Starting phenix.real_space_refine on Thu Jun 12 15:21:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rtb_19485/06_2025/8rtb_19485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rtb_19485/06_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_19485/06_2025/8rtb_19485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rtb_19485/06_2025/8rtb_19485.map" model { file = "/net/cci-nas-00/data/ceres_data/8rtb_19485/06_2025/8rtb_19485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rtb_19485/06_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-5710/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: 9.33, per 1000 atoms: 0.66 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: 3.55 Conformation dependent library (CDL) restraints added in 1.9 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: 2.00 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: 5.12 Time building geometry restraints manager: 4.24 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: 43.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 36.300 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.690 ------------------------------------------------------------------------------- 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= 0.247 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 Details of bonding type rmsd hydrogen bonds : bond 0.15150 ( 703) hydrogen bonds : angle 6.62726 ( 2004) covalent geometry : bond 0.00561 (14467) covalent geometry : angle 0.78948 (19611) *********************** 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: 0.2793 time to fit residues: 135.9908 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 : 1.550 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.062518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.050314 restraints weight = 76804.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051884 restraints weight = 43889.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052974 restraints weight = 30041.048| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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= 0.162 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 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 703) hydrogen bonds : angle 5.31291 ( 2004) covalent geometry : bond 0.00360 (14467) covalent geometry : angle 0.70850 (19611) *********************** 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 : 1.948 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: 0.9481 (OUTLIER) cc_final: 0.9122 (mm) REVERT: A 216 ASP cc_start: 0.9196 (m-30) cc_final: 0.8893 (p0) REVERT: A 245 MET cc_start: 0.8998 (ttm) cc_final: 0.8620 (ttm) REVERT: A 323 MET cc_start: 0.8598 (mmm) cc_final: 0.8083 (mmm) REVERT: A 365 LEU cc_start: 0.8649 (tp) cc_final: 0.8424 (tp) REVERT: A 527 LYS cc_start: 0.9683 (tppt) cc_final: 0.9480 (ttpt) REVERT: A 634 MET cc_start: 0.9554 (ttt) cc_final: 0.9191 (ttt) REVERT: A 650 MET cc_start: 0.9512 (mtp) cc_final: 0.9182 (mmm) REVERT: A 771 GLU cc_start: 0.9337 (mt-10) cc_final: 0.9100 (mp0) REVERT: B 62 ARG cc_start: 0.9493 (mtt180) cc_final: 0.9251 (mtm-85) REVERT: B 80 THR cc_start: 0.9574 (m) cc_final: 0.9336 (p) REVERT: B 199 LEU cc_start: 0.9773 (tp) cc_final: 0.9526 (tp) REVERT: B 260 LEU cc_start: 0.9252 (pt) cc_final: 0.9005 (pp) REVERT: B 401 MET cc_start: 0.8659 (tmm) cc_final: 0.8424 (tmm) REVERT: B 643 MET cc_start: 0.8818 (tmm) cc_final: 0.8381 (ppp) REVERT: B 650 MET cc_start: 0.9290 (ttm) cc_final: 0.9043 (ttm) REVERT: B 759 MET cc_start: 0.8901 (tmm) cc_final: 0.8585 (tmm) REVERT: E 18 TYR cc_start: 0.8713 (m-10) cc_final: 0.8050 (m-10) REVERT: E 20 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9144 (mm-30) REVERT: D 19 GLU cc_start: 0.9566 (tm-30) cc_final: 0.9306 (pp20) REVERT: D 20 GLU cc_start: 0.9033 (pp20) cc_final: 0.8796 (pp20) REVERT: D 49 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8166 (t80) REVERT: J 40 LEU cc_start: 0.9612 (tp) cc_final: 0.9316 (tp) REVERT: J 63 PHE cc_start: 0.8737 (m-80) cc_final: 0.7843 (m-80) outliers start: 29 outliers final: 11 residues processed: 270 average time/residue: 0.3885 time to fit residues: 161.0311 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 : 1.936 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.9990 chunk 108 optimal weight: 0.0070 chunk 174 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 169 optimal weight: 6.9990 overall best weight: 2.2804 ------------------------------------------------------------------------------- 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 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 = 0.3262 r_free = 0.3262 target = 0.059414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.047581 restraints weight = 79607.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.049075 restraints weight = 45060.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050100 restraints weight = 30771.205| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3085 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= 0.228 Angle : 0.684 8.789 19611 Z= 0.353 Chirality : 0.042 0.218 2148 Planarity : 0.005 0.054 2531 Dihedral : 4.846 26.999 1953 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.81 % Allowed : 13.85 % Favored : 83.33 % 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: -0.73 (0.20), residues: 1774 helix: 0.91 (0.18), residues: 872 sheet: -2.05 (0.32), residues: 259 loop : -1.67 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 657 HIS 0.007 0.001 HIS A 320 PHE 0.023 0.002 PHE J 44 TYR 0.047 0.002 TYR D 18 ARG 0.005 0.001 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 703) hydrogen bonds : angle 5.14148 ( 2004) covalent geometry : bond 0.00477 (14467) covalent geometry : angle 0.68436 (19611) *********************** 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 269 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9508 (OUTLIER) cc_final: 0.9274 (mm) REVERT: C 84 ASN cc_start: 0.9268 (t0) cc_final: 0.8975 (t0) REVERT: C 101 ARG cc_start: 0.8637 (pmt170) cc_final: 0.8341 (pmt170) REVERT: A 216 ASP cc_start: 0.9154 (m-30) cc_final: 0.8953 (p0) REVERT: A 218 MET cc_start: 0.9397 (ttt) cc_final: 0.8958 (tpp) REVERT: A 245 MET cc_start: 0.9075 (ttm) cc_final: 0.8771 (ttm) REVERT: A 294 ASN cc_start: 0.9619 (m-40) cc_final: 0.9012 (t0) REVERT: A 295 LEU cc_start: 0.9618 (tp) cc_final: 0.9127 (tp) REVERT: A 305 GLN cc_start: 0.8671 (tp-100) cc_final: 0.7846 (tp-100) REVERT: A 323 MET cc_start: 0.8484 (mmm) cc_final: 0.8127 (mmm) REVERT: A 448 MET cc_start: 0.9018 (tpt) cc_final: 0.8651 (tpt) REVERT: A 484 MET cc_start: 0.9507 (OUTLIER) cc_final: 0.9169 (ptp) REVERT: A 527 LYS cc_start: 0.9684 (tppt) cc_final: 0.9469 (ttpt) REVERT: A 634 MET cc_start: 0.9581 (ttt) cc_final: 0.9165 (ttt) REVERT: A 650 MET cc_start: 0.9502 (mtp) cc_final: 0.9012 (mmm) REVERT: B 62 ARG cc_start: 0.9495 (mtt180) cc_final: 0.9247 (mtm-85) REVERT: B 80 THR cc_start: 0.9628 (m) cc_final: 0.9360 (p) REVERT: B 199 LEU cc_start: 0.9795 (tp) cc_final: 0.9550 (tp) REVERT: B 401 MET cc_start: 0.8794 (tmm) cc_final: 0.8481 (tmm) REVERT: E 26 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8751 (ttp80) REVERT: E 31 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8678 (pp20) REVERT: J 63 PHE cc_start: 0.8815 (m-80) cc_final: 0.7902 (m-80) outliers start: 41 outliers final: 21 residues processed: 252 average time/residue: 0.2714 time to fit residues: 102.9834 Evaluate side-chains 232 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 ILE 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 332 VAL Chi-restraints excluded: chain B residue 361 VAL 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: 1.9990 chunk 104 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.058035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046462 restraints weight = 80127.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047927 restraints weight = 45372.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048923 restraints weight = 30889.140| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14467 Z= 0.245 Angle : 0.688 8.074 19611 Z= 0.354 Chirality : 0.043 0.240 2148 Planarity : 0.005 0.045 2531 Dihedral : 4.773 27.207 1953 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.81 % Allowed : 16.94 % Favored : 80.25 % 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: -0.60 (0.20), residues: 1774 helix: 0.98 (0.18), residues: 865 sheet: -1.91 (0.32), residues: 265 loop : -1.56 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.007 0.001 HIS A 320 PHE 0.035 0.002 PHE J 44 TYR 0.031 0.002 TYR H 64 ARG 0.013 0.001 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 703) hydrogen bonds : angle 5.09028 ( 2004) covalent geometry : bond 0.00509 (14467) covalent geometry : angle 0.68756 (19611) *********************** 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 256 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 1.674 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 84 ASN cc_start: 0.9296 (t0) cc_final: 0.9013 (t0) REVERT: A 10 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9260 (mt) REVERT: A 37 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8397 (mm-30) REVERT: A 323 MET cc_start: 0.8444 (mmm) cc_final: 0.8186 (mmm) REVERT: A 448 MET cc_start: 0.9043 (tpt) cc_final: 0.8667 (tpt) REVERT: A 484 MET cc_start: 0.9566 (OUTLIER) cc_final: 0.9246 (ptp) REVERT: A 527 LYS cc_start: 0.9690 (tppt) cc_final: 0.9467 (ttpt) REVERT: A 634 MET cc_start: 0.9565 (ttt) cc_final: 0.9223 (ttt) REVERT: A 650 MET cc_start: 0.9487 (mtp) cc_final: 0.8905 (mmm) REVERT: A 771 GLU cc_start: 0.9349 (mt-10) cc_final: 0.9123 (mt-10) REVERT: B 62 ARG cc_start: 0.9476 (mtt180) cc_final: 0.9221 (mtm-85) REVERT: B 80 THR cc_start: 0.9622 (m) cc_final: 0.9354 (p) REVERT: B 199 LEU cc_start: 0.9789 (tp) cc_final: 0.9558 (tp) REVERT: B 323 MET cc_start: 0.9475 (mmm) cc_final: 0.9187 (mmm) REVERT: B 401 MET cc_start: 0.8705 (tmm) cc_final: 0.8424 (tmm) REVERT: B 448 MET cc_start: 0.8295 (mtt) cc_final: 0.8083 (mtt) REVERT: E 14 LEU cc_start: 0.9542 (mt) cc_final: 0.9121 (tt) REVERT: E 26 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8802 (ttp80) REVERT: J 58 MET cc_start: 0.9138 (mpp) cc_final: 0.8564 (pmm) REVERT: J 63 PHE cc_start: 0.8838 (m-80) cc_final: 0.7828 (m-80) outliers start: 41 outliers final: 24 residues processed: 239 average time/residue: 0.2538 time to fit residues: 90.3519 Evaluate side-chains 229 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain A residue 361 VAL 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 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 H residue 54 VAL 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: 0.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 121 optimal weight: 0.0170 chunk 158 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 overall best weight: 0.9422 ------------------------------------------------------------------------------- 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 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 187 HIS ** 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 = 0.3271 r_free = 0.3271 target = 0.059346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047669 restraints weight = 79768.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049213 restraints weight = 44776.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050272 restraints weight = 30277.754| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14467 Z= 0.135 Angle : 0.646 11.148 19611 Z= 0.322 Chirality : 0.043 0.374 2148 Planarity : 0.004 0.044 2531 Dihedral : 4.505 24.085 1953 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.47 % Allowed : 18.59 % Favored : 78.94 % 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: -0.29 (0.21), residues: 1774 helix: 1.20 (0.18), residues: 861 sheet: -1.69 (0.33), residues: 257 loop : -1.40 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 808 HIS 0.006 0.001 HIS B 274 PHE 0.035 0.001 PHE J 44 TYR 0.018 0.001 TYR D 18 ARG 0.007 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 703) hydrogen bonds : angle 4.75024 ( 2004) covalent geometry : bond 0.00302 (14467) covalent geometry : angle 0.64560 (19611) *********************** 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 261 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.985 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: C 50 TRP cc_start: 0.8614 (m100) cc_final: 0.8304 (m100) REVERT: C 84 ASN cc_start: 0.9257 (t0) cc_final: 0.8939 (t0) REVERT: A 218 MET cc_start: 0.9321 (ttt) cc_final: 0.8498 (tpt) REVERT: A 294 ASN cc_start: 0.9601 (m-40) cc_final: 0.8991 (t0) REVERT: A 305 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8077 (tp-100) REVERT: A 325 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8697 (mp0) REVERT: A 401 MET cc_start: 0.8171 (ttp) cc_final: 0.7481 (mtp) REVERT: A 448 MET cc_start: 0.9081 (tpt) cc_final: 0.8637 (tpt) REVERT: A 484 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.9243 (ptp) REVERT: A 634 MET cc_start: 0.9521 (ttt) cc_final: 0.9186 (ttt) REVERT: A 650 MET cc_start: 0.9475 (mtp) cc_final: 0.8952 (mmm) REVERT: A 694 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8965 (mp) REVERT: A 771 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9107 (mt-10) REVERT: B 62 ARG cc_start: 0.9467 (mtt180) cc_final: 0.9182 (mtm-85) REVERT: B 80 THR cc_start: 0.9630 (m) cc_final: 0.9371 (p) REVERT: B 207 MET cc_start: 0.8100 (pmm) cc_final: 0.7679 (pmm) REVERT: B 323 MET cc_start: 0.9501 (mmm) cc_final: 0.9281 (mmm) REVERT: B 401 MET cc_start: 0.8707 (tmm) cc_final: 0.8435 (tmm) REVERT: B 448 MET cc_start: 0.8313 (mtt) cc_final: 0.8009 (mtt) REVERT: E 14 LEU cc_start: 0.9474 (mt) cc_final: 0.9058 (tt) REVERT: E 26 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8755 (ttp80) REVERT: D 19 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9230 (pp20) REVERT: D 20 GLU cc_start: 0.9125 (pp20) cc_final: 0.8851 (pp20) REVERT: F 31 GLU cc_start: 0.9167 (tp30) cc_final: 0.8943 (tp30) outliers start: 36 outliers final: 27 residues processed: 247 average time/residue: 0.2739 time to fit residues: 100.6230 Evaluate side-chains 232 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 344 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 458 THR 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 126 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 158 optimal weight: 6.9990 chunk 119 optimal weight: 0.0570 chunk 161 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 0.0010 overall best weight: 0.3504 ------------------------------------------------------------------------------- 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 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 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 = 0.3294 r_free = 0.3294 target = 0.060168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048519 restraints weight = 78929.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050084 restraints weight = 44166.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051161 restraints weight = 29759.230| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3988 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= 0.118 Angle : 0.654 12.931 19611 Z= 0.319 Chirality : 0.043 0.393 2148 Planarity : 0.004 0.044 2531 Dihedral : 4.355 22.231 1953 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.02 % Allowed : 19.07 % Favored : 77.91 % 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: -0.08 (0.21), residues: 1774 helix: 1.33 (0.18), residues: 848 sheet: -1.38 (0.34), residues: 256 loop : -1.27 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 808 HIS 0.006 0.001 HIS B 274 PHE 0.040 0.001 PHE J 44 TYR 0.018 0.001 TYR D 18 ARG 0.005 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 703) hydrogen bonds : angle 4.59251 ( 2004) covalent geometry : bond 0.00271 (14467) covalent geometry : angle 0.65419 (19611) *********************** 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 271 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 1.820 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 50 TRP cc_start: 0.8555 (m100) cc_final: 0.8252 (m100) REVERT: C 84 ASN cc_start: 0.9226 (t0) cc_final: 0.8882 (t0) REVERT: C 103 ARG cc_start: 0.7320 (mmm160) cc_final: 0.6351 (tpt170) REVERT: A 117 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8189 (ptp) REVERT: A 218 MET cc_start: 0.9229 (ttt) cc_final: 0.8967 (tpt) REVERT: A 286 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9059 (tm-30) REVERT: A 294 ASN cc_start: 0.9573 (m-40) cc_final: 0.8998 (t0) REVERT: A 325 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8809 (mp0) REVERT: A 401 MET cc_start: 0.8228 (ttp) cc_final: 0.7600 (mtp) REVERT: A 448 MET cc_start: 0.9075 (tpt) cc_final: 0.8664 (tpt) REVERT: A 484 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9304 (ptp) REVERT: A 650 MET cc_start: 0.9443 (mtp) cc_final: 0.8865 (mmm) REVERT: A 694 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8806 (mp) REVERT: A 771 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9084 (mt-10) REVERT: B 62 ARG cc_start: 0.9450 (mtt180) cc_final: 0.9186 (mtm-85) REVERT: B 68 LEU cc_start: 0.9810 (tt) cc_final: 0.9514 (pp) REVERT: B 80 THR cc_start: 0.9625 (m) cc_final: 0.9363 (p) REVERT: B 199 LEU cc_start: 0.9789 (tp) cc_final: 0.9551 (tt) REVERT: B 323 MET cc_start: 0.9498 (mmm) cc_final: 0.9292 (mmm) REVERT: B 401 MET cc_start: 0.8660 (tmm) cc_final: 0.8311 (tmm) REVERT: B 448 MET cc_start: 0.8402 (mtt) cc_final: 0.8079 (mtt) REVERT: B 629 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8044 (mtt-85) REVERT: E 14 LEU cc_start: 0.9458 (mt) cc_final: 0.9095 (tt) REVERT: E 20 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8924 (mm-30) REVERT: E 22 ARG cc_start: 0.9482 (mtt180) cc_final: 0.8842 (mtt90) REVERT: E 61 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: J 58 MET cc_start: 0.8761 (pmm) cc_final: 0.8179 (pmm) outliers start: 44 outliers final: 27 residues processed: 255 average time/residue: 0.2804 time to fit residues: 107.5987 Evaluate side-chains 239 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 458 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 630 THR 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 126 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 260 LEU 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 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 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: 0.0470 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 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 372 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 = 0.3292 r_free = 0.3292 target = 0.059984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048392 restraints weight = 79264.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049943 restraints weight = 44333.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.051008 restraints weight = 29882.161| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4142 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= 0.124 Angle : 0.665 13.068 19611 Z= 0.325 Chirality : 0.043 0.403 2148 Planarity : 0.004 0.043 2531 Dihedral : 4.282 21.661 1953 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.36 % Allowed : 19.41 % Favored : 77.23 % 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: 1.29 (0.18), residues: 854 sheet: -1.22 (0.34), residues: 256 loop : -1.17 (0.24), residues: 664 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 0.043 0.001 PHE J 44 TYR 0.020 0.001 TYR D 18 ARG 0.006 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 703) hydrogen bonds : angle 4.55677 ( 2004) covalent geometry : bond 0.00285 (14467) covalent geometry : angle 0.66460 (19611) *********************** 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 262 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 1.580 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: C 50 TRP cc_start: 0.8506 (m100) cc_final: 0.8212 (m100) REVERT: C 84 ASN cc_start: 0.9274 (t0) cc_final: 0.8916 (t0) REVERT: A 117 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8187 (ptp) REVERT: A 286 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9053 (tm-30) REVERT: A 325 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8786 (mp0) REVERT: A 401 MET cc_start: 0.8039 (ttp) cc_final: 0.7498 (mtp) REVERT: A 448 MET cc_start: 0.9090 (tpt) cc_final: 0.8674 (tpt) REVERT: A 484 MET cc_start: 0.9552 (OUTLIER) cc_final: 0.9311 (ptp) REVERT: A 633 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8607 (mpp) REVERT: A 650 MET cc_start: 0.9421 (mtp) cc_final: 0.8829 (mmm) REVERT: A 694 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8900 (mp) REVERT: A 771 GLU cc_start: 0.9278 (mt-10) cc_final: 0.9075 (mt-10) REVERT: B 62 ARG cc_start: 0.9448 (mtt180) cc_final: 0.9164 (mtm-85) REVERT: B 68 LEU cc_start: 0.9804 (tt) cc_final: 0.9508 (pp) REVERT: B 80 THR cc_start: 0.9620 (m) cc_final: 0.9356 (p) REVERT: B 199 LEU cc_start: 0.9795 (tp) cc_final: 0.9571 (tt) REVERT: B 401 MET cc_start: 0.8656 (tmm) cc_final: 0.8294 (tmm) REVERT: B 448 MET cc_start: 0.8423 (mtt) cc_final: 0.8113 (mtt) REVERT: B 629 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8057 (mtt-85) REVERT: E 14 LEU cc_start: 0.9400 (mt) cc_final: 0.9071 (tt) REVERT: D 54 MET cc_start: 0.9005 (tmm) cc_final: 0.8399 (ppp) REVERT: J 58 MET cc_start: 0.8836 (pmm) cc_final: 0.8623 (pmm) outliers start: 49 outliers final: 29 residues processed: 249 average time/residue: 0.2695 time to fit residues: 100.6058 Evaluate side-chains 239 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 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 458 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 630 THR 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 248 ILE 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 D residue 24 LEU Chi-restraints excluded: chain D residue 32 PHE 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: 4.9990 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.0170 chunk 80 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- 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 59 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048331 restraints weight = 80092.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049832 restraints weight = 45605.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.050851 restraints weight = 31015.583| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4236 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= 0.133 Angle : 0.677 13.652 19611 Z= 0.330 Chirality : 0.043 0.378 2148 Planarity : 0.004 0.042 2531 Dihedral : 4.241 22.119 1953 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.09 % Allowed : 20.58 % Favored : 76.34 % 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: 0.07 (0.21), residues: 1774 helix: 1.32 (0.18), residues: 855 sheet: -1.10 (0.34), residues: 256 loop : -1.12 (0.25), residues: 663 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 0.040 0.001 PHE J 44 TYR 0.020 0.001 TYR D 18 ARG 0.006 0.000 ARG E 26 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 703) hydrogen bonds : angle 4.56715 ( 2004) covalent geometry : bond 0.00301 (14467) covalent geometry : angle 0.67679 (19611) *********************** 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 253 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 1.785 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: C 50 TRP cc_start: 0.8616 (m100) cc_final: 0.8309 (m100) REVERT: C 84 ASN cc_start: 0.9289 (t0) cc_final: 0.8928 (t0) REVERT: A 117 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8068 (ptp) REVERT: A 286 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9054 (tm-30) REVERT: A 325 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8818 (mp0) REVERT: A 401 MET cc_start: 0.8039 (ttp) cc_final: 0.7458 (mtp) REVERT: A 448 MET cc_start: 0.9069 (tpt) cc_final: 0.8654 (tpt) REVERT: A 484 MET cc_start: 0.9582 (OUTLIER) cc_final: 0.9317 (ptp) REVERT: A 633 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8506 (mpp) REVERT: A 650 MET cc_start: 0.9457 (mtp) cc_final: 0.8859 (mmm) REVERT: A 694 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8885 (mp) REVERT: B 68 LEU cc_start: 0.9815 (tt) cc_final: 0.9508 (pp) REVERT: B 80 THR cc_start: 0.9643 (m) cc_final: 0.9389 (p) REVERT: B 199 LEU cc_start: 0.9784 (tp) cc_final: 0.9573 (tt) REVERT: B 329 THR cc_start: 0.9581 (p) cc_final: 0.9253 (t) REVERT: B 401 MET cc_start: 0.8710 (tmm) cc_final: 0.8335 (tmm) REVERT: B 448 MET cc_start: 0.8473 (mtt) cc_final: 0.8141 (mtt) REVERT: B 629 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8098 (mtt-85) REVERT: E 14 LEU cc_start: 0.9376 (mt) cc_final: 0.8979 (tt) REVERT: E 26 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8737 (ttp80) REVERT: J 58 MET cc_start: 0.8906 (pmm) cc_final: 0.8677 (pmm) outliers start: 45 outliers final: 28 residues processed: 239 average time/residue: 0.2585 time to fit residues: 92.6596 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 : 1.512 ------------------------------------------------------------------------------- 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 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 484 MET Chi-restraints excluded: chain A residue 630 THR 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 248 ILE Chi-restraints excluded: chain B residue 260 LEU 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 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: 7.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** 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 = 0.3278 r_free = 0.3278 target = 0.059375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.047831 restraints weight = 80029.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049337 restraints weight = 45522.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050380 restraints weight = 31046.262| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4359 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= 0.139 Angle : 0.696 14.166 19611 Z= 0.340 Chirality : 0.043 0.387 2148 Planarity : 0.004 0.042 2531 Dihedral : 4.222 22.118 1953 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 21.33 % Favored : 75.86 % 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: 0.12 (0.21), residues: 1774 helix: 1.31 (0.18), residues: 855 sheet: -0.97 (0.34), residues: 256 loop : -1.07 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.005 0.001 HIS B 274 PHE 0.048 0.001 PHE J 44 TYR 0.021 0.001 TYR D 18 ARG 0.024 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 703) hydrogen bonds : angle 4.60153 ( 2004) covalent geometry : bond 0.00313 (14467) covalent geometry : angle 0.69603 (19611) *********************** 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 257 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.745 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: C 50 TRP cc_start: 0.8586 (m100) cc_final: 0.8280 (m100) REVERT: C 84 ASN cc_start: 0.9262 (t0) cc_final: 0.8906 (t0) REVERT: A 59 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8959 (tm-30) REVERT: A 117 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.7986 (ptp) REVERT: A 286 GLU cc_start: 0.9334 (tm-30) cc_final: 0.9015 (tm-30) REVERT: A 325 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8794 (mp0) REVERT: A 401 MET cc_start: 0.7999 (ttp) cc_final: 0.7447 (mtp) REVERT: A 448 MET cc_start: 0.9083 (tpt) cc_final: 0.8693 (tpt) REVERT: A 484 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.9315 (ptp) REVERT: A 650 MET cc_start: 0.9442 (mtp) cc_final: 0.8856 (mmm) REVERT: B 68 LEU cc_start: 0.9815 (tt) cc_final: 0.9519 (pp) REVERT: B 80 THR cc_start: 0.9630 (m) cc_final: 0.9381 (p) REVERT: B 199 LEU cc_start: 0.9797 (tp) cc_final: 0.9561 (tt) REVERT: B 329 THR cc_start: 0.9570 (p) cc_final: 0.9246 (t) REVERT: B 401 MET cc_start: 0.8725 (tmm) cc_final: 0.8363 (tmm) REVERT: B 448 MET cc_start: 0.8450 (mtt) cc_final: 0.8106 (mtt) REVERT: B 629 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8101 (mtt-85) REVERT: E 14 LEU cc_start: 0.9340 (mt) cc_final: 0.8955 (tp) REVERT: E 26 ARG cc_start: 0.8986 (ttp80) cc_final: 0.8767 (ttp80) REVERT: D 54 MET cc_start: 0.9046 (tmm) cc_final: 0.8553 (ppp) REVERT: J 58 MET cc_start: 0.8928 (pmm) cc_final: 0.8691 (pmm) outliers start: 41 outliers final: 32 residues processed: 242 average time/residue: 0.2530 time to fit residues: 90.8937 Evaluate side-chains 246 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 16 VAL 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 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 458 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 630 THR 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 248 ILE Chi-restraints excluded: chain B residue 260 LEU 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 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 64 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 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 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 = 0.3251 r_free = 0.3251 target = 0.058082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.046695 restraints weight = 81861.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.048152 restraints weight = 46991.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049138 restraints weight = 32228.747| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14467 Z= 0.172 Angle : 0.713 14.255 19611 Z= 0.351 Chirality : 0.044 0.357 2148 Planarity : 0.004 0.066 2531 Dihedral : 4.291 23.106 1953 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 22.09 % Favored : 75.31 % 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: 0.04 (0.21), residues: 1774 helix: 1.24 (0.18), residues: 861 sheet: -0.96 (0.33), residues: 271 loop : -1.15 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 808 HIS 0.005 0.001 HIS A 320 PHE 0.051 0.001 PHE J 44 TYR 0.025 0.001 TYR H 64 ARG 0.015 0.001 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 703) hydrogen bonds : angle 4.72336 ( 2004) covalent geometry : bond 0.00375 (14467) covalent geometry : angle 0.71335 (19611) ********************** 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 244 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.678 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 50 TRP cc_start: 0.8557 (m100) cc_final: 0.8222 (m100) REVERT: C 84 ASN cc_start: 0.9276 (t0) cc_final: 0.8942 (t0) REVERT: A 59 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8939 (tm-30) REVERT: A 325 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8699 (mp0) REVERT: A 448 MET cc_start: 0.9140 (tpt) cc_final: 0.8740 (tpt) REVERT: A 484 MET cc_start: 0.9569 (OUTLIER) cc_final: 0.9271 (ptp) REVERT: A 633 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8569 (mpp) REVERT: A 634 MET cc_start: 0.9269 (ppp) cc_final: 0.8714 (ppp) REVERT: A 650 MET cc_start: 0.9414 (mtp) cc_final: 0.8876 (mmm) REVERT: B 80 THR cc_start: 0.9627 (m) cc_final: 0.9373 (p) REVERT: B 199 LEU cc_start: 0.9801 (tp) cc_final: 0.9547 (tt) REVERT: B 329 THR cc_start: 0.9565 (p) cc_final: 0.9255 (t) REVERT: B 401 MET cc_start: 0.8776 (tmm) cc_final: 0.8466 (tmm) REVERT: B 448 MET cc_start: 0.8409 (mtt) cc_final: 0.8052 (mtt) REVERT: B 629 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8004 (mtt180) REVERT: E 14 LEU cc_start: 0.9348 (mt) cc_final: 0.8959 (tp) REVERT: E 26 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8794 (ttp80) REVERT: D 54 MET cc_start: 0.9071 (tmm) cc_final: 0.8548 (ppp) REVERT: J 58 MET cc_start: 0.8970 (pmm) cc_final: 0.8730 (pmm) outliers start: 38 outliers final: 33 residues processed: 230 average time/residue: 0.3517 time to fit residues: 125.8079 Evaluate side-chains 240 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 16 VAL 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 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 458 THR Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 633 MET 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 248 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 122 optimal weight: 0.4980 chunk 159 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- 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 ** 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 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 = 0.3280 r_free = 0.3280 target = 0.059223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047806 restraints weight = 80065.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.049317 restraints weight = 45090.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050368 restraints weight = 30462.650| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4637 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= 0.125 Angle : 0.720 15.034 19611 Z= 0.343 Chirality : 0.044 0.390 2148 Planarity : 0.004 0.049 2531 Dihedral : 4.189 21.855 1953 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.54 % Allowed : 22.63 % Favored : 74.83 % 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: 0.22 (0.21), residues: 1774 helix: 1.37 (0.18), residues: 843 sheet: -0.78 (0.35), residues: 254 loop : -1.00 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 370 HIS 0.004 0.001 HIS B 274 PHE 0.049 0.001 PHE J 44 TYR 0.016 0.001 TYR D 18 ARG 0.015 0.000 ARG C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 703) hydrogen bonds : angle 4.62821 ( 2004) covalent geometry : bond 0.00285 (14467) covalent geometry : angle 0.72044 (19611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.85 seconds wall clock time: 106 minutes 54.54 seconds (6414.54 seconds total)