Starting phenix.real_space_refine on Sun Dec 29 23:21:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6j_41069/12_2024/8t6j_41069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6j_41069/12_2024/8t6j_41069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6j_41069/12_2024/8t6j_41069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6j_41069/12_2024/8t6j_41069.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6j_41069/12_2024/8t6j_41069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6j_41069/12_2024/8t6j_41069.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 7473 2.51 5 N 1940 2.21 5 O 2127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5803 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 317 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 150 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5793 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 156 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'YKU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.63, per 1000 atoms: 0.65 Number of scatterers: 11652 At special positions: 0 Unit cell: (123.555, 82.6537, 188.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 2127 8.00 N 1940 7.00 C 7473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 51.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.670A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.500A pdb=" N ALA B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.896A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.889A pdb=" N SER B 180 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing helix chain 'B' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.975A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.666A pdb=" N ARG B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.378A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.807A pdb=" N ASN B 349 " --> pdb=" O PRO B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.923A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 removed outlier: 3.929A pdb=" N LEU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.833A pdb=" N VAL B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.694A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 630 Processing helix chain 'B' and resid 631 through 637 removed outlier: 3.723A pdb=" N ALA B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 673 removed outlier: 4.223A pdb=" N CYS B 644 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.272A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 removed outlier: 3.535A pdb=" N GLN B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 761 Proline residue: B 743 - end of helix removed outlier: 4.097A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 750 " --> pdb=" O TYR B 746 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 793 removed outlier: 3.594A pdb=" N ASN B 769 " --> pdb=" O PRO B 765 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 797 through 816 removed outlier: 3.931A pdb=" N VAL B 806 " --> pdb=" O MET B 802 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 807 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 827 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.742A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.685A pdb=" N ILE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.883A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.893A pdb=" N SER A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.588A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.729A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.655A pdb=" N ARG A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.558A pdb=" N VAL A 313 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 4.388A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.790A pdb=" N ASN A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.930A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 4.072A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 3.895A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.859A pdb=" N VAL A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.697A pdb=" N ILE A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 631 through 637 removed outlier: 3.662A pdb=" N ALA A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 673 removed outlier: 4.241A pdb=" N CYS A 644 " --> pdb=" O LYS A 640 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 4.298A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 715 removed outlier: 3.523A pdb=" N GLN A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 761 Proline residue: A 743 - end of helix removed outlier: 4.044A pdb=" N LEU A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 750 " --> pdb=" O TYR A 746 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 793 removed outlier: 3.582A pdb=" N ASN A 769 " --> pdb=" O PRO A 765 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 797 through 816 removed outlier: 3.927A pdb=" N VAL A 806 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 827 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.262A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 213 through 216 removed outlier: 7.768A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.291A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 468 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 485 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AA5, first strand: chain 'B' and resid 471 through 475 removed outlier: 3.570A pdb=" N LYS B 472 " --> pdb=" O ASP B 480 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 480 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AA7, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AA8, first strand: chain 'B' and resid 556 through 558 Processing sheet with id=AA9, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.609A pdb=" N ASP B 722 " --> pdb=" O TYR B 730 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.258A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 213 through 216 removed outlier: 7.759A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 472 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 480 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 274 through 276 removed outlier: 3.714A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 326 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 468 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AB6, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AB7, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB8, first strand: chain 'A' and resid 556 through 558 Processing sheet with id=AB9, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.606A pdb=" N ASP A 722 " --> pdb=" O TYR A 730 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1527 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: 3.87 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1887 1.27 - 1.41: 3001 1.41 - 1.55: 6857 1.55 - 1.68: 11 1.68 - 1.82: 162 Bond restraints: 11918 Sorted by residual: bond pdb=" C19 YKU B 901 " pdb=" C21 YKU B 901 " ideal model delta sigma weight residual 1.429 1.527 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C19 YKU A 901 " pdb=" C21 YKU A 901 " ideal model delta sigma weight residual 1.429 1.526 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C13 YKU A 901 " pdb=" N12 YKU A 901 " ideal model delta sigma weight residual 1.359 1.454 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C13 YKU B 901 " pdb=" N12 YKU B 901 " ideal model delta sigma weight residual 1.359 1.453 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C04 YKU B 901 " pdb=" C07 YKU B 901 " ideal model delta sigma weight residual 1.465 1.528 -0.063 2.00e-02 2.50e+03 9.87e+00 ... (remaining 11913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 15964 2.00 - 4.00: 222 4.00 - 6.00: 19 6.00 - 7.99: 3 7.99 - 9.99: 2 Bond angle restraints: 16210 Sorted by residual: angle pdb=" CB LYS B 51 " pdb=" CG LYS B 51 " pdb=" CD LYS B 51 " ideal model delta sigma weight residual 111.30 117.90 -6.60 2.30e+00 1.89e-01 8.23e+00 angle pdb=" CA LEU B 295 " pdb=" CB LEU B 295 " pdb=" CG LEU B 295 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.15e+00 angle pdb=" CB ARG B 114 " pdb=" CG ARG B 114 " pdb=" CD ARG B 114 " ideal model delta sigma weight residual 111.30 104.76 6.54 2.30e+00 1.89e-01 8.09e+00 angle pdb=" CB MET A 474 " pdb=" CG MET A 474 " pdb=" SD MET A 474 " ideal model delta sigma weight residual 112.70 121.19 -8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" CB LYS A 51 " pdb=" CG LYS A 51 " pdb=" CD LYS A 51 " ideal model delta sigma weight residual 111.30 117.26 -5.96 2.30e+00 1.89e-01 6.71e+00 ... (remaining 16205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6401 17.97 - 35.94: 567 35.94 - 53.91: 105 53.91 - 71.88: 20 71.88 - 89.85: 3 Dihedral angle restraints: 7096 sinusoidal: 2638 harmonic: 4458 Sorted by residual: dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 135.61 -42.61 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual -86.00 -44.07 -41.93 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual 93.00 134.68 -41.68 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 7093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1000 0.027 - 0.054: 531 0.054 - 0.082: 203 0.082 - 0.109: 84 0.109 - 0.136: 34 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA ILE B 568 " pdb=" N ILE B 568 " pdb=" C ILE B 568 " pdb=" CB ILE B 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 568 " pdb=" N ILE A 568 " pdb=" C ILE A 568 " pdb=" CB ILE A 568 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL B 217 " pdb=" N VAL B 217 " pdb=" C VAL B 217 " pdb=" CB VAL B 217 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1849 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 789 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 790 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 790 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 790 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 789 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO B 790 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 790 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 790 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 764 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 765 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 765 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 765 " 0.017 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 791 2.74 - 3.28: 11449 3.28 - 3.82: 18007 3.82 - 4.36: 19638 4.36 - 4.90: 36335 Nonbonded interactions: 86220 Sorted by model distance: nonbonded pdb=" OG SER B 152 " pdb=" OG SER B 176 " model vdw 2.196 3.040 nonbonded pdb=" OG SER A 152 " pdb=" OG SER A 176 " model vdw 2.221 3.040 nonbonded pdb=" O ARG B 435 " pdb=" NH1 ARG B 435 " model vdw 2.228 3.120 nonbonded pdb=" O ARG A 435 " pdb=" NH1 ARG A 435 " model vdw 2.229 3.120 nonbonded pdb=" O GLY A 253 " pdb=" OG SER A 256 " model vdw 2.274 3.040 ... (remaining 86215 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 26 through 515 or (resid 516 through 517 and (name N or na \ me CA or name C or name O or name CB )) or resid 518 through 827 or resid 901)) selection = (chain 'B' and (resid 26 through 378 or (resid 379 and (name N or name CA or nam \ e C or name O or name CB )) or resid 380 through 552 or (resid 553 and (name N o \ r name CA or name C or name O or name CB )) or resid 554 through 559 or (resid 5 \ 60 through 561 and (name N or name CA or name C or name O or name CB )) or resid \ 562 through 827 or resid 901)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.860 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.003 0.098 11918 Z= 0.238 Angle : 0.563 9.992 16210 Z= 0.289 Chirality : 0.041 0.136 1852 Planarity : 0.003 0.036 2058 Dihedral : 13.807 89.854 4184 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1522 helix: 1.52 (0.21), residues: 648 sheet: -1.22 (0.42), residues: 172 loop : -1.14 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS B 30 PHE 0.013 0.001 PHE B 544 TYR 0.010 0.001 TYR B 223 ARG 0.013 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: B 657 MET cc_start: 0.6699 (ptm) cc_final: 0.6420 (ptt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2161 time to fit residues: 50.1215 Evaluate side-chains 124 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 747 ASN A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 11918 Z= 0.535 Angle : 0.734 6.763 16210 Z= 0.386 Chirality : 0.049 0.165 1852 Planarity : 0.005 0.071 2058 Dihedral : 5.354 34.200 1662 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.73 % Allowed : 11.40 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1522 helix: 1.09 (0.21), residues: 662 sheet: -1.51 (0.40), residues: 182 loop : -1.44 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 487 HIS 0.006 0.002 HIS B 30 PHE 0.020 0.002 PHE A 712 TYR 0.020 0.002 TYR B 340 ARG 0.009 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLU cc_start: 0.6333 (mt-10) cc_final: 0.6107 (mt-10) outliers start: 21 outliers final: 12 residues processed: 142 average time/residue: 0.2316 time to fit residues: 48.8909 Evaluate side-chains 136 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 GLN A 571 GLN A 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11918 Z= 0.195 Angle : 0.529 5.761 16210 Z= 0.278 Chirality : 0.042 0.148 1852 Planarity : 0.004 0.032 2058 Dihedral : 4.726 29.133 1662 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.48 % Allowed : 12.47 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1522 helix: 1.51 (0.21), residues: 654 sheet: -1.45 (0.40), residues: 184 loop : -1.22 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.003 0.001 HIS A 218 PHE 0.019 0.001 PHE A 712 TYR 0.013 0.001 TYR A 629 ARG 0.007 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 MET cc_start: 0.8016 (ttp) cc_final: 0.7786 (ttp) REVERT: A 497 ASP cc_start: 0.7224 (t0) cc_final: 0.6998 (t0) outliers start: 30 outliers final: 16 residues processed: 147 average time/residue: 0.2143 time to fit residues: 47.8478 Evaluate side-chains 141 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 571 GLN A 571 GLN A 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11918 Z= 0.237 Angle : 0.537 6.048 16210 Z= 0.280 Chirality : 0.042 0.148 1852 Planarity : 0.004 0.032 2058 Dihedral : 4.595 25.689 1662 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.39 % Allowed : 15.11 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1522 helix: 1.57 (0.21), residues: 654 sheet: -1.49 (0.39), residues: 184 loop : -1.18 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.004 0.001 HIS A 218 PHE 0.025 0.001 PHE A 712 TYR 0.014 0.001 TYR A 629 ARG 0.005 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 0.2219 time to fit residues: 49.5195 Evaluate side-chains 148 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11918 Z= 0.320 Angle : 0.575 6.326 16210 Z= 0.302 Chirality : 0.044 0.151 1852 Planarity : 0.004 0.042 2058 Dihedral : 4.687 23.224 1662 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.56 % Allowed : 16.35 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1522 helix: 1.49 (0.21), residues: 654 sheet: -1.59 (0.39), residues: 184 loop : -1.25 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 487 HIS 0.005 0.001 HIS B 218 PHE 0.026 0.002 PHE A 712 TYR 0.019 0.001 TYR A 340 ARG 0.005 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8070 (mmp) cc_final: 0.7864 (mmm) REVERT: B 688 MET cc_start: 0.6911 (mmt) cc_final: 0.6538 (mmt) REVERT: A 79 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7669 (tt) outliers start: 31 outliers final: 26 residues processed: 155 average time/residue: 0.2187 time to fit residues: 50.7552 Evaluate side-chains 156 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11918 Z= 0.308 Angle : 0.585 8.657 16210 Z= 0.304 Chirality : 0.044 0.154 1852 Planarity : 0.004 0.041 2058 Dihedral : 4.687 21.583 1662 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.63 % Allowed : 16.52 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1522 helix: 1.44 (0.21), residues: 654 sheet: -1.64 (0.38), residues: 184 loop : -1.26 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 487 HIS 0.005 0.001 HIS A 218 PHE 0.028 0.002 PHE A 712 TYR 0.016 0.001 TYR A 340 ARG 0.006 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8054 (mmp) cc_final: 0.7807 (mmp) REVERT: B 601 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.6600 (t80) REVERT: B 688 MET cc_start: 0.6926 (mmt) cc_final: 0.6553 (mmt) REVERT: A 79 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7687 (tt) REVERT: A 601 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6599 (t80) outliers start: 44 outliers final: 35 residues processed: 170 average time/residue: 0.2151 time to fit residues: 54.9411 Evaluate side-chains 166 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11918 Z= 0.168 Angle : 0.528 7.597 16210 Z= 0.271 Chirality : 0.041 0.154 1852 Planarity : 0.003 0.033 2058 Dihedral : 4.375 20.290 1662 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.22 % Allowed : 17.42 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1522 helix: 1.59 (0.21), residues: 660 sheet: -1.46 (0.39), residues: 184 loop : -1.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 575 HIS 0.003 0.001 HIS A 30 PHE 0.026 0.001 PHE A 712 TYR 0.016 0.001 TYR A 629 ARG 0.007 0.000 ARG B 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8074 (mmp) cc_final: 0.7856 (mmp) REVERT: B 601 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6521 (t80) REVERT: B 688 MET cc_start: 0.6822 (mmt) cc_final: 0.6465 (mmt) REVERT: A 497 ASP cc_start: 0.7290 (t0) cc_final: 0.7064 (t0) REVERT: A 588 CYS cc_start: 0.6500 (m) cc_final: 0.6289 (m) REVERT: A 601 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6552 (t80) outliers start: 39 outliers final: 29 residues processed: 168 average time/residue: 0.2270 time to fit residues: 56.4603 Evaluate side-chains 164 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 808 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11918 Z= 0.217 Angle : 0.539 7.553 16210 Z= 0.277 Chirality : 0.042 0.152 1852 Planarity : 0.004 0.039 2058 Dihedral : 4.348 18.954 1662 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.30 % Allowed : 17.59 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1522 helix: 1.57 (0.20), residues: 660 sheet: -1.46 (0.39), residues: 184 loop : -1.07 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 575 HIS 0.004 0.001 HIS B 218 PHE 0.024 0.001 PHE A 712 TYR 0.016 0.001 TYR A 629 ARG 0.010 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 474 MET cc_start: 0.8070 (mmp) cc_final: 0.7827 (mmp) REVERT: B 601 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6552 (t80) REVERT: B 688 MET cc_start: 0.6839 (mmt) cc_final: 0.6478 (mmt) REVERT: A 79 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7764 (tt) REVERT: A 497 ASP cc_start: 0.7307 (t0) cc_final: 0.7065 (t0) REVERT: A 588 CYS cc_start: 0.6504 (m) cc_final: 0.6299 (m) REVERT: A 601 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6567 (t80) outliers start: 40 outliers final: 33 residues processed: 163 average time/residue: 0.2223 time to fit residues: 54.3068 Evaluate side-chains 165 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 777 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 41 optimal weight: 0.0170 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11918 Z= 0.151 Angle : 0.521 8.402 16210 Z= 0.264 Chirality : 0.041 0.151 1852 Planarity : 0.003 0.036 2058 Dihedral : 4.175 18.198 1662 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.73 % Allowed : 18.17 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1522 helix: 1.69 (0.20), residues: 660 sheet: -1.01 (0.42), residues: 160 loop : -1.07 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 575 HIS 0.002 0.001 HIS A 30 PHE 0.024 0.001 PHE A 712 TYR 0.015 0.001 TYR A 629 ARG 0.008 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7665 (tt) REVERT: B 474 MET cc_start: 0.8101 (mmp) cc_final: 0.7863 (mmp) REVERT: B 601 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6559 (t80) REVERT: B 688 MET cc_start: 0.6801 (mmt) cc_final: 0.6442 (mmt) REVERT: B 788 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6554 (t80) REVERT: A 79 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7767 (tt) REVERT: A 474 MET cc_start: 0.8363 (mmm) cc_final: 0.8148 (mmp) REVERT: A 588 CYS cc_start: 0.6496 (m) cc_final: 0.6296 (m) REVERT: A 601 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6499 (t80) outliers start: 33 outliers final: 25 residues processed: 163 average time/residue: 0.2111 time to fit residues: 51.7570 Evaluate side-chains 158 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 788 PHE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11918 Z= 0.190 Angle : 0.555 13.943 16210 Z= 0.275 Chirality : 0.042 0.150 1852 Planarity : 0.004 0.050 2058 Dihedral : 4.154 20.899 1662 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.73 % Allowed : 18.50 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1522 helix: 1.67 (0.20), residues: 660 sheet: -1.32 (0.39), residues: 184 loop : -1.02 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 575 HIS 0.003 0.001 HIS B 30 PHE 0.024 0.001 PHE A 712 TYR 0.015 0.001 TYR A 629 ARG 0.007 0.000 ARG B 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7643 (tt) REVERT: B 474 MET cc_start: 0.8112 (mmp) cc_final: 0.7870 (mmp) REVERT: B 601 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6519 (t80) REVERT: B 625 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7965 (mt) REVERT: B 688 MET cc_start: 0.6786 (mmt) cc_final: 0.6439 (mmt) REVERT: A 79 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7784 (tt) REVERT: A 588 CYS cc_start: 0.6499 (m) cc_final: 0.6275 (m) REVERT: A 601 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6498 (t80) outliers start: 33 outliers final: 27 residues processed: 153 average time/residue: 0.2084 time to fit residues: 49.0592 Evaluate side-chains 158 residues out of total 1334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 629 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 747 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.143514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118321 restraints weight = 21910.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117357 restraints weight = 16442.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118036 restraints weight = 18589.791| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 11918 Z= 0.192 Angle : 0.813 59.200 16210 Z= 0.473 Chirality : 0.042 0.359 1852 Planarity : 0.004 0.066 2058 Dihedral : 4.185 20.999 1662 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.97 % Allowed : 18.25 % Favored : 78.78 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1522 helix: 1.64 (0.20), residues: 660 sheet: -1.32 (0.39), residues: 184 loop : -1.02 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 575 HIS 0.003 0.001 HIS A 218 PHE 0.023 0.001 PHE A 712 TYR 0.017 0.001 TYR A 746 ARG 0.007 0.000 ARG B 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.99 seconds wall clock time: 42 minutes 30.43 seconds (2550.43 seconds total)