: A 312 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.4266 (mp0) REVERT: A 364 ARG cc_start: 0.6013 (ppt-90) cc_final: 0.5140 (ttt90) REVERT: A 404 SER cc_start: 0.7404 (m) cc_final: 0.6809 (p) REVERT: A 494 GLN cc_start: 0.6327 (mt0) cc_final: 0.5830 (mm-40) REVERT: A 503 MET cc_start: 0.5360 (mpt) cc_final: 0.5028 (mpm) REVERT: B 201 LYS cc_start: 0.4210 (tptp) cc_final: 0.3700 (mmpt) REVERT: B 235 ASP cc_start: 0.4346 (m-30) cc_final: 0.3852 (m-30) REVERT: B 281 ARG cc_start: 0.5400 (mpt-90) cc_final: 0.4704 (mtm180) REVERT: B 364 ARG cc_start: 0.5968 (ppt-90) cc_final: 0.5133 (ttt90) REVERT: B 404 SER cc_start: 0.7262 (m) cc_final: 0.6728 (p) REVERT: B 494 GLN cc_start: 0.6251 (mt0) cc_final: 0.5773 (mm-40) REVERT: B 503 MET cc_start: 0.5371 (mpt) cc_final: 0.5079 (mpm) REVERT: B 725 LYS cc_start: 0.5789 (OUTLIER) cc_final: 0.5354 (mtmm) REVERT: C 201 LYS cc_start: 0.4225 (tptp) cc_final: 0.3728 (mmpt) REVERT: C 235 ASP cc_start: 0.4366 (m-30) cc_final: 0.3878 (m-30) REVERT: C 281 ARG cc_start: 0.5419 (mpt-90) cc_final: 0.4724 (mtm180) REVERT: C 364 ARG cc_start: 0.5969 (ppt-90) cc_final: 0.5134 (ttt90) REVERT: C 404 SER cc_start: 0.7264 (m) cc_final: 0.6729 (p) REVERT: C 494 GLN cc_start: 0.6296 (mt0) cc_final: 0.5809 (mm-40) REVERT: C 503 MET cc_start: 0.5416 (mpt) cc_final: 0.5128 (mpm) REVERT: C 725 LYS cc_start: 0.5828 (OUTLIER) cc_final: 0.5374 (mtmm) REVERT: D 281 ARG cc_start: 0.5394 (mpt-90) cc_final: 0.4715 (mtm180) REVERT: D 312 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.4332 (mp0) REVERT: D 364 ARG cc_start: 0.5888 (ppt-90) cc_final: 0.5080 (ttt90) REVERT: D 404 SER cc_start: 0.7407 (m) cc_final: 0.6812 (p) REVERT: D 417 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: D 494 GLN cc_start: 0.6258 (mt0) cc_final: 0.5678 (pt0) REVERT: D 503 MET cc_start: 0.5420 (mpt) cc_final: 0.5131 (mpm) REVERT: D 600 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6645 (mt-10) REVERT: D 725 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5379 (mtmm) outliers start: 37 outliers final: 14 residues processed: 226 average time/residue: 1.1714 time to fit residues: 301.9538 Evaluate side-chains 220 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 651 THR 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 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 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 417 GLU Chi-restraints excluded: chain D residue 475 VAL 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: 1.9990 chunk 136 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 311 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.207847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153590 restraints weight = 53910.866| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.92 r_work: 0.3651 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4631 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= 0.164 Angle : 0.522 5.038 25758 Z= 0.276 Chirality : 0.036 0.119 2708 Planarity : 0.004 0.045 3012 Dihedral : 19.598 140.079 4020 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.00 % Favored : 93.81 % Rotamer: Outliers : 1.74 % Allowed : 12.39 % Favored : 85.87 % 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: -0.92 (0.18), residues: 2068 helix: 0.63 (0.14), residues: 1240 sheet: -2.81 (0.51), residues: 76 loop : -2.53 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 421 TYR 0.011 0.002 TYR A 511 PHE 0.017 0.002 PHE A 248 TRP 0.011 0.001 TRP D 698 HIS 0.003 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (19300) covalent geometry : angle 0.52208 / 0.28 (25744) SS BOND : bond 0.00034 / 0.02 ( 3) SS BOND : angle 0.27229 / 0.18 ( 14) hydrogen bonds : bond 0.04028 / 2.64 ( 884) hydrogen bonds : angle 4.36207 / 3.04 ( 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 227 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.4099 (tptp) cc_final: 0.3637 (mmpt) REVERT: A 235 ASP cc_start: 0.4309 (m-30) cc_final: 0.3837 (m-30) REVERT: A 248 PHE cc_start: 0.6297 (p90) cc_final: 0.6028 (p90) REVERT: A 281 ARG cc_start: 0.5316 (mpt-90) cc_final: 0.4626 (mtm180) REVERT: A 312 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.4155 (mp0) REVERT: A 364 ARG cc_start: 0.5947 (ppt-90) cc_final: 0.5091 (ttt90) REVERT: A 404 SER cc_start: 0.7320 (m) cc_final: 0.6769 (p) REVERT: A 494 GLN cc_start: 0.6162 (mt0) cc_final: 0.5676 (mm-40) REVERT: A 503 MET cc_start: 0.5295 (mpt) cc_final: 0.4967 (mpm) REVERT: B 201 LYS cc_start: 0.4133 (tptp) cc_final: 0.3639 (mmpt) REVERT: B 235 ASP cc_start: 0.4299 (m-30) cc_final: 0.3817 (m-30) REVERT: B 281 ARG cc_start: 0.5302 (mpt-90) cc_final: 0.4608 (mtm180) REVERT: B 364 ARG cc_start: 0.5938 (ppt-90) cc_final: 0.5090 (ttt90) REVERT: B 404 SER cc_start: 0.7240 (m) cc_final: 0.6707 (p) REVERT: B 494 GLN cc_start: 0.6164 (mt0) cc_final: 0.5697 (mm-40) REVERT: B 503 MET cc_start: 0.5297 (mpt) cc_final: 0.5002 (mpm) REVERT: C 201 LYS cc_start: 0.4142 (tptp) cc_final: 0.3647 (mmpt) REVERT: C 235 ASP cc_start: 0.4313 (m-30) cc_final: 0.3832 (m-30) REVERT: C 281 ARG cc_start: 0.5335 (mpt-90) cc_final: 0.4650 (mtm180) REVERT: C 364 ARG cc_start: 0.5898 (ppt-90) cc_final: 0.5077 (ttt90) REVERT: C 404 SER cc_start: 0.7241 (m) cc_final: 0.6707 (p) REVERT: C 466 MET cc_start: 0.6309 (mtp) cc_final: 0.5959 (mpp) REVERT: C 494 GLN cc_start: 0.6223 (mt0) cc_final: 0.5755 (mm-40) REVERT: C 503 MET cc_start: 0.5306 (mpt) cc_final: 0.5022 (mpm) REVERT: C 725 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.5174 (mtmm) REVERT: D 235 ASP cc_start: 0.4836 (m-30) cc_final: 0.4396 (m-30) REVERT: D 281 ARG cc_start: 0.5344 (mpt-90) cc_final: 0.4670 (mtm180) REVERT: D 364 ARG cc_start: 0.5780 (ppt-90) cc_final: 0.4974 (ttt90) REVERT: D 404 SER cc_start: 0.7130 (m) cc_final: 0.6549 (p) REVERT: D 466 MET cc_start: 0.6302 (mtp) cc_final: 0.5899 (mpp) REVERT: D 494 GLN cc_start: 0.6194 (mt0) cc_final: 0.5612 (pt0) REVERT: D 503 MET cc_start: 0.5298 (mpt) cc_final: 0.5015 (mpm) REVERT: D 708 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7791 (t0) outliers start: 32 outliers final: 14 residues processed: 218 average time/residue: 1.1996 time to fit residues: 299.4211 Evaluate side-chains 213 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 651 THR 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 678 MET Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL 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 475 VAL Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 708 ASP 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: 2.9990 chunk 198 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 311 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.210205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.157396 restraints weight = 53986.648| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.83 r_work: 0.3693 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19303 Z= 0.108 Angle : 0.482 4.626 25758 Z= 0.257 Chirality : 0.034 0.122 2708 Planarity : 0.004 0.041 3012 Dihedral : 18.925 132.964 4020 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.24 % Favored : 93.57 % Rotamer: Outliers : 0.98 % Allowed : 13.21 % Favored : 85.82 % 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: -0.59 (0.18), residues: 2068 helix: 0.93 (0.15), residues: 1236 sheet: -2.87 (0.50), residues: 76 loop : -2.42 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 421 TYR 0.010 0.001 TYR D 511 PHE 0.015 0.001 PHE A 248 TRP 0.012 0.001 TRP C 698 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (19300) covalent geometry : angle 0.48188 / 0.26 (25744) SS BOND : bond 0.00042 / 0.02 ( 3) SS BOND : angle 0.32777 / 0.21 ( 14) hydrogen bonds : bond 0.03729 / 2.44 ( 884) hydrogen bonds : angle 4.18171 / 2.92 ( 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 220 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.927 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: 0.4189 (tptp) cc_final: 0.3726 (mmpt) REVERT: A 235 ASP cc_start: 0.4418 (m-30) cc_final: 0.3900 (m-30) REVERT: A 248 PHE cc_start: 0.6452 (p90) cc_final: 0.6161 (p90) REVERT: A 281 ARG cc_start: 0.5435 (mpt-90) cc_final: 0.4749 (mtm180) REVERT: A 364 ARG cc_start: 0.5951 (ppt-90) cc_final: 0.5099 (ttt90) REVERT: A 404 SER cc_start: 0.7406 (m) cc_final: 0.6840 (p) REVERT: A 406 GLU cc_start: 0.6825 (pm20) cc_final: 0.6572 (pm20) REVERT: A 494 GLN cc_start: 0.6237 (mt0) cc_final: 0.5757 (mm-40) REVERT: A 503 MET cc_start: 0.5252 (mpt) cc_final: 0.4936 (mpm) REVERT: B 201 LYS cc_start: 0.4215 (tptp) cc_final: 0.3732 (mmpt) REVERT: B 235 ASP cc_start: 0.4402 (m-30) cc_final: 0.3891 (m-30) REVERT: B 281 ARG cc_start: 0.5419 (mpt-90) cc_final: 0.4720 (mtm180) REVERT: B 364 ARG cc_start: 0.5941 (ppt-90) cc_final: 0.5099 (ttt90) REVERT: B 404 SER cc_start: 0.7309 (m) cc_final: 0.6814 (p) REVERT: B 494 GLN cc_start: 0.6263 (mt0) cc_final: 0.5780 (mm-40) REVERT: B 503 MET cc_start: 0.5309 (mpt) cc_final: 0.5014 (mpm) REVERT: C 201 LYS cc_start: 0.4211 (tptp) cc_final: 0.3737 (mmpt) REVERT: C 235 ASP cc_start: 0.4418 (m-30) cc_final: 0.3903 (m-30) REVERT: C 281 ARG cc_start: 0.5414 (mpt-90) cc_final: 0.4731 (mtm180) REVERT: C 364 ARG cc_start: 0.5949 (ppt-90) cc_final: 0.5107 (ttt90) REVERT: C 466 MET cc_start: 0.6392 (mtp) cc_final: 0.6074 (mpp) REVERT: C 494 GLN cc_start: 0.6284 (mt0) cc_final: 0.5793 (mm-40) REVERT: C 503 MET cc_start: 0.5304 (mpt) cc_final: 0.5033 (mpm) REVERT: C 725 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.5266 (mtmm) REVERT: D 235 ASP cc_start: 0.4886 (m-30) cc_final: 0.4418 (m-30) REVERT: D 281 ARG cc_start: 0.5417 (mpt-90) cc_final: 0.4787 (mtm180) REVERT: D 364 ARG cc_start: 0.5822 (ppt-90) cc_final: 0.5033 (ttt90) REVERT: D 404 SER cc_start: 0.7333 (m) cc_final: 0.6794 (p) REVERT: D 421 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7727 (mtt-85) REVERT: D 466 MET cc_start: 0.6384 (mtp) cc_final: 0.6019 (mpp) REVERT: D 494 GLN cc_start: 0.6263 (mt0) cc_final: 0.5679 (pt0) REVERT: D 503 MET cc_start: 0.5343 (mpt) cc_final: 0.5045 (mpm) outliers start: 18 outliers final: 13 residues processed: 214 average time/residue: 1.2133 time to fit residues: 297.3436 Evaluate side-chains 206 residues out of total 1840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 651 THR 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 C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL 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 475 VAL Chi-restraints excluded: chain D residue 486 VAL 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: 6.9990 chunk 96 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 311 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.207043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153070 restraints weight = 53912.670| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.86 r_work: 0.3646 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 19303 Z= 0.205 Angle : 0.544 5.298 25758 Z= 0.286 Chirality : 0.037 0.114 2708 Planarity : 0.004 0.045 3012 Dihedral : 19.292 138.729 4020 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.58 % Favored : 93.23 % Rotamer: Outliers : 1.14 % Allowed : 13.64 % 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: -0.80 (0.18), residues: 2068 helix: 0.71 (0.14), residues: 1240 sheet: -2.84 (0.51), residues: 76 loop : -2.42 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 421 TYR 0.012 0.002 TYR A 442 PHE 0.017 0.002 PHE B 248 TRP 0.010 0.001 TRP C 698 HIS 0.004 0.001 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (19300) covalent geometry : angle 0.54373 / 0.29 (25744) SS BOND : bond 0.00057 / 0.03 ( 3) SS BOND : angle 0.24026 / 0.15 ( 14) hydrogen bonds : bond 0.04082 / 2.68 ( 884) hydrogen bonds : angle 4.37733 / 3.06 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13934.53 seconds wall clock time: 236 minutes 10.04 seconds (14170.04 seconds total)