Starting phenix.real_space_refine on Sun Jan 19 17:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rtb_19485/01_2025/8rtb_19485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rtb_19485/01_2025/8rtb_19485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rtb_19485/01_2025/8rtb_19485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rtb_19485/01_2025/8rtb_19485.map" model { file = "/net/cci-nas-00/data/ceres_data/8rtb_19485/01_2025/8rtb_19485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rtb_19485/01_2025/8rtb_19485.cif" } resolution = 3.83 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= 0.007 sd= 0.029 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 57 5.16 5 C 9069 2.51 5 N 2413 2.21 5 O 2593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14132 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 835 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 5992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5992 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 36, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5284 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 630} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 367 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 49} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 450 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "F" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 279 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 240 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 350 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 335 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 11.60, per 1000 atoms: 0.82 Number of scatterers: 14132 At special positions: 0 Unit cell: (134.442, 89.628, 158.983, 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 57 16.00 O 2593 8.00 N 2413 7.00 C 9069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 19 sheets defined 52.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'C' and resid 28 through 45 Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.019A pdb=" N TRP C 50 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 51 " --> pdb=" O TRP C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.950A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.788A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 4.071A pdb=" N TRP C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.791A pdb=" N SER A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.576A pdb=" N PHE A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 132 through 140 removed outlier: 3.822A pdb=" N PHE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.934A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.834A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.946A pdb=" N TYR A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 removed outlier: 4.300A pdb=" N VAL A 262 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 266 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 297 Processing helix chain 'A' and resid 305 through 318 removed outlier: 4.066A pdb=" N ILE A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.550A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 469 through 472 Processing helix chain 'A' and resid 484 through 491 Processing helix chain 'A' and resid 507 through 511 removed outlier: 4.527A pdb=" N GLN A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.534A pdb=" N LEU A 623 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP A 624 " --> pdb=" O GLU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 642 removed outlier: 3.607A pdb=" N SER A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 689 through 695 removed outlier: 3.519A pdb=" N ALA A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.832A pdb=" N LYS A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 removed outlier: 3.635A pdb=" N TYR A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 777 through 785 removed outlier: 4.305A pdb=" N VAL A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 801 removed outlier: 3.782A pdb=" N SER A 796 " --> pdb=" O GLU A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 Proline residue: A 810 - end of helix Processing helix chain 'B' and resid 53 through 71 removed outlier: 3.926A pdb=" N VAL B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 71 " --> pdb=" O THR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 148 through 171 Processing helix chain 'B' and resid 191 through 202 removed outlier: 4.061A pdb=" N PHE B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 196 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.353A pdb=" N TYR B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 280 through 297 Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.858A pdb=" N ASN B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 469 through 472 Processing helix chain 'B' and resid 484 through 491 Processing helix chain 'B' and resid 628 through 643 removed outlier: 3.584A pdb=" N MET B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 677 removed outlier: 4.195A pdb=" N ASP B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 695 removed outlier: 3.802A pdb=" N ALA B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.920A pdb=" N LYS B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 725 removed outlier: 3.630A pdb=" N TYR B 722 " --> pdb=" O ASP B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 739 removed outlier: 3.607A pdb=" N LEU B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 785 Processing helix chain 'B' and resid 787 through 802 Processing helix chain 'B' and resid 804 through 821 removed outlier: 4.283A pdb=" N TRP B 808 " --> pdb=" O ASP B 804 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) Proline residue: B 810 - end of helix Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 27 through 62 removed outlier: 4.357A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 60 removed outlier: 3.644A pdb=" N TYR D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 61 Processing helix chain 'G' and resid 23 through 61 Processing helix chain 'H' and resid 43 through 69 Processing helix chain 'J' and resid 31 through 49 Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 60 through 82 removed outlier: 4.515A pdb=" N CYS J 67 " --> pdb=" O PHE J 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.587A pdb=" N ARG A 222 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.754A pdb=" N ILE A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 127 removed outlier: 3.534A pdb=" N SER A 40 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 38 " --> pdb=" O TYR A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA8, first strand: chain 'A' and resid 248 through 250 removed outlier: 3.523A pdb=" N ARG A 249 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU A 357 " --> pdb=" O ARG A 249 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.555A pdb=" N HIS A 326 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 415 through 417 Processing sheet with id=AB2, first strand: chain 'A' and resid 495 through 496 removed outlier: 5.897A pdb=" N ILE A 475 " --> pdb=" O TYR A 615 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 617 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA A 477 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 474 " --> pdb=" O MET A 650 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 652 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A 476 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL A 684 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR A 651 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 447 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N MET A 448 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A 709 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 removed outlier: 3.648A pdb=" N VAL A 768 " --> pdb=" O GLU A 771 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.660A pdb=" N HIS B 24 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 177 through 178 removed outlier: 3.693A pdb=" N TYR B 38 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 121 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 331 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB7, first strand: chain 'B' and resid 277 through 278 Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.878A pdb=" N THR B 415 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 684 through 687 removed outlier: 6.002A pdb=" N THR B 447 " --> pdb=" O PHE B 685 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR B 687 " --> pdb=" O THR B 447 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 449 " --> pdb=" O THR B 687 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET B 448 " --> pdb=" O ILE B 710 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 615 through 618 removed outlier: 6.269A pdb=" N ALA B 477 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 476 " --> pdb=" O VAL B 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 703 hydrogen bonds defined for protein. 2004 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: 4.84 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4603 1.34 - 1.46: 2939 1.46 - 1.58: 6825 1.58 - 1.70: 1 1.70 - 1.81: 99 Bond restraints: 14467 Sorted by residual: bond pdb=" CB PRO A 497 " pdb=" CG PRO A 497 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" N PRO A 497 " pdb=" CA PRO A 497 " ideal model delta sigma weight residual 1.481 1.444 0.038 1.85e-02 2.92e+03 4.12e+00 bond pdb=" CD LYS H 65 " pdb=" CE LYS H 65 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CG GLU A 154 " pdb=" CD GLU A 154 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.86e+00 bond pdb=" CG1 ILE A 82 " pdb=" CD1 ILE A 82 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.81e+00 ... (remaining 14462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 19294 2.59 - 5.18: 286 5.18 - 7.77: 28 7.77 - 10.36: 2 10.36 - 12.95: 1 Bond angle restraints: 19611 Sorted by residual: angle pdb=" CA PRO A 497 " pdb=" N PRO A 497 " pdb=" CD PRO A 497 " ideal model delta sigma weight residual 112.00 99.05 12.95 1.40e+00 5.10e-01 8.56e+01 angle pdb=" C GLU F 31 " pdb=" N PHE F 32 " pdb=" CA PHE F 32 " ideal model delta sigma weight residual 120.68 113.22 7.46 1.70e+00 3.46e-01 1.93e+01 angle pdb=" CA TYR H 64 " pdb=" CB TYR H 64 " pdb=" CG TYR H 64 " ideal model delta sigma weight residual 113.90 121.50 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 112.12 108.70 3.42 8.40e-01 1.42e+00 1.65e+01 angle pdb=" N VAL A 26 " pdb=" CA VAL A 26 " pdb=" C VAL A 26 " ideal model delta sigma weight residual 111.81 108.37 3.44 8.60e-01 1.35e+00 1.60e+01 ... (remaining 19606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7703 17.87 - 35.75: 727 35.75 - 53.62: 106 53.62 - 71.49: 18 71.49 - 89.36: 14 Dihedral angle restraints: 8568 sinusoidal: 3357 harmonic: 5211 Sorted by residual: dihedral pdb=" CA GLN A 305 " pdb=" C GLN A 305 " pdb=" N ILE A 306 " pdb=" CA ILE A 306 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR A 664 " pdb=" C TYR A 664 " pdb=" N PHE A 665 " pdb=" CA PHE A 665 " ideal model delta harmonic sigma weight residual 180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN B 314 " pdb=" C ASN B 314 " pdb=" N GLN B 315 " pdb=" CA GLN B 315 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 8565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1704 0.054 - 0.108: 381 0.108 - 0.162: 56 0.162 - 0.215: 5 0.215 - 0.269: 2 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CB ILE A 82 " pdb=" CA ILE A 82 " pdb=" CG1 ILE A 82 " pdb=" CG2 ILE A 82 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 416 " pdb=" CA ILE A 416 " pdb=" CG1 ILE A 416 " pdb=" CG2 ILE A 416 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR D 18 " pdb=" N TYR D 18 " pdb=" C TYR D 18 " pdb=" CB TYR D 18 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2145 not shown) Planarity restraints: 2531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 20 " -0.073 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 21 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 496 " -0.080 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A 497 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 33 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO J 34 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO J 34 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO J 34 " 0.061 5.00e-02 4.00e+02 ... (remaining 2528 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 249 2.68 - 3.24: 14144 3.24 - 3.79: 21172 3.79 - 4.35: 27517 4.35 - 4.90: 46506 Nonbonded interactions: 109588 Sorted by model distance: nonbonded pdb=" NH2 ARG A 211 " pdb=" OD1 ASP B 252 " model vdw 2.126 3.120 nonbonded pdb=" NH1 ARG A 222 " pdb=" OD2 ASP B 362 " model vdw 2.132 3.120 nonbonded pdb=" O LEU A 609 " pdb=" OH TYR A 615 " model vdw 2.167 3.040 nonbonded pdb=" NZ LYS A 106 " pdb=" O ASP A 776 " model vdw 2.210 3.120 nonbonded pdb=" OG1 THR A 640 " pdb=" OH TYR A 651 " model vdw 2.213 3.040 ... (remaining 109583 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 15 through 130 or (resid 147 through 150 and (name N or na \ me CA or name C or name O or name CB )) or resid 151 through 235 or resid 240 th \ rough 431 or (resid 432 through 433 and (name N or name CA or name C or name O o \ r name CB )) or resid 442 through 498 or resid 607 through 662 or (resid 663 and \ (name N or name CA or name C or name O or name CB )) or resid 664 through 688 o \ r (resid 689 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 90 through 691 or (resid 692 through 693 and (name N or name CA or name C or nam \ e O or name CB )) or resid 694 through 764 or (resid 765 and (name N or name CA \ or name C or name O or name CB )) or (resid 776 and (name N or name CA or name C \ or name O or name CB )) or resid 777 or (resid 778 and (name N or name CA or na \ me C or name O or name CB )) or resid 779 through 816 or (resid 817 through 818 \ and (name N or name CA or name C or name O or name CB )) or resid 819 or (resid \ 820 and (name N or name CA or name C or name O or name CB )) or resid 821)) selection = (chain 'B' and (resid 15 through 254 or (resid 255 and (name N or name CA or nam \ e C or name O or name CB )) or resid 256 through 607 or (resid 608 and (name N o \ r name CA or name C or name O or name CB )) or resid 609 through 720 or (resid 7 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 722 through \ 731 or (resid 732 and (name N or name CA or name C or name O or name CB )) or r \ esid 733 through 821)) } ncs_group { reference = (chain 'D' and ((resid 13 and (name N or name CA or name C or name O or name CB \ )) or resid 14 or (resid 15 and (name N or name CA or name C or name O or name C \ B )) or resid 16 through 33 or (resid 34 and (name N or name CA or name C or nam \ e O or name CB )) or resid 35 through 40 or (resid 41 and (name N or name CA or \ name C or name O or name CB )) or resid 42 through 47 or (resid 48 and (name N o \ r name CA or name C or name O or name CB )) or resid 49 through 62)) selection = chain 'E' } ncs_group { reference = (chain 'F' and ((resid 22 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 or (resid 31 and (name N or name CA or name C or name \ O or name CB )) or resid 32 or (resid 33 through 39 and (name N or name CA or na \ me C or name O or name CB )) or resid 40 or (resid 41 through 45 and (name N or \ name CA or name C or name O or name CB )) or resid 46 through 55 or (resid 56 an \ d (name N or name CA or name C or name O or name CB )) or resid 57 through 61 or \ (resid 62 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 22 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 57 or (resid 58 through 59 and (na \ me N or name CA or name C or name O or name CB )) or resid 60 through 62)) } 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: 8.780 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 36.660 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.006 0.163 14467 Z= 0.373 Angle : 0.789 12.955 19611 Z= 0.455 Chirality : 0.046 0.269 2148 Planarity : 0.007 0.113 2531 Dihedral : 14.187 89.364 5208 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.20), residues: 1774 helix: 0.50 (0.18), residues: 824 sheet: -2.74 (0.32), residues: 265 loop : -1.83 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 50 HIS 0.008 0.001 HIS A 326 PHE 0.034 0.002 PHE A 520 TYR 0.043 0.002 TYR H 64 ARG 0.010 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.529 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.6817 (tp) cc_final: 0.6581 (tp) REVERT: A 305 GLN cc_start: 0.6633 (tp40) cc_final: 0.6410 (tp-100) REVERT: A 322 VAL cc_start: 0.7554 (t) cc_final: 0.7287 (t) REVERT: B 260 LEU cc_start: 0.7453 (pt) cc_final: 0.7142 (pp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2854 time to fit residues: 138.4592 Evaluate side-chains 222 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 0.0170 chunk 160 optimal weight: 3.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 408 ASN B 428 ASN B 673 GLN B 705 GLN B 750 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.050172 restraints weight = 76298.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051765 restraints weight = 43074.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.052873 restraints weight = 29297.609| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14467 Z= 0.238 Angle : 0.709 11.376 19611 Z= 0.361 Chirality : 0.043 0.226 2148 Planarity : 0.006 0.083 2531 Dihedral : 5.091 25.302 1953 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.99 % Allowed : 10.63 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.20), residues: 1774 helix: 0.85 (0.18), residues: 857 sheet: -2.44 (0.32), residues: 256 loop : -1.72 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 50 HIS 0.009 0.001 HIS B 274 PHE 0.025 0.002 PHE B 391 TYR 0.032 0.002 TYR D 18 ARG 0.008 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 1.907 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9126 (mm) REVERT: A 216 ASP cc_start: 0.9203 (m-30) cc_final: 0.8898 (p0) REVERT: A 245 MET cc_start: 0.9001 (ttm) cc_final: 0.8619 (ttm) REVERT: A 323 MET cc_start: 0.8616 (mmm) cc_final: 0.8101 (mmm) REVERT: A 365 LEU cc_start: 0.8642 (tp) cc_final: 0.8417 (tp) REVERT: A 465 LEU cc_start: 0.9676 (mt) cc_final: 0.9473 (pp) REVERT: A 527 LYS cc_start: 0.9687 (tppt) cc_final: 0.9475 (ttpt) REVERT: A 634 MET cc_start: 0.9568 (ttt) cc_final: 0.9211 (ttt) REVERT: A 650 MET cc_start: 0.9532 (mtp) cc_final: 0.9197 (mmm) REVERT: A 771 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9098 (mp0) REVERT: B 62 ARG cc_start: 0.9504 (mtt180) cc_final: 0.9256 (mtm-85) REVERT: B 80 THR cc_start: 0.9589 (m) cc_final: 0.9346 (p) REVERT: B 199 LEU cc_start: 0.9770 (tp) cc_final: 0.9527 (tp) REVERT: B 260 LEU cc_start: 0.9250 (pt) cc_final: 0.9004 (pp) REVERT: B 401 MET cc_start: 0.8663 (tmm) cc_final: 0.8428 (tmm) REVERT: B 643 MET cc_start: 0.8822 (tmm) cc_final: 0.8380 (ppp) REVERT: B 650 MET cc_start: 0.9278 (ttm) cc_final: 0.9034 (ttm) REVERT: B 759 MET cc_start: 0.8890 (tmm) cc_final: 0.8576 (tmm) REVERT: E 18 TYR cc_start: 0.8727 (m-10) cc_final: 0.8064 (m-10) REVERT: E 20 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9147 (mm-30) REVERT: D 19 GLU cc_start: 0.9576 (tm-30) cc_final: 0.9312 (pp20) REVERT: D 20 GLU cc_start: 0.9043 (pp20) cc_final: 0.8802 (pp20) REVERT: D 49 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8153 (t80) REVERT: J 40 LEU cc_start: 0.9612 (tp) cc_final: 0.9317 (tp) REVERT: J 63 PHE cc_start: 0.8747 (m-80) cc_final: 0.7854 (m-80) outliers start: 29 outliers final: 11 residues processed: 270 average time/residue: 0.2645 time to fit residues: 106.3876 Evaluate side-chains 235 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 31 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 174 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 GLN B 673 GLN B 750 GLN ** B 790 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 = 0.3261 r_free = 0.3261 target = 0.059429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.047589 restraints weight = 79571.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.049083 restraints weight = 45013.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050108 restraints weight = 30704.216| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14467 Z= 0.331 Angle : 0.696 8.752 19611 Z= 0.359 Chirality : 0.043 0.225 2148 Planarity : 0.005 0.055 2531 Dihedral : 4.885 27.546 1953 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 13.44 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.20), residues: 1774 helix: 0.87 (0.18), residues: 872 sheet: -2.07 (0.32), residues: 259 loop : -1.69 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 657 HIS 0.008 0.001 HIS A 320 PHE 0.030 0.002 PHE J 44 TYR 0.045 0.002 TYR D 18 ARG 0.010 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 1.692 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9262 (mm) REVERT: C 84 ASN cc_start: 0.9268 (t0) cc_final: 0.8976 (t0) REVERT: C 101 ARG cc_start: 0.8732 (pmt170) cc_final: 0.8431 (pmt170) REVERT: A 216 ASP cc_start: 0.9148 (m-30) cc_final: 0.8941 (p0) REVERT: A 218 MET cc_start: 0.9399 (ttt) cc_final: 0.8931 (tpp) REVERT: A 245 MET cc_start: 0.9079 (ttm) cc_final: 0.8739 (ttm) REVERT: A 294 ASN cc_start: 0.9617 (m-40) cc_final: 0.9006 (t0) REVERT: A 295 LEU cc_start: 0.9617 (tp) cc_final: 0.9124 (tp) REVERT: A 305 GLN cc_start: 0.8694 (tp-100) cc_final: 0.7881 (tp-100) REVERT: A 323 MET cc_start: 0.8489 (mmm) cc_final: 0.8145 (mmm) REVERT: A 448 MET cc_start: 0.9003 (tpt) cc_final: 0.8645 (tpt) REVERT: A 465 LEU cc_start: 0.9684 (mt) cc_final: 0.9459 (pp) REVERT: A 484 MET cc_start: 0.9544 (OUTLIER) cc_final: 0.9159 (ptp) REVERT: A 527 LYS cc_start: 0.9686 (tppt) cc_final: 0.9472 (ttpt) REVERT: A 634 MET cc_start: 0.9581 (ttt) cc_final: 0.9164 (ttt) REVERT: A 650 MET cc_start: 0.9512 (mtp) cc_final: 0.9009 (mmm) REVERT: B 62 ARG cc_start: 0.9492 (mtt180) cc_final: 0.9243 (mtm-85) REVERT: B 80 THR cc_start: 0.9630 (m) cc_final: 0.9358 (p) REVERT: B 199 LEU cc_start: 0.9788 (tp) cc_final: 0.9540 (tp) REVERT: B 323 MET cc_start: 0.9493 (mmm) cc_final: 0.9271 (mmm) REVERT: B 401 MET cc_start: 0.8769 (tmm) cc_final: 0.8486 (tmm) REVERT: E 26 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8828 (ttp80) REVERT: H 25 GLU cc_start: 0.9060 (mp0) cc_final: 0.8834 (pm20) REVERT: J 63 PHE cc_start: 0.8811 (m-80) cc_final: 0.7891 (m-80) outliers start: 38 outliers final: 18 residues processed: 250 average time/residue: 0.2694 time to fit residues: 101.4664 Evaluate side-chains 231 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 49 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 58 optimal weight: 0.0010 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 GLN ** B 790 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 = 0.3248 r_free = 0.3248 target = 0.058626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047003 restraints weight = 80562.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.048465 restraints weight = 46082.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049488 restraints weight = 31553.973| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14467 Z= 0.297 Angle : 0.670 9.250 19611 Z= 0.343 Chirality : 0.043 0.265 2148 Planarity : 0.005 0.046 2531 Dihedral : 4.751 26.837 1953 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.95 % Allowed : 16.94 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.20), residues: 1774 helix: 0.98 (0.18), residues: 865 sheet: -1.93 (0.32), residues: 265 loop : -1.55 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.006 0.001 HIS B 274 PHE 0.034 0.002 PHE J 44 TYR 0.029 0.002 TYR H 64 ARG 0.014 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 1.726 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 ASN cc_start: 0.9293 (t0) cc_final: 0.8996 (t0) REVERT: C 103 ARG cc_start: 0.7534 (mmm160) cc_final: 0.6430 (tpt170) REVERT: A 37 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 218 MET cc_start: 0.9373 (ttt) cc_final: 0.8968 (tpp) REVERT: A 294 ASN cc_start: 0.9626 (m-40) cc_final: 0.9011 (t0) REVERT: A 323 MET cc_start: 0.8443 (mmm) cc_final: 0.8190 (mmm) REVERT: A 448 MET cc_start: 0.9053 (tpt) cc_final: 0.8668 (tpt) REVERT: A 465 LEU cc_start: 0.9675 (mt) cc_final: 0.9459 (pp) REVERT: A 484 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.9336 (ptp) REVERT: A 634 MET cc_start: 0.9564 (ttt) cc_final: 0.8917 (ttt) REVERT: A 650 MET cc_start: 0.9499 (mtp) cc_final: 0.8996 (mmm) REVERT: A 694 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 771 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9125 (mt-10) REVERT: B 62 ARG cc_start: 0.9486 (mtt180) cc_final: 0.9224 (mtm-85) REVERT: B 80 THR cc_start: 0.9628 (m) cc_final: 0.9353 (p) REVERT: B 199 LEU cc_start: 0.9785 (tp) cc_final: 0.9551 (tp) REVERT: B 401 MET cc_start: 0.8762 (tmm) cc_final: 0.8470 (tmm) REVERT: E 14 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9100 (tt) REVERT: E 26 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8808 (ttp80) REVERT: H 25 GLU cc_start: 0.9029 (mp0) cc_final: 0.8827 (pm20) REVERT: J 58 MET cc_start: 0.9126 (mpp) cc_final: 0.8517 (pmm) REVERT: J 63 PHE cc_start: 0.8858 (m-80) cc_final: 0.7836 (m-80) outliers start: 43 outliers final: 26 residues processed: 246 average time/residue: 0.2575 time to fit residues: 94.4103 Evaluate side-chains 233 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 158 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.045722 restraints weight = 82734.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047152 restraints weight = 47683.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048129 restraints weight = 32846.277| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14467 Z= 0.346 Angle : 0.692 8.909 19611 Z= 0.358 Chirality : 0.044 0.311 2148 Planarity : 0.005 0.047 2531 Dihedral : 4.759 26.770 1953 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.16 % Allowed : 18.11 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.20), residues: 1774 helix: 0.96 (0.18), residues: 870 sheet: -1.79 (0.32), residues: 269 loop : -1.49 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.008 0.001 HIS A 320 PHE 0.035 0.002 PHE J 44 TYR 0.032 0.002 TYR H 64 ARG 0.007 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 1.576 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 PHE cc_start: 0.9050 (m-80) cc_final: 0.8836 (m-80) REVERT: C 84 ASN cc_start: 0.9332 (t0) cc_final: 0.9044 (t0) REVERT: A 10 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9268 (mt) REVERT: A 245 MET cc_start: 0.9010 (mtp) cc_final: 0.8593 (ttm) REVERT: A 294 ASN cc_start: 0.9606 (m-40) cc_final: 0.9001 (t0) REVERT: A 305 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8176 (tp-100) REVERT: A 323 MET cc_start: 0.8459 (mmm) cc_final: 0.8185 (mmm) REVERT: A 448 MET cc_start: 0.9076 (tpt) cc_final: 0.8688 (tpt) REVERT: A 465 LEU cc_start: 0.9684 (mt) cc_final: 0.9458 (pp) REVERT: A 484 MET cc_start: 0.9567 (OUTLIER) cc_final: 0.9351 (ptp) REVERT: A 527 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7753 (pttt) REVERT: A 650 MET cc_start: 0.9465 (mtp) cc_final: 0.8894 (mmm) REVERT: A 694 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9028 (mp) REVERT: A 771 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9171 (mt-10) REVERT: B 62 ARG cc_start: 0.9472 (mtt180) cc_final: 0.9198 (mtm-85) REVERT: B 75 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.9020 (p0) REVERT: B 80 THR cc_start: 0.9628 (m) cc_final: 0.9356 (p) REVERT: B 207 MET cc_start: 0.8030 (pmm) cc_final: 0.7579 (pmm) REVERT: B 323 MET cc_start: 0.9519 (mmm) cc_final: 0.9290 (mmm) REVERT: B 401 MET cc_start: 0.8736 (tmm) cc_final: 0.8418 (tmm) REVERT: E 14 LEU cc_start: 0.9500 (mt) cc_final: 0.9080 (tt) REVERT: E 26 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8815 (ttp80) REVERT: H 25 GLU cc_start: 0.9074 (mp0) cc_final: 0.8865 (pm20) REVERT: J 58 MET cc_start: 0.9155 (mpp) cc_final: 0.8595 (pmm) REVERT: J 63 PHE cc_start: 0.8868 (m-80) cc_final: 0.7839 (m-80) outliers start: 46 outliers final: 33 residues processed: 243 average time/residue: 0.2618 time to fit residues: 94.6550 Evaluate side-chains 235 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 158 optimal weight: 0.6980 chunk 119 optimal weight: 0.0970 chunk 161 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN A 65 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 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 = 0.3267 r_free = 0.3267 target = 0.059155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.047709 restraints weight = 80229.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049209 restraints weight = 45940.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.050234 restraints weight = 31339.823| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14467 Z= 0.191 Angle : 0.665 12.591 19611 Z= 0.328 Chirality : 0.043 0.370 2148 Planarity : 0.004 0.044 2531 Dihedral : 4.507 23.022 1953 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.36 % Allowed : 19.07 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1774 helix: 1.26 (0.18), residues: 851 sheet: -1.52 (0.34), residues: 249 loop : -1.28 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 808 HIS 0.005 0.001 HIS B 274 PHE 0.037 0.001 PHE J 44 TYR 0.016 0.001 TYR D 18 ARG 0.005 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 1.593 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: 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: symmetry clash REVERT: C 71 PHE cc_start: 0.9010 (m-80) cc_final: 0.8784 (m-80) REVERT: A 117 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8216 (ptp) REVERT: A 218 MET cc_start: 0.9337 (ttt) cc_final: 0.8696 (tpt) REVERT: A 305 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8140 (tp-100) REVERT: A 325 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8751 (mp0) REVERT: A 401 MET cc_start: 0.8018 (ttp) cc_final: 0.7367 (mtp) REVERT: A 448 MET cc_start: 0.9101 (tpt) cc_final: 0.8690 (tpt) REVERT: A 465 LEU cc_start: 0.9644 (mt) cc_final: 0.9403 (pp) REVERT: A 484 MET cc_start: 0.9527 (OUTLIER) cc_final: 0.9259 (ptp) REVERT: A 650 MET cc_start: 0.9427 (mtp) cc_final: 0.8883 (mmm) REVERT: A 692 ASP cc_start: 0.9656 (t0) cc_final: 0.9404 (t0) REVERT: A 694 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8985 (mp) REVERT: A 771 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9124 (mt-10) REVERT: B 62 ARG cc_start: 0.9441 (mtt180) cc_final: 0.9196 (mtm-85) REVERT: B 80 THR cc_start: 0.9612 (m) cc_final: 0.9338 (p) REVERT: B 199 LEU cc_start: 0.9802 (tp) cc_final: 0.9531 (tt) REVERT: B 351 MET cc_start: 0.9512 (ptp) cc_final: 0.9186 (ptp) REVERT: B 401 MET cc_start: 0.8696 (tmm) cc_final: 0.8390 (tmm) REVERT: E 14 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9027 (tt) REVERT: E 61 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7523 (m-80) outliers start: 49 outliers final: 28 residues processed: 252 average time/residue: 0.2868 time to fit residues: 110.1535 Evaluate side-chains 241 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 125 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.046315 restraints weight = 81894.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047770 restraints weight = 46546.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.048779 restraints weight = 31801.124| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14467 Z= 0.259 Angle : 0.678 11.731 19611 Z= 0.339 Chirality : 0.043 0.359 2148 Planarity : 0.004 0.044 2531 Dihedral : 4.477 23.089 1953 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.36 % Allowed : 19.96 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.20), residues: 1774 helix: 1.20 (0.18), residues: 858 sheet: -1.43 (0.33), residues: 269 loop : -1.30 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 808 HIS 0.005 0.001 HIS A 320 PHE 0.039 0.001 PHE J 44 TYR 0.024 0.001 TYR H 64 ARG 0.005 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 1.763 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 PHE cc_start: 0.9068 (m-80) cc_final: 0.8794 (m-80) REVERT: C 103 ARG cc_start: 0.7346 (mmm160) cc_final: 0.6323 (tpt170) REVERT: A 218 MET cc_start: 0.9407 (ttt) cc_final: 0.8966 (tpt) REVERT: A 305 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8255 (tp-100) REVERT: A 325 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8735 (mp0) REVERT: A 401 MET cc_start: 0.8149 (ttp) cc_final: 0.7527 (mtp) REVERT: A 448 MET cc_start: 0.9099 (tpt) cc_final: 0.8689 (tpt) REVERT: A 465 LEU cc_start: 0.9674 (mt) cc_final: 0.9426 (pp) REVERT: A 484 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9260 (ptp) REVERT: A 650 MET cc_start: 0.9446 (mtp) cc_final: 0.8913 (mmm) REVERT: A 692 ASP cc_start: 0.9661 (t0) cc_final: 0.9422 (t0) REVERT: A 694 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9076 (mp) REVERT: B 62 ARG cc_start: 0.9447 (mtt180) cc_final: 0.9172 (mtm-85) REVERT: B 80 THR cc_start: 0.9631 (m) cc_final: 0.9371 (p) REVERT: B 199 LEU cc_start: 0.9797 (tp) cc_final: 0.9550 (tt) REVERT: B 351 MET cc_start: 0.9529 (ptp) cc_final: 0.9203 (ptp) REVERT: B 401 MET cc_start: 0.8768 (tmm) cc_final: 0.8487 (tmm) REVERT: B 629 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8221 (mtt-85) REVERT: E 14 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9067 (tt) REVERT: E 20 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8929 (mm-30) REVERT: E 22 ARG cc_start: 0.9387 (mtt180) cc_final: 0.8770 (mtt90) REVERT: E 61 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7513 (m-80) outliers start: 49 outliers final: 34 residues processed: 242 average time/residue: 0.2497 time to fit residues: 90.5550 Evaluate side-chains 234 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN B 705 GLN ** B 790 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 = 0.3267 r_free = 0.3267 target = 0.058902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047488 restraints weight = 80673.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.048947 restraints weight = 46427.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.049962 restraints weight = 31920.361| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14467 Z= 0.201 Angle : 0.693 14.173 19611 Z= 0.339 Chirality : 0.044 0.386 2148 Planarity : 0.004 0.043 2531 Dihedral : 4.414 23.442 1953 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.22 % Allowed : 20.99 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1774 helix: 1.25 (0.18), residues: 852 sheet: -1.29 (0.34), residues: 256 loop : -1.17 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 808 HIS 0.003 0.001 HIS A 25 PHE 0.044 0.001 PHE J 44 TYR 0.017 0.001 TYR H 64 ARG 0.006 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 1.732 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 PHE cc_start: 0.9060 (m-80) cc_final: 0.8777 (m-80) REVERT: C 103 ARG cc_start: 0.7329 (mmm160) cc_final: 0.6643 (tpt170) REVERT: A 117 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.7931 (ptp) REVERT: A 218 MET cc_start: 0.9366 (ttt) cc_final: 0.8985 (tpt) REVERT: A 286 GLU cc_start: 0.9374 (tm-30) cc_final: 0.9067 (tm-30) REVERT: A 325 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8839 (mp0) REVERT: A 401 MET cc_start: 0.8156 (ttp) cc_final: 0.7496 (mtp) REVERT: A 448 MET cc_start: 0.9101 (tpt) cc_final: 0.8675 (tpt) REVERT: A 465 LEU cc_start: 0.9679 (mt) cc_final: 0.9426 (pp) REVERT: A 484 MET cc_start: 0.9571 (OUTLIER) cc_final: 0.9309 (ptp) REVERT: A 650 MET cc_start: 0.9463 (mtp) cc_final: 0.8870 (mmm) REVERT: A 692 ASP cc_start: 0.9672 (t0) cc_final: 0.9415 (t0) REVERT: A 694 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9087 (mp) REVERT: B 62 ARG cc_start: 0.9453 (mtt180) cc_final: 0.9231 (mtm-85) REVERT: B 80 THR cc_start: 0.9639 (m) cc_final: 0.9368 (p) REVERT: B 199 LEU cc_start: 0.9778 (tp) cc_final: 0.9543 (tt) REVERT: B 351 MET cc_start: 0.9549 (ptp) cc_final: 0.9206 (ptp) REVERT: B 401 MET cc_start: 0.8739 (tmm) cc_final: 0.8368 (tmm) REVERT: B 448 MET cc_start: 0.8316 (mtt) cc_final: 0.7823 (mpp) REVERT: B 629 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8135 (mtt-85) REVERT: E 14 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9029 (tt) REVERT: E 61 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: D 19 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9185 (pp20) REVERT: D 20 GLU cc_start: 0.9172 (pp20) cc_final: 0.8911 (pp20) outliers start: 47 outliers final: 29 residues processed: 242 average time/residue: 0.2564 time to fit residues: 93.5340 Evaluate side-chains 239 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.047653 restraints weight = 79988.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049159 restraints weight = 45508.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050209 restraints weight = 30954.507| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14467 Z= 0.197 Angle : 0.710 14.861 19611 Z= 0.346 Chirality : 0.045 0.368 2148 Planarity : 0.004 0.043 2531 Dihedral : 4.328 26.497 1953 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.02 % Allowed : 20.92 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.21), residues: 1774 helix: 1.25 (0.18), residues: 852 sheet: -1.14 (0.34), residues: 256 loop : -1.09 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 808 HIS 0.003 0.001 HIS A 25 PHE 0.049 0.001 PHE J 44 TYR 0.053 0.001 TYR D 18 ARG 0.007 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 1.535 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 LYS cc_start: 0.9421 (mtmm) cc_final: 0.9094 (pttt) REVERT: C 71 PHE cc_start: 0.9067 (m-80) cc_final: 0.8826 (m-80) REVERT: C 103 ARG cc_start: 0.7702 (mmm160) cc_final: 0.6799 (tpt170) REVERT: A 218 MET cc_start: 0.9322 (ttt) cc_final: 0.8984 (tpt) REVERT: A 286 GLU cc_start: 0.9372 (tm-30) cc_final: 0.9044 (tm-30) REVERT: A 325 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8839 (mp0) REVERT: A 401 MET cc_start: 0.8069 (ttp) cc_final: 0.7414 (mtp) REVERT: A 448 MET cc_start: 0.9111 (tpt) cc_final: 0.8692 (tpt) REVERT: A 465 LEU cc_start: 0.9666 (mt) cc_final: 0.9416 (pp) REVERT: A 484 MET cc_start: 0.9569 (OUTLIER) cc_final: 0.9332 (ptp) REVERT: A 650 MET cc_start: 0.9453 (mtp) cc_final: 0.8861 (mmm) REVERT: A 692 ASP cc_start: 0.9646 (t0) cc_final: 0.9390 (t0) REVERT: A 694 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9082 (mp) REVERT: B 62 ARG cc_start: 0.9413 (mtt180) cc_final: 0.9168 (mtm-85) REVERT: B 80 THR cc_start: 0.9634 (m) cc_final: 0.9360 (p) REVERT: B 199 LEU cc_start: 0.9794 (tp) cc_final: 0.9527 (tt) REVERT: B 401 MET cc_start: 0.8733 (tmm) cc_final: 0.8358 (tmm) REVERT: B 629 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7986 (mtt180) REVERT: E 14 LEU cc_start: 0.9399 (mt) cc_final: 0.8971 (tt) REVERT: E 61 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: D 19 GLU cc_start: 0.9539 (tm-30) cc_final: 0.9181 (pp20) REVERT: D 20 GLU cc_start: 0.9198 (pp20) cc_final: 0.8926 (pp20) REVERT: D 54 MET cc_start: 0.9058 (tmm) cc_final: 0.8555 (ppp) outliers start: 44 outliers final: 31 residues processed: 239 average time/residue: 0.2524 time to fit residues: 89.9592 Evaluate side-chains 240 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 64 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047167 restraints weight = 81318.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048638 restraints weight = 46709.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049650 restraints weight = 32004.717| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14467 Z= 0.221 Angle : 0.715 15.092 19611 Z= 0.351 Chirality : 0.045 0.365 2148 Planarity : 0.004 0.042 2531 Dihedral : 4.336 31.931 1953 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.33 % Allowed : 21.88 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1774 helix: 1.24 (0.18), residues: 853 sheet: -1.07 (0.34), residues: 261 loop : -1.05 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.004 0.001 HIS A 25 PHE 0.051 0.001 PHE J 44 TYR 0.032 0.001 TYR D 18 ARG 0.008 0.000 ARG E 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 1.774 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASP cc_start: 0.7989 (p0) cc_final: 0.7070 (p0) REVERT: C 69 LYS cc_start: 0.9379 (mtmm) cc_final: 0.9131 (ptpp) REVERT: C 71 PHE cc_start: 0.9048 (m-80) cc_final: 0.8835 (m-80) REVERT: A 59 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8956 (tm-30) REVERT: A 286 GLU cc_start: 0.9360 (tm-30) cc_final: 0.9036 (tm-30) REVERT: A 325 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8797 (mp0) REVERT: A 401 MET cc_start: 0.7978 (ttp) cc_final: 0.7398 (mtp) REVERT: A 448 MET cc_start: 0.9112 (tpt) cc_final: 0.8711 (tpt) REVERT: A 465 LEU cc_start: 0.9663 (mt) cc_final: 0.9408 (pp) REVERT: A 484 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9332 (ptp) REVERT: A 650 MET cc_start: 0.9424 (mtp) cc_final: 0.8861 (mmm) REVERT: A 692 ASP cc_start: 0.9660 (t0) cc_final: 0.9405 (t0) REVERT: A 694 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9118 (mp) REVERT: B 80 THR cc_start: 0.9619 (m) cc_final: 0.9358 (p) REVERT: B 199 LEU cc_start: 0.9794 (tp) cc_final: 0.9526 (tt) REVERT: B 401 MET cc_start: 0.8757 (tmm) cc_final: 0.8409 (tmm) REVERT: B 629 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7979 (mtt180) REVERT: E 14 LEU cc_start: 0.9365 (mt) cc_final: 0.8958 (tp) REVERT: E 61 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: D 54 MET cc_start: 0.9034 (tmm) cc_final: 0.8512 (ppp) REVERT: G 54 MET cc_start: 0.7337 (ppp) cc_final: 0.7119 (ppp) outliers start: 34 outliers final: 29 residues processed: 229 average time/residue: 0.2436 time to fit residues: 84.0396 Evaluate side-chains 240 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 24 HIS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain F residue 32 PHE Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain H residue 28 TYR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 122 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046817 restraints weight = 81359.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.048300 restraints weight = 46050.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049326 restraints weight = 31323.185| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14467 Z= 0.227 Angle : 0.732 14.571 19611 Z= 0.357 Chirality : 0.044 0.337 2148 Planarity : 0.004 0.055 2531 Dihedral : 4.344 30.461 1953 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.47 % Allowed : 22.09 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1774 helix: 1.18 (0.18), residues: 853 sheet: -1.02 (0.34), residues: 262 loop : -1.05 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.003 0.001 HIS A 25 PHE 0.024 0.001 PHE E 49 TYR 0.029 0.001 TYR D 18 ARG 0.021 0.001 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4787.39 seconds wall clock time: 87 minutes 56.30 seconds (5276.30 seconds total)